Welcome to pyPESTO’s documentation!¶
Install and upgrade¶
Requirements¶
This package requires Python 3.6 or later. It is tested on Linux using Travis continuous integration.
I cannot use my system’s Python distribution, what now?¶
Several Python distributions can co-exist on a single system. If you don’t have access to a recent Python version via your system’s package manager (this might be the case for old operating systems), it is recommended to install the latest version of the Anaconda Python 3 distribution.
Also, there is the possibility to use multiple virtual environments via:
python3 -m virtualenv ENV_NAME
source ENV_NAME/bin/activate
where ENV_NAME denotes an individual environment name, if you do not want to mess up the system environment.
Install from PIP¶
The package can be installed from the Python Package Index PyPI via pip:
pip3 install pypesto
Install from GIT¶
If you want the bleeding edge version, install directly from github:
pip3 install git+https://github.com/icb-dcm/pypesto.git
If you need to have access to the source code, you can download it via:
git clone https://github.com/icb-dcm/pypesto.git
and then install from the local repository via:
cd pypesto
pip3 install .
Upgrade¶
If you want to upgrade from an existing previous version, replace
install by ìnstall --upgrade in the above commands.
Install optional packages and external dependencies¶
pyPESTO includes multiple convenience methods to simplify parameter estimation for models generated using the toolbox AMICI. To use AMICI, install it via pip:
pip3 install amici
or, in case of problems, follow the full instructions from the AMICI documentation.
This package inherently supports optimization using the dlib toolbox. To use it, install dlib via:
pip3 install dlib
All external dependencies can be installed through this shell script.
Examples¶
The following examples cover typical use cases and should help get a better idea of how to use this package:
Rosenbrock banana¶
Here, we perform optimization for the Rosenbrock banana function, which does not require an AMICI model. In particular, we try several ways of specifying derivative information.
[1]:
import pypesto
import pypesto.visualize as visualize
import numpy as np
import scipy as sp
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
%matplotlib inline
Define the objective and problem¶
[2]:
# first type of objective
objective1 = pypesto.Objective(fun=sp.optimize.rosen,
grad=sp.optimize.rosen_der,
hess=sp.optimize.rosen_hess)
# second type of objective
def rosen2(x):
return (sp.optimize.rosen(x),
sp.optimize.rosen_der(x),
sp.optimize.rosen_hess(x))
objective2 = pypesto.Objective(fun=rosen2, grad=True, hess=True)
dim_full = 10
lb = -5 * np.ones((dim_full, 1))
ub = 5 * np.ones((dim_full, 1))
problem1 = pypesto.Problem(objective=objective1, lb=lb, ub=ub)
problem2 = pypesto.Problem(objective=objective2, lb=lb, ub=ub)
Illustration¶
[3]:
x = np.arange(-2, 2, 0.1)
y = np.arange(-2, 2, 0.1)
x, y = np.meshgrid(x, y)
z = np.zeros_like(x)
for j in range(0, x.shape[0]):
for k in range(0, x.shape[1]):
z[j,k] = objective1([x[j,k], y[j,k]], (0,))
[4]:
fig = plt.figure()
fig.set_size_inches(*(14,10))
ax = plt.axes(projection='3d')
ax.plot_surface(X=x, Y=y, Z=z)
plt.xlabel('x axis')
plt.ylabel('y axis')
ax.set_title('cost function values')
[4]:
Text(0.5, 0.92, 'cost function values')
Run optimization¶
[5]:
import pypesto.optimize as optimize
[6]:
%%time
# create different optimizers
optimizer_bfgs = optimize.ScipyOptimizer(method='l-bfgs-b')
optimizer_tnc = optimize.ScipyOptimizer(method='TNC')
optimizer_dogleg = optimize.ScipyOptimizer(method='dogleg')
# set number of starts
n_starts = 20
# save optimizer trace
history_options = pypesto.HistoryOptions(trace_record=True)
# Run optimizaitons for different optimzers
result1_bfgs = optimize.minimize(
problem=problem1, optimizer=optimizer_bfgs,
n_starts=n_starts, history_options=history_options)
result1_tnc = optimize.minimize(
problem=problem1, optimizer=optimizer_tnc,
n_starts=n_starts, history_options=history_options)
result1_dogleg = optimize.minimize(
problem=problem1, optimizer=optimizer_dogleg,
n_starts=n_starts, history_options=history_options)
# Optimize second type of objective
result2 = optimize.minimize(
problem=problem2, optimizer=optimizer_tnc, n_starts=n_starts)
Function values from history and optimizer do not match: 2.685929315976887, 2.9820162443657527
Parameters obtained from history and optimizer do not match: [ 9.81668828e-01 9.70664899e-01 9.44081691e-01 8.86185728e-01
7.98866760e-01 6.27503392e-01 3.49193984e-01 1.00863999e-01
1.18119992e-02 -4.83096174e-04], [0.98232811 0.9607169 0.93006041 0.86376905 0.72679074 0.51464422
0.25715153 0.03390018 0.0134388 0.00224348]
Function values from history and optimizer do not match: 2.932320470464073, 3.104833804292291
Parameters obtained from history and optimizer do not match: [9.85695690e-01 9.66998320e-01 9.34405532e-01 8.72211105e-01
7.61716907e-01 5.82160864e-01 2.90132686e-01 5.88015713e-02
1.02493152e-02 1.44786818e-04], [9.76820249e-01 9.49203293e-01 9.03611145e-01 8.32711736e-01
6.92021069e-01 4.71244784e-01 2.26981271e-01 1.93600745e-02
9.06285841e-03 3.00716108e-04]
Function values from history and optimizer do not match: 7.128857018893593, 7.737539574292646
Parameters obtained from history and optimizer do not match: [-9.74521002e-01 9.48916364e-01 8.98382180e-01 7.95485807e-01
6.32334509e-01 3.95389632e-01 1.55262583e-01 2.24615758e-02
9.92812211e-03 4.70538835e-05], [-0.95137113 0.92287756 0.85600385 0.74220324 0.53469862 0.25223695
0.05388462 0.01175751 0.01035533 0.00121333]
Function values from history and optimizer do not match: 4.047666500407507, 4.8092850089870245
Parameters obtained from history and optimizer do not match: [9.57097378e-01 9.15272882e-01 8.35583627e-01 6.92924153e-01
4.69156347e-01 1.98916115e-01 2.87951418e-02 1.21495892e-02
1.14276335e-02 2.48487865e-04], [9.37837181e-01 8.73541886e-01 7.61292462e-01 5.64720865e-01
2.84119482e-01 6.17767487e-02 1.53662912e-02 1.54992154e-02
1.49513982e-02 2.98560604e-04]
Function values from history and optimizer do not match: 4.760963749486806, 5.255690010134404
Parameters obtained from history and optimizer do not match: [-0.98990379 0.98886801 0.98189121 0.96587616 0.93451723 0.87262109
0.75889559 0.56883791 0.31364781 0.07883034], [-0.99248035 0.99162316 0.97889433 0.95364865 0.91078502 0.8261375
0.68236478 0.45820395 0.17444197 0.01383626]
Function values from history and optimizer do not match: 1.8159939922237558, 2.5425135960926237
Parameters obtained from history and optimizer do not match: [9.90583524e-01 9.80917081e-01 9.63072632e-01 9.30325108e-01
8.61713989e-01 7.40678602e-01 5.38268550e-01 2.71328618e-01
5.43996813e-02 7.89698144e-04], [9.89162276e-01 9.78043570e-01 9.51094059e-01 9.02211862e-01
8.07645490e-01 6.35406055e-01 3.75384767e-01 1.11075371e-01
1.30319964e-02 2.11963742e-04]
Function values from history and optimizer do not match: 2.2546577084566284, 2.988463828057193
Parameters obtained from history and optimizer do not match: [9.86890406e-01 9.73738159e-01 9.51089323e-01 9.02086672e-01
8.09027663e-01 6.46629154e-01 4.04671023e-01 1.51442890e-01
1.94187285e-02 2.45054194e-04], [9.81148194e-01 9.60640784e-01 9.21690034e-01 8.55030060e-01
7.31180374e-01 5.23069013e-01 2.44624625e-01 3.39441804e-02
1.03741576e-02 2.45306769e-05]
Function values from history and optimizer do not match: 0.3545683077008359, 0.5906121485206447
Parameters obtained from history and optimizer do not match: [0.99668472 0.99262575 0.98945665 0.98129911 0.96532923 0.93081497
0.86315388 0.74328951 0.53910453 0.2736718 ], [0.9963228 0.99215562 0.98514259 0.97132273 0.94683482 0.89670025
0.80300196 0.64224614 0.40061592 0.14210795]
Function values from history and optimizer do not match: 1.442951465698237, 2.117657844069939
Parameters obtained from history and optimizer do not match: [0.99253701 0.98698288 0.97438388 0.94864025 0.89249411 0.79343394
0.62110958 0.37154848 0.12142293 0.00337751], [9.85576055e-01 9.72515609e-01 9.52500598e-01 9.14984751e-01
8.40282960e-01 7.07108893e-01 4.93844010e-01 2.19299261e-01
1.80684261e-02 2.39353088e-04]
Function values from history and optimizer do not match: 0.4310215367360306, 0.7200757805862191
Parameters obtained from history and optimizer do not match: [0.99728801 0.99265292 0.98655945 0.97724776 0.95330363 0.91375386
0.83290125 0.68949822 0.4687524 0.21461214], [0.99666432 0.99530499 0.9871224 0.96976884 0.94230384 0.89383977
0.79420195 0.62752848 0.3793222 0.11129682]
Function values from history and optimizer do not match: 6.33997905147026, 7.069668392692864
Parameters obtained from history and optimizer do not match: [7.84450616e-01 6.10188497e-01 3.64032562e-01 1.19476022e-01
1.25200919e-02 9.74166479e-03 1.00503247e-02 8.51949533e-03
9.92120699e-03 1.97235559e-04], [ 7.13358486e-01 4.93846146e-01 2.05601150e-01 2.46828697e-02
1.00531820e-02 8.83759494e-03 9.93584452e-03 1.16356575e-02
1.00772170e-02 -9.19777874e-05]
Function values from history and optimizer do not match: 1.080010188007246, 1.638996874292531
Parameters obtained from history and optimizer do not match: [0.99354151 0.98796198 0.97743947 0.96147507 0.92290179 0.84825176
0.71159467 0.49318554 0.223647 0.03035961], [0.99093761 0.98310117 0.96952353 0.94165684 0.88399848 0.77718421
0.59296742 0.3287277 0.08605952 0.00216266]
Function values from history and optimizer do not match: 6.334069745693479, 7.027921368861192
Parameters obtained from history and optimizer do not match: [-0.98264119 0.97390376 0.94694027 0.8905699 0.79188661 0.62198099
0.37540054 0.12148722 0.01380672 0.00504649], [-0.97385408 0.95844934 0.9257917 0.85697013 0.71970238 0.49533252
0.21270446 0.03011495 0.00979574 -0.00651404]
CPU times: user 2.74 s, sys: 37.7 ms, total: 2.78 s
Wall time: 2.74 s
Visualize and compare optimization results¶
[7]:
# plot separated waterfalls
visualize.waterfall(result1_bfgs, size=(15,6))
visualize.waterfall(result1_tnc, size=(15,6))
visualize.waterfall(result1_dogleg, size=(15,6))
[7]:
<matplotlib.axes._subplots.AxesSubplot at 0x7fb3be1ba0d0>
We can now have a closer look, which method perfomred better: Let’s first compare bfgs and TNC, since both methods gave good results. How does the fine convergence look like?
[8]:
# plot one list of waterfalls
visualize.waterfall([result1_bfgs, result1_tnc],
legends=['L-BFGS-B', 'TNC'],
start_indices=10,
scale_y='lin')
[8]:
<matplotlib.axes._subplots.AxesSubplot at 0x7fb3bf463760>
[9]:
# retrieve second optimum
all_x = result1_bfgs.optimize_result.get_for_key('x')
all_fval = result1_bfgs.optimize_result.get_for_key('fval')
x = all_x[19]
fval = all_fval[19]
print('Second optimum at: ' + str(fval))
# create a reference point from it
ref = {'x': x, 'fval': fval, 'color': [
0.2, 0.4, 1., 1.], 'legend': 'second optimum'}
ref = visualize.create_references(ref)
# new waterfall plot with reference point for second optimum
visualize.waterfall(result1_dogleg, size=(15,6),
scale_y='lin', y_limits=[-1, 101],
reference=ref, colors=[0., 0., 0., 1.])
Second optimum at: 3.9865791142048876
[9]:
<matplotlib.axes._subplots.AxesSubplot at 0x7fb3bde83940>
Visualize parameters¶
There seems to be a second local optimum. We want to see whether it was also found by the dogleg method
[10]:
visualize.parameters([result1_bfgs, result1_tnc],
legends=['L-BFGS-B', 'TNC'],
balance_alpha=False)
visualize.parameters(result1_dogleg,
legends='dogleg',
reference=ref,
size=(15,10),
start_indices=[0, 1, 2, 3, 4, 5],
balance_alpha=False)
[10]:
<matplotlib.axes._subplots.AxesSubplot at 0x7fb3bdd5b430>
If the result needs to be examined in more detail, it can easily be exported as a pandas.DataFrame:
[11]:
df = result1_tnc.optimize_result.as_dataframe(
['fval', 'n_fval', 'n_grad', 'n_hess', 'n_res', 'n_sres', 'time'])
df.head()
[11]:
| fval | n_fval | n_grad | n_hess | n_res | n_sres | time | |
|---|---|---|---|---|---|---|---|
| 0 | 0.590612 | 101 | 101 | 0 | 0 | 0 | 0.052775 |
| 1 | 1.779748 | 101 | 101 | 0 | 0 | 0 | 0.049476 |
| 2 | 2.117658 | 101 | 101 | 0 | 0 | 0 | 0.039615 |
| 3 | 2.542514 | 101 | 101 | 0 | 0 | 0 | 0.064188 |
| 4 | 2.982016 | 101 | 101 | 0 | 0 | 0 | 0.024157 |
Optimizer history¶
Let’s compare optimzer progress over time.
[12]:
# plot one list of waterfalls
visualize.optimizer_history([result1_bfgs, result1_tnc],
legends=['L-BFGS-B', 'TNC'],
reference=ref)
# plot one list of waterfalls
visualize.optimizer_history(result1_dogleg,
reference=ref)
[12]:
<matplotlib.axes._subplots.AxesSubplot at 0x7fb3bdbcc820>
We can also visualize this usign other scalings or offsets…
[13]:
# plot one list of waterfalls
visualize.optimizer_history([result1_bfgs, result1_tnc],
legends=['L-BFGS-B', 'TNC'],
reference=ref,
offset_y=0.)
# plot one list of waterfalls
visualize.optimizer_history([result1_bfgs, result1_tnc],
legends=['L-BFGS-B', 'TNC'],
reference=ref,
scale_y='lin',
y_limits=[-1., 11.])
[13]:
<matplotlib.axes._subplots.AxesSubplot at 0x7fb3be01d130>
Compute profiles¶
The profiling routine needs a problem, a results object and an optimizer.
Moreover it accepts an index of integer (profile_index), whether or not a profile should be computed.
Finally, an integer (result_index) can be passed, in order to specify the local optimum, from which profiling should be started.
[14]:
import pypesto.profile as profile
[15]:
%%time
# compute profiles
profile_options = profile.ProfileOptions(min_step_size=0.0005,
delta_ratio_max=0.05,
default_step_size=0.005,
ratio_min=0.01)
result1_bfgs = profile.parameter_profile(
problem=problem1,
result=result1_bfgs,
optimizer=optimizer_bfgs,
profile_index=np.array([1, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0]),
result_index=0,
profile_options=profile_options)
# compute profiles from second optimum
result1_bfgs = profile.parameter_profile(
problem=problem1,
result=result1_bfgs,
optimizer=optimizer_bfgs,
profile_index=np.array([1, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0]),
result_index=19,
profile_options=profile_options)
CPU times: user 1.31 s, sys: 4.28 ms, total: 1.32 s
Wall time: 1.32 s
Visualize and analyze results¶
pypesto offers easy-to-use visualization routines:
[16]:
# specify the parameters, for which profiles should be computed
ax = visualize.profiles(result1_bfgs, profile_indices = [0,1,2,5,7],
reference=ref, profile_list_ids=[0, 1])
Approximate profiles¶
When computing the profiles is computationally too demanding, it is possible to employ to at least consider a normal approximation with covariance matrix given by the Hessian or FIM at the optimal parameters.
[17]:
%%time
result1_tnc = profile.approximate_parameter_profile(
problem=problem1,
result=result1_bfgs,
profile_index=np.array([1, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0]),
result_index=0,
n_steps=1000)
CPU times: user 25 ms, sys: 16.3 ms, total: 41.4 ms
Wall time: 24.2 ms
These approximate profiles require at most one additional function evaluation, can however yield substantial approximation errors:
[18]:
axes = visualize.profiles(
result1_bfgs, profile_indices = [0,1,2,5,7], profile_list_ids=[0, 2],
ratio_min=0.01, colors=[(1,0,0,1), (0,0,1,1)],
legends=["Optimization-based profile", "Local profile approximation"])
We can also plot approximate confidence intervals based on profiles:
[19]:
visualize.profile_cis(
result1_bfgs, confidence_level=0.95, profile_list=2)
[19]:
<matplotlib.axes._subplots.AxesSubplot at 0x7fb3bda13f10>
Conversion reaction¶
[1]:
import importlib
import os
import sys
import numpy as np
import amici
import amici.plotting
import pypesto
import pypesto.optimize as optimize
import pypesto.visualize as visualize
# sbml file we want to import
sbml_file = 'conversion_reaction/model_conversion_reaction.xml'
# name of the model that will also be the name of the python module
model_name = 'model_conversion_reaction'
# directory to which the generated model code is written
model_output_dir = 'tmp/' + model_name
Compile AMICI model¶
[2]:
# import sbml model, compile and generate amici module
sbml_importer = amici.SbmlImporter(sbml_file)
sbml_importer.sbml2amici(model_name,
model_output_dir,
verbose=False)
Load AMICI model¶
[3]:
# load amici module (the usual starting point later for the analysis)
sys.path.insert(0, os.path.abspath(model_output_dir))
model_module = importlib.import_module(model_name)
model = model_module.getModel()
model.requireSensitivitiesForAllParameters()
model.setTimepoints(np.linspace(0, 10, 11))
model.setParameterScale(amici.ParameterScaling.log10)
model.setParameters([-0.3,-0.7])
solver = model.getSolver()
solver.setSensitivityMethod(amici.SensitivityMethod.forward)
solver.setSensitivityOrder(amici.SensitivityOrder.first)
# how to run amici now:
rdata = amici.runAmiciSimulation(model, solver, None)
amici.plotting.plotStateTrajectories(rdata)
edata = amici.ExpData(rdata, 0.2, 0.0)
Optimize¶
[4]:
# create objective function from amici model
# pesto.AmiciObjective is derived from pesto.Objective,
# the general pesto objective function class
objective = pypesto.AmiciObjective(model, solver, [edata], 1)
# create optimizer object which contains all information for doing the optimization
optimizer = optimize.ScipyOptimizer(method='ls_trf')
# create problem object containing all information on the problem to be solved
problem = pypesto.Problem(objective=objective,
lb=[-2,-2], ub=[2,2])
# do the optimization
result = optimize.minimize(problem=problem,
optimizer=optimizer,
n_starts=10)
Visualize¶
[5]:
visualize.waterfall(result)
visualize.parameters(result)
visualize.optimizer_convergence(result)
[5]:
<AxesSubplot:xlabel='fval', ylabel='gradient norm'>
Profiles¶
[6]:
import pypesto.profile as profile
profile_options = profile.ProfileOptions(min_step_size=0.0005,
delta_ratio_max=0.05,
default_step_size=0.005,
ratio_min=0.01)
result = profile.parameter_profile(
problem=problem,
result=result,
optimizer=optimizer,
profile_index=np.array([1, 1, 1, 0, 0, 1, 0, 1, 0, 0, 0]),
result_index=0,
profile_options=profile_options)
Parameters obtained from history and optimizer do not match: [-0.17103023], [-0.17102486]
Parameters obtained from history and optimizer do not match: [-0.92272262], [-0.92270649]
[7]:
# specify the parameters, for which profiles should be computed
ax = visualize.profiles(result)
Sampling¶
[8]:
import pypesto.sample as sample
sampler = sample.AdaptiveParallelTemperingSampler(
internal_sampler=sample.AdaptiveMetropolisSampler(),
n_chains=3)
result = sample.sample(problem, n_samples=10000, sampler=sampler, result=result)
100%|██████████| 10000/10000 [00:33<00:00, 295.74it/s]
[9]:
ax = visualize.sampling_scatter(result, size=[13,6])
Burn in index not found in the results, the full chain will be shown.
You may want to use, e.g., 'pypesto.sample.geweke_test'.
Predict¶
[10]:
# Let's create a function, which predicts the ratio of x_1 and x_0
import pypesto.predict as predict
def ratio_function(amici_output_list):
# This (optional) function post-processes the results from AMICI and must accept one input:
# a list of dicts, with the fields t, x, y[, sx, sy - if sensi_orders includes 1]
# We need to specify the simulation condition: here, we only have one, i.e., it's [0]
x = amici_output_list[0]['x']
ratio = x[:,1] / x[:,0]
# we need to output also at least one simulation condition
return [ratio]
# create pypesto prediction function
predictor = predict.AmiciPredictor(objective, post_processor=ratio_function, output_ids=['ratio'])
# run prediction
prediction = predictor(x=model.getUnscaledParameters())
[11]:
dict(prediction)
[11]:
{'conditions': [{'timepoints': array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10.]),
'output_ids': ['ratio'],
'x_names': ['k1', 'k2'],
'output': array([0. , 1.95196396, 2.00246152, 2.00290412, 2.00290796,
2.00290801, 2.00290801, 2.00290799, 2.002908 , 2.00290801,
2.002908 ]),
'output_sensi': None}],
'condition_ids': ['condition_0'],
'comment': None,
'parameter_ids': ['k1', 'k2']}
Analyze parameter ensembles¶
[12]:
# We want to use the sample result to create a prediction
from pypesto.ensemble import ensemble
# first collect some vectors from the sampling result
vectors = result.sample_result.trace_x[0, ::20, :]
# create the collection
my_ensemble = ensemble.Ensemble(vectors,
x_names=problem.x_names,
ensemble_type=ensemble.EnsembleType.sample,
lower_bound=problem.lb,
upper_bound=problem.ub)
# we can also perform an approximative identifiability analysis
summary = my_ensemble.compute_summary()
identifiability = my_ensemble.check_identifiability()
print(identifiability.transpose())
parameterId k1 k2
parameterId k1 k2
lowerBound -2 -2
upperBound 2 2
ensemble_mean -0.559689 -0.810604
ensemble_std 0.287255 0.364753
ensemble_median -0.559689 -0.810604
within lb: 1 std True True
within ub: 1 std True True
within lb: 2 std True True
within ub: 2 std True True
within lb: 3 std True True
within ub: 3 std True True
within lb: perc 5 True True
within lb: perc 20 True True
within ub: perc 80 True True
within ub: perc 95 True True
[13]:
# run a prediction
ensemble_prediction = my_ensemble.predict(predictor, prediction_id='ratio_over_time')
# go for some analysis
prediction_summary = ensemble_prediction.compute_summary(percentiles_list=(1, 5, 10, 25, 75, 90, 95, 99))
dict(prediction_summary)
[13]:
{'mean': <pypesto.predict.result.PredictionResult at 0x7fe734b68760>,
'std': <pypesto.predict.result.PredictionResult at 0x7fe734b698b0>,
'median': <pypesto.predict.result.PredictionResult at 0x7fe734b69d60>,
'percentile 1': <pypesto.predict.result.PredictionResult at 0x7fe734b69a30>,
'percentile 5': <pypesto.predict.result.PredictionResult at 0x7fe734b69a60>,
'percentile 10': <pypesto.predict.result.PredictionResult at 0x7fe734b69640>,
'percentile 25': <pypesto.predict.result.PredictionResult at 0x7fe734b69610>,
'percentile 75': <pypesto.predict.result.PredictionResult at 0x7fe734b693d0>,
'percentile 90': <pypesto.predict.result.PredictionResult at 0x7fe734b69e20>,
'percentile 95': <pypesto.predict.result.PredictionResult at 0x7fe734b692e0>,
'percentile 99': <pypesto.predict.result.PredictionResult at 0x7fe734b69730>}
Fixed parameters¶
In this notebook we will show how to use fixed parameters. Therefore, we employ our Rosenbrock example. We define two problems, where for the first problem all parameters are optimized, and for the second we fix some of them to specified values.
Define problem¶
[1]:
import pypesto
import pypesto.optimize as optimize
import pypesto.visualize as visualize
import numpy as np
import scipy as sp
import matplotlib.pyplot as plt
%matplotlib inline
[2]:
objective = pypesto.Objective(fun=sp.optimize.rosen,
grad=sp.optimize.rosen_der,
hess=sp.optimize.rosen_hess)
dim_full = 5
lb = -2 * np.ones((dim_full,1))
ub = 2 * np.ones((dim_full,1))
problem1 = pypesto.Problem(objective=objective, lb=lb, ub=ub)
x_fixed_indices = [1, 3]
x_fixed_vals = [1, 1]
problem2 = pypesto.Problem(objective=objective, lb=lb, ub=ub,
x_fixed_indices=x_fixed_indices,
x_fixed_vals=x_fixed_vals)
Optimize¶
[3]:
optimizer = optimize.ScipyOptimizer()
n_starts = 10
result1 = optimize.minimize(problem=problem1, optimizer=optimizer,
n_starts=n_starts)
result2 = optimize.minimize(problem=problem2, optimizer=optimizer,
n_starts=n_starts)
Visualize¶
[4]:
fig, ax = plt.subplots()
visualize.waterfall(result1, ax)
visualize.waterfall(result2, ax)
visualize.parameters(result1)
visualize.parameters(result2)
visualize.parameters(result2, parameter_indices='all')
[4]:
<matplotlib.axes._subplots.AxesSubplot at 0x7ff3da236a20>
[5]:
result1.optimize_result.as_dataframe(['fval', 'x', 'grad'])
[5]:
| fval | x | grad | |
|---|---|---|---|
| 0 | 2.563931e-14 | [0.9999999859217336, 0.9999999812160436, 0.999... | [-3.7771869883630873e-06, 3.2004378806360524e-... |
| 1 | 4.103854e-14 | [1.0000000033181213, 1.00000001070042, 1.00000... | [-1.6190347383411735e-06, 5.768553691118231e-0... |
| 2 | 2.430040e-13 | [0.9999999979980921, 0.9999999872750013, 0.999... | [3.4844693764909735e-06, 4.6873211372756083e-0... |
| 3 | 2.993261e-12 | [1.0000000655628785, 1.0000002137366326, 1.000... | [-3.291322500031286e-05, 6.600823794056182e-07... |
| 4 | 3.028019e-11 | [1.0000002263273202, 0.9999999457510741, 1.000... | [0.00020321414758544783, -0.000184783444508992... |
| 5 | 1.504857e-10 | [1.0000008747306284, 1.000001813929941, 1.0000... | [-2.4037728901340504e-05, -1.168240814877157e-... |
| 6 | 3.713657e-10 | [1.0000011952242212, 1.000001771893066, 1.0000... | [0.00024981346612303615, 0.0001962351003382311... |
| 7 | 4.012393e-10 | [0.9999986079063197, 0.9999988670990364, 0.999... | [-0.000663297051531534, 0.000537723456872972, ... |
| 8 | 5.247717e-10 | [1.000000368254703, 1.0000009022274876, 0.9999... | [-6.555069341760695e-05, 0.0009407121705420637... |
| 9 | 3.930839e+00 | [-0.9620510415103535, 0.9357394330313418, 0.88... | [-1.109923131625834e-06, 5.109232684041842e-06... |
[6]:
result2.optimize_result.as_dataframe(['fval', 'x', 'grad'])
[6]:
| fval | x | grad | |
|---|---|---|---|
| 0 | 4.679771e-17 | [0.9999999998641961, 1.0, 1.0000000002266116, ... | [-1.0891474676223493e-07, nan, 2.2706484163692... |
| 1 | 4.825331e-16 | [0.9999999995848748, 1.0, 0.9999999991941183, ... | [-3.329303753527845e-07, nan, -8.0749345757971... |
| 2 | 1.394704e-14 | [1.0000000026325193, 1.0, 0.9999999987812758, ... | [2.1112804950914665e-06, nan, -1.2211616799204... |
| 3 | 3.989975e+00 | [-0.9949747468838975, 1.0, 0.9999999999585671,... | [-4.2116658605095836e-08, nan, -4.151572285811... |
| 4 | 3.989975e+00 | [-0.9949747461383964, 1.0, 0.9999999963588824,... | [5.468066182068299e-07, nan, -3.64839985427999... |
| 5 | 3.989975e+00 | [-0.9949747436177196, 1.0, 0.9999999894437084,... | [2.5380648831507813e-06, nan, -1.0577404068293... |
| 6 | 3.989975e+00 | [-0.9949747458936441, 1.0, 0.99999997533737, 1... | [7.40153570877311e-07, nan, -2.471195460075688... |
| 7 | 3.989975e+00 | [-0.9949747793023977, 1.0, 1.000000023888003, ... | [-2.5651750697797127e-05, nan, 2.3935779637870... |
| 8 | 3.989975e+00 | [-0.9949748033666262, 1.0, 1.0000000080319777,... | [-4.466176453288284e-05, nan, 8.0480417566767e... |
| 9 | 3.989975e+00 | [-0.994974648260114, 1.0, 0.9999999725753793, ... | [7.78676721049365e-05, nan, -2.747946901432181... |
AMICI Python example “Boehm”¶
This is an example using the “boehm_ProteomeRes2014.xml” model to demonstrate and test SBML import and AMICI Python interface.
[1]:
import libsbml
import importlib
import amici
import pypesto
import os
import sys
import numpy as np
import matplotlib.pyplot as plt
# temporarily add the simulate file
sys.path.insert(0, 'boehm_JProteomeRes2014')
from benchmark_import import DataProvider
# sbml file
sbml_file = 'boehm_JProteomeRes2014/boehm_JProteomeRes2014.xml'
# name of the model that will also be the name of the python module
model_name = 'boehm_JProteomeRes2014'
# output directory
model_output_dir = 'tmp/' + model_name
The example model¶
Here we use libsbml to show the reactions and species described by the model (this is independent of AMICI).
[2]:
sbml_reader = libsbml.SBMLReader()
sbml_doc = sbml_reader.readSBML(os.path.abspath(sbml_file))
sbml_model = sbml_doc.getModel()
dir(sbml_doc)
print(os.path.abspath(sbml_file))
print('Species: ', [s.getId() for s in sbml_model.getListOfSpecies()])
print('\nReactions:')
for reaction in sbml_model.getListOfReactions():
reactants = ' + '.join(
['%s %s'%(int(r.getStoichiometry())
if r.getStoichiometry() > 1 else '', r.getSpecies())
for r in reaction.getListOfReactants()])
products = ' + '.join(
['%s %s'%(int(r.getStoichiometry())
if r.getStoichiometry() > 1 else '', r.getSpecies())
for r in reaction.getListOfProducts()])
reversible = '<' if reaction.getReversible() else ''
print('%3s: %10s %1s->%10s\t\t[%s]' % (
reaction.getId(),
reactants,
reversible,
products,
libsbml.formulaToL3String(reaction.getKineticLaw().getMath())))
/home/yannik/pypesto/doc/example/boehm_JProteomeRes2014/boehm_JProteomeRes2014.xml
Species: ['STAT5A', 'STAT5B', 'pApB', 'pApA', 'pBpB', 'nucpApA', 'nucpApB', 'nucpBpB']
Reactions:
v1_v_0: 2 STAT5A -> pApA [cyt * BaF3_Epo * STAT5A^2 * k_phos]
v2_v_1: STAT5A + STAT5B -> pApB [cyt * BaF3_Epo * STAT5A * STAT5B * k_phos]
v3_v_2: 2 STAT5B -> pBpB [cyt * BaF3_Epo * STAT5B^2 * k_phos]
v4_v_3: pApA -> nucpApA [cyt * k_imp_homo * pApA]
v5_v_4: pApB -> nucpApB [cyt * k_imp_hetero * pApB]
v6_v_5: pBpB -> nucpBpB [cyt * k_imp_homo * pBpB]
v7_v_6: nucpApA -> 2 STAT5A [nuc * k_exp_homo * nucpApA]
v8_v_7: nucpApB -> STAT5A + STAT5B [nuc * k_exp_hetero * nucpApB]
v9_v_8: nucpBpB -> 2 STAT5B [nuc * k_exp_homo * nucpBpB]
Importing an SBML model, compiling and generating an AMICI module¶
Before we can use AMICI to simulate our model, the SBML model needs to be translated to C++ code. This is done by amici.SbmlImporter.
[3]:
# Create an SbmlImporter instance for our SBML model
sbml_importer = amici.SbmlImporter(sbml_file)
In this example, we want to specify fixed parameters, observables and a \(\sigma\) parameter. Unfortunately, the latter two are not part of the SBML standard. However, they can be provided to amici.SbmlImporter.sbml2amici as demonstrated in the following.
Constant parameters¶
Constant parameters, i.e. parameters with respect to which no sensitivities are to be computed (these are often parameters specifying a certain experimental condition) are provided as a list of parameter names.
[4]:
constantParameters = ['ratio', 'specC17']
Observables¶
We used SBML’s `AssignmentRule <http://sbml.org/Software/libSBML/5.13.0/docs//python-api/classlibsbml_1_1_rule.html>`__ as a non-standard way to specify Model outputs within the SBML file. These rules need to be removed prior to the model import (AMICI does at this time not support these Rules). This can be easily done using amici.assignmentRules2observables().
In this example, we introduced parameters named observable_* as targets of the observable AssignmentRules. Where applicable we have observable_*_sigma parameters for \(\sigma\) parameters (see below).
[5]:
# Retrieve model output names and formulae from AssignmentRules and remove the respective rules
observables = amici.assignmentRules2observables(
sbml_importer.sbml, # the libsbml model object
filter_function=lambda variable: variable.getId().startswith('observable_') and not variable.getId().endswith('_sigma')
)
print('Observables:', observables)
Observables: {'observable_pSTAT5A_rel': {'name': 'observable_pSTAT5A_rel', 'formula': '(100 * pApB + 200 * pApA * specC17) / (pApB + STAT5A * specC17 + 2 * pApA * specC17)'}, 'observable_pSTAT5B_rel': {'name': 'observable_pSTAT5B_rel', 'formula': '-(100 * pApB - 200 * pBpB * (specC17 - 1)) / (STAT5B * (specC17 - 1) - pApB + 2 * pBpB * (specC17 - 1))'}, 'observable_rSTAT5A_rel': {'name': 'observable_rSTAT5A_rel', 'formula': '(100 * pApB + 100 * STAT5A * specC17 + 200 * pApA * specC17) / (2 * pApB + STAT5A * specC17 + 2 * pApA * specC17 - STAT5B * (specC17 - 1) - 2 * pBpB * (specC17 - 1))'}}
\(\sigma\) parameters¶
To specify measurement noise as a parameter, we simply provide a dictionary with (preexisting) parameter names as keys and a list of observable names as values to indicate which sigma parameter is to be used for which observable.
[6]:
sigma_vals = ['sd_pSTAT5A_rel', 'sd_pSTAT5B_rel', 'sd_rSTAT5A_rel']
observable_names = observables.keys()
sigmas = dict(zip(list(observable_names), sigma_vals))
print(sigmas)
{'observable_pSTAT5A_rel': 'sd_pSTAT5A_rel', 'observable_pSTAT5B_rel': 'sd_pSTAT5B_rel', 'observable_rSTAT5A_rel': 'sd_rSTAT5A_rel'}
Generating the module¶
Now we can generate the python module for our model. amici.SbmlImporter.sbml2amici will symbolically derive the sensitivity equations, generate C++ code for model simulation, and assemble the python module.
[7]:
sbml_importer.sbml2amici(model_name,
model_output_dir,
verbose=False,
observables=observables,
constantParameters=constantParameters,
sigmas=sigmas,
)
Importing the module and loading the model¶
If everything went well, we need to add the previously selected model output directory to our PYTHON_PATH and are then ready to load newly generated model:
[8]:
sys.path.insert(0, os.path.abspath(model_output_dir))
model_module = importlib.import_module(model_name)
And get an instance of our model from which we can retrieve information such as parameter names:
[9]:
model = model_module.getModel()
print("Model parameters:", list(model.getParameterIds()))
print("Model outputs: ", list(model.getObservableIds()))
print("Model states: ", list(model.getStateIds()))
Model parameters: ['Epo_degradation_BaF3', 'k_exp_hetero', 'k_exp_homo', 'k_imp_hetero', 'k_imp_homo', 'k_phos', 'sd_pSTAT5A_rel', 'sd_pSTAT5B_rel', 'sd_rSTAT5A_rel']
Model outputs: ['observable_pSTAT5A_rel', 'observable_pSTAT5B_rel', 'observable_rSTAT5A_rel']
Model states: ['STAT5A', 'STAT5B', 'pApB', 'pApA', 'pBpB', 'nucpApA', 'nucpApB', 'nucpBpB']
Running simulations and analyzing results¶
After importing the model, we can run simulations using amici.runAmiciSimulation. This requires a Model instance and a Solver instance. Optionally you can provide measurements inside an ExpData instance, as shown later in this notebook.
[10]:
h5_file = 'boehm_JProteomeRes2014/data_boehm_JProteomeRes2014.h5'
dp = DataProvider(h5_file)
[11]:
# set timepoints for which we want to simulate the model
timepoints = amici.DoubleVector(dp.get_timepoints())
model.setTimepoints(timepoints)
# set fixed parameters for which we want to simulate the model
model.setFixedParameters(amici.DoubleVector(np.array([0.693, 0.107])))
# set parameters to optimal values found in the benchmark collection
model.setParameterScale(2)
model.setParameters(amici.DoubleVector(np.array(
[-1.568917588,
-4.999704894,
-2.209698782,
-1.786006548,
4.990114009,
4.197735488,
0.585755271,
0.818982819,
0.498684404,
]
)))
# Create solver instance
solver = model.getSolver()
# Run simulation using model parameters from the benchmark collection and default solver options
rdata = amici.runAmiciSimulation(model, solver)
[12]:
# Create edata
edata = amici.ExpData(rdata, 1.0, 0)
# set observed data
edata.setObservedData(amici.DoubleVector(dp.get_measurements()[0][:, 0]), 0)
edata.setObservedData(amici.DoubleVector(dp.get_measurements()[0][:, 1]), 1)
edata.setObservedData(amici.DoubleVector(dp.get_measurements()[0][:, 2]), 2)
# set standard deviations to optimal values found in the benchmark collection
edata.setObservedDataStdDev(amici.DoubleVector(np.array(16*[10**0.585755271])), 0)
edata.setObservedDataStdDev(amici.DoubleVector(np.array(16*[10**0.818982819])), 1)
edata.setObservedDataStdDev(amici.DoubleVector(np.array(16*[10**0.498684404])), 2)
[13]:
rdata = amici.runAmiciSimulation(model, solver, edata)
print('Chi2 value reported in benchmark collection: 47.9765479')
print('chi2 value using AMICI:')
print(rdata['chi2'])
Chi2 value reported in benchmark collection: 47.9765479
chi2 value using AMICI:
47.97654321200259
Run optimization using pyPESTO¶
[14]:
# create objective function from amici model
# pesto.AmiciObjective is derived from pesto.Objective,
# the general pesto objective function class
model.requireSensitivitiesForAllParameters()
solver.setSensitivityMethod(amici.SensitivityMethod_forward)
solver.setSensitivityOrder(amici.SensitivityOrder_first)
objective = pypesto.AmiciObjective(model, solver, [edata], 1)
[15]:
import pypesto.optimize as optimize
# create optimizer object which contains all information for doing the optimization
optimizer = optimize.ScipyOptimizer()
optimizer.solver = 'bfgs'
[16]:
# create problem object containing all information on the problem to be solved
x_names = ['x' + str(j) for j in range(0, 9)]
problem = pypesto.Problem(objective=objective,
lb=-5*np.ones((9)), ub=5*np.ones((9)),
x_names=x_names)
[17]:
# do the optimization
result = optimize.minimize(problem=problem,
optimizer=optimizer,
n_starts=10) # 200
0%| | 0/10 [00:00<?, ?it/s][Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 27.1575 and h = 3.02895e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 27.157468:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 27.1575 and h = 3.02895e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 27.157468:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 27.1575 and h = 3.02895e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 27.157468:
AMICI failed to integrate the forward problem
20%|██ | 2/10 [00:04<00:16, 2.01s/it][Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 198.1 and h = 2.52411e-05, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 198.099706:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 197.924 and h = 2.91098e-05, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 197.924166:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 197.924 and h = 2.91098e-05, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 197.924166:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 197.924 and h = 2.91098e-05, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 197.924166:
AMICI failed to integrate the forward problem
30%|███ | 3/10 [00:05<00:13, 1.92s/it][Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 125.014 and h = 1.7682e-05, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 125.014377:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 125.014 and h = 1.7682e-05, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 125.014377:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 125.014 and h = 1.7682e-05, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 125.014377:
AMICI failed to integrate the forward problem
50%|█████ | 5/10 [00:08<00:08, 1.74s/it][Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 162.24 and h = 3.05789e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 162.239689:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 162.24 and h = 3.05789e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 162.239689:
AMICI failed to integrate the forward problem
70%|███████ | 7/10 [00:18<00:08, 2.96s/it][Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 25.5245 and h = 5.70238e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 25.524541:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 25.5245 and h = 5.70238e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 25.524541:
AMICI failed to integrate the forward problem
100%|██████████| 10/10 [00:23<00:00, 2.37s/it]
Visualization¶
Create waterfall and parameter plot
[18]:
# waterfall, parameter space,
import pypesto.visualize as visualize
visualize.waterfall(result)
visualize.parameters(result)
[18]:
<AxesSubplot:title={'center':'Estimated parameters'}, xlabel='Parameter value', ylabel='Parameter'>
Model import using the Petab format¶
In this notebook, we illustrate how to use pyPESTO together with PEtab and AMICI. We employ models from the benchmark collection, which we first download:
[1]:
import pypesto
import pypesto.petab
import pypesto.optimize as optimize
import pypesto.visualize as visualize
import amici
import petab
import os
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline
!git clone --depth 1 https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git tmp/benchmark-models || (cd tmp/benchmark-models && git pull)
folder_base = "tmp/benchmark-models/Benchmark-Models/"
fatal: destination path 'tmp/benchmark-models' already exists and is not an empty directory.
Already up to date.
Import¶
Manage PEtab model¶
A PEtab problem comprises all the information on the model, the data and the parameters to perform parameter estimation. We import a model as a petab.Problem.
[2]:
# a collection of models that can be simulated
#model_name = "Zheng_PNAS2012"
model_name = "Boehm_JProteomeRes2014"
#model_name = "Fujita_SciSignal2010"
#model_name = "Sneyd_PNAS2002"
#model_name = "Borghans_BiophysChem1997"
#model_name = "Elowitz_Nature2000"
#model_name = "Crauste_CellSystems2017"
#model_name = "Lucarelli_CellSystems2018"
#model_name = "Schwen_PONE2014"
#model_name = "Blasi_CellSystems2016"
# the yaml configuration file links to all needed files
yaml_config = os.path.join(folder_base, model_name, model_name + '.yaml')
# create a petab problem
petab_problem = petab.Problem.from_yaml(yaml_config)
Import model to AMICI¶
The model must be imported to pyPESTO and AMICI. Therefore, we create a pypesto.PetabImporter from the problem, and create an AMICI model.
[3]:
importer = pypesto.petab.PetabImporter(petab_problem)
model = importer.create_model()
# some model properties
print("Model parameters:", list(model.getParameterIds()), '\n')
print("Model const parameters:", list(model.getFixedParameterIds()), '\n')
print("Model outputs: ", list(model.getObservableIds()), '\n')
print("Model states: ", list(model.getStateIds()), '\n')
Model parameters: ['Epo_degradation_BaF3', 'k_exp_hetero', 'k_exp_homo', 'k_imp_hetero', 'k_imp_homo', 'k_phos', 'ratio', 'specC17', 'noiseParameter1_pSTAT5A_rel', 'noiseParameter1_pSTAT5B_rel', 'noiseParameter1_rSTAT5A_rel']
Model const parameters: []
Model outputs: ['pSTAT5A_rel', 'pSTAT5B_rel', 'rSTAT5A_rel']
Model states: ['STAT5A', 'STAT5B', 'pApB', 'pApA', 'pBpB', 'nucpApA', 'nucpApB', 'nucpBpB']
Create objective function¶
To perform parameter estimation, we need to define an objective function, which integrates the model, data, and noise model defined in the PEtab problem.
[4]:
import libsbml
converter_config = libsbml.SBMLLocalParameterConverter()\
.getDefaultProperties()
petab_problem.sbml_document.convert(converter_config)
obj = importer.create_objective()
# for some models, hyperparamters need to be adjusted
#obj.amici_solver.setMaxSteps(10000)
#obj.amici_solver.setRelativeTolerance(1e-7)
#obj.amici_solver.setAbsoluteTolerance(1e-7)
We can request variable derivatives via sensi_orders, or function values or residuals as specified via mode. Passing return_dict, we obtain the direct result of the AMICI simulation.
[5]:
ret = obj(petab_problem.x_nominal_scaled, mode='mode_fun', sensi_orders=(0,1), return_dict=True)
print(ret)
{'fval': 138.22199677513575, 'grad': array([ 2.20386015e-02, 5.53227506e-02, 5.78886452e-03, 5.40656415e-03,
-4.51595809e-05, 7.91163446e-03, 0.00000000e+00, 1.07840959e-02,
2.40378735e-02, 1.91919657e-02, 0.00000000e+00]), 'hess': array([[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.]]), 'rdatas': [<amici.numpy.ReturnDataView object at 0x7fb394714cd0>]}
The problem defined in PEtab also defines the fixing of parameters, and parameter bounds. This information is contained in a pypesto.Problem.
[6]:
problem = importer.create_problem(obj)
In particular, the problem accounts for the fixing of parametes.
[7]:
print(problem.x_fixed_indices, problem.x_free_indices)
[6, 10] [0, 1, 2, 3, 4, 5, 7, 8, 9]
The problem creates a copy of he objective function that takes into account the fixed parameters. The objective function is able to calculate function values and derivatives. A finite difference check whether the computed gradient is accurate:
[8]:
objective = problem.objective
ret = objective(petab_problem.x_nominal_free_scaled, sensi_orders=(0,1))
print(ret)
(138.22199677513575, array([ 2.20386015e-02, 5.53227506e-02, 5.78886452e-03, 5.40656415e-03,
-4.51595809e-05, 7.91163446e-03, 1.07840959e-02, 2.40378735e-02,
1.91919657e-02]))
[9]:
eps = 1e-4
def fd(x):
grad = np.zeros_like(x)
j = 0
for i, xi in enumerate(x):
mask = np.zeros_like(x)
mask[i] += eps
valinc, _ = objective(x+mask, sensi_orders=(0,1))
valdec, _ = objective(x-mask, sensi_orders=(0,1))
grad[j] = (valinc - valdec) / (2*eps)
j += 1
return grad
fdval = fd(petab_problem.x_nominal_free_scaled)
print("fd: ", fdval)
print("l2 difference: ", np.linalg.norm(ret[1] - fdval))
fd: [0.02493368 0.05309659 0.00530587 0.01291083 0.00587754 0.01473653
0.01078279 0.02403657 0.01919066]
l2 difference: 0.012310244824532846
In short¶
All of the previous steps can be shortened by directly creating an importer object and then a problem:
[10]:
importer = pypesto.petab.PetabImporter.from_yaml(yaml_config)
problem = importer.create_problem()
Run optimization¶
Given the problem, we can perform optimization. We can specify an optimizer to use, and a parallelization engine to speed things up.
[11]:
optimizer = optimize.ScipyOptimizer()
# engine = pypesto.engine.SingleCoreEngine()
engine = pypesto.engine.MultiProcessEngine()
# do the optimization
result = optimize.minimize(problem=problem, optimizer=optimizer,
n_starts=10, engine=engine)
Engine set up to use up to 4 processes in total. The number was automatically determined and might not be appropriate on some systems.
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
[Warning] AMICI:CVODES:CVode:ERR_FAILURE: AMICI ERROR: in module CVODES in function CVode : At t = 129.296 and h = 7.99525e-06, the error test failed repeatedly or with |h| = hmin.
[Warning] AMICI:simulation: AMICI forward simulation failed at t = 129.295950:
AMICI failed to integrate the forward problem
Visualize¶
The results are contained in a pypesto.Result object. It contains e.g. the optimal function values.
[12]:
result.optimize_result.get_for_key('fval')
[12]:
[145.75941164508708,
150.66829665808604,
151.0111203508512,
156.3408523704166,
158.80993946232553,
171.1342910354579,
209.9307084952844,
249.7459886904473,
249.74599725959808,
249.7459974434843]
We can use the standard pyPESTO plotting routines to visualize and analyze the results.
[13]:
ref = visualize.create_references(
x=petab_problem.x_nominal_scaled, fval=obj(petab_problem.x_nominal_scaled))
visualize.waterfall(result, reference=ref, scale_y='lin')
visualize.parameters(result, reference=ref)
[13]:
<matplotlib.axes._subplots.AxesSubplot at 0x7fb345161310>
Storage¶
This notebook illustrates how simulations and results can be saved to file.
[1]:
import pypesto
import pypesto.optimize as optimize
import pypesto.visualize as visualize
from pypesto.store import (save_to_hdf5, read_from_hdf5)
import numpy as np
import scipy as sp
import matplotlib.pyplot as plt
import tempfile
%matplotlib inline
Define the objective and problem¶
[2]:
objective = pypesto.Objective(fun=sp.optimize.rosen,
grad=sp.optimize.rosen_der,
hess=sp.optimize.rosen_hess)
dim_full = 10
lb = -3 * np.ones((dim_full, 1))
ub = 3 * np.ones((dim_full, 1))
problem = pypesto.Problem(objective=objective, lb=lb, ub=ub)
# create optimizers
optimizer = optimize.ScipyOptimizer(method='l-bfgs-b')
# set number of starts
n_starts = 20
Objective function traces¶
During optimization, it is possible to regularly write the objective function trace to file. This is useful e.g. when runs fail, or for various diagnostics. Currently, pyPESTO can save histories to 3 backends: in-memory, as CSV files, or to HDF5 files.
Memory History¶
To record the history in-memory, just set trace_record=True in the pypesto.HistoryOptions. Then, the optimization result contains those histories:
[3]:
# record the history
history_options = pypesto.HistoryOptions(trace_record=True)
# Run optimizaitons
result = optimize.minimize(
problem=problem, optimizer=optimizer,
n_starts=n_starts, history_options=history_options)
0%| | 0/20 [00:00<?, ?it/s]Executing task 0.
Final fval=0.0000, time=0.0218s, n_fval=94.
Executing task 1.
Final fval=0.0000, time=0.0142s, n_fval=61.
Executing task 2.
Final fval=0.0000, time=0.0191s, n_fval=72.
Executing task 3.
Final fval=0.0000, time=0.0185s, n_fval=76.
Executing task 4.
Final fval=0.0000, time=0.0227s, n_fval=81.
25%|██▌ | 5/20 [00:00<00:00, 48.89it/s]Executing task 5.
Final fval=0.0000, time=0.0258s, n_fval=83.
Executing task 6.
Final fval=0.0000, time=0.0270s, n_fval=90.
Executing task 7.
Final fval=3.9866, time=0.0278s, n_fval=77.
Executing task 8.
Final fval=0.0000, time=0.0308s, n_fval=98.
Executing task 9.
Final fval=0.0000, time=0.0256s, n_fval=96.
50%|█████ | 10/20 [00:00<00:00, 39.43it/s]Executing task 10.
Final fval=0.0000, time=0.0224s, n_fval=68.
Executing task 11.
Final fval=0.0000, time=0.0172s, n_fval=64.
Executing task 12.
Final fval=0.0000, time=0.0220s, n_fval=79.
Executing task 13.
Final fval=0.0000, time=0.0277s, n_fval=92.
Executing task 14.
Final fval=0.0000, time=0.0198s, n_fval=70.
75%|███████▌ | 15/20 [00:00<00:00, 41.09it/s]Executing task 15.
Final fval=0.0000, time=0.0253s, n_fval=81.
Executing task 16.
Final fval=3.9866, time=0.0226s, n_fval=61.
Executing task 17.
Final fval=3.9866, time=0.0307s, n_fval=74.
Executing task 18.
Final fval=3.9866, time=0.0236s, n_fval=71.
Executing task 19.
Final fval=0.0000, time=0.0175s, n_fval=74.
100%|██████████| 20/20 [00:00<00:00, 40.68it/s]
Now, in addition to queries on the result, we can also access the
[4]:
print("History type: ", type(result.optimize_result.list[0].history))
# print("Function value trace of best run: ", result.optimize_result.list[0].history.get_fval_trace())
fig, ax = plt.subplots(1, 2)
visualize.waterfall(result, ax=ax[0])
visualize.optimizer_history(result, ax=ax[1])
fig.set_size_inches((15, 5))
History type: <class 'pypesto.objective.history.MemoryHistory'>
CSV History¶
The in-memory storage is however not stored anywhere. To do that, it is possible to store either to CSV or HDF5. This is specified via the storage_file option. If it ends in .csv, a pypesto.objective.history.CsvHistory will be employed; if it ends in .hdf5 a pypesto.objective.history.Hdf5History. Occurrences of the substring {id} in the filename are replaced by the multistart id, allowing to maintain a separate file per run (this is necessary for CSV as otherwise runs are
overwritten).
[5]:
# record the history and store to CSV
history_options = pypesto.HistoryOptions(trace_record=True, storage_file='history_{id}.csv')
# Run optimizaitons
result = optimize.minimize(
problem=problem, optimizer=optimizer,
n_starts=n_starts, history_options=history_options)
0%| | 0/20 [00:00<?, ?it/s]Executing task 0.
Final fval=0.0000, time=1.3848s, n_fval=87.
5%|▌ | 1/20 [00:01<00:26, 1.39s/it]Executing task 1.
Final fval=0.0000, time=1.0376s, n_fval=66.
10%|█ | 2/20 [00:02<00:21, 1.18s/it]Executing task 2.
Final fval=0.0000, time=1.3995s, n_fval=87.
15%|█▌ | 3/20 [00:03<00:21, 1.28s/it]Executing task 3.
Final fval=0.0000, time=1.3883s, n_fval=87.
20%|██ | 4/20 [00:05<00:21, 1.33s/it]Executing task 4.
Final fval=0.0000, time=1.1283s, n_fval=74.
25%|██▌ | 5/20 [00:06<00:18, 1.25s/it]Executing task 5.
Final fval=0.0000, time=1.2335s, n_fval=81.
30%|███ | 6/20 [00:07<00:17, 1.25s/it]Executing task 6.
Final fval=3.9866, time=1.6121s, n_fval=106.
35%|███▌ | 7/20 [00:09<00:17, 1.37s/it]Executing task 7.
Final fval=0.0000, time=1.2220s, n_fval=77.
40%|████ | 8/20 [00:10<00:15, 1.32s/it]Executing task 8.
Final fval=0.0000, time=1.0812s, n_fval=71.
45%|████▌ | 9/20 [00:11<00:13, 1.25s/it]Executing task 9.
Final fval=0.0000, time=1.5227s, n_fval=78.
50%|█████ | 10/20 [00:13<00:13, 1.33s/it]Executing task 10.
Final fval=0.0000, time=1.9653s, n_fval=97.
55%|█████▌ | 11/20 [00:14<00:13, 1.53s/it]Executing task 11.
Final fval=0.0000, time=1.9667s, n_fval=94.
60%|██████ | 12/20 [00:16<00:13, 1.66s/it]Executing task 12.
Final fval=0.0000, time=1.0537s, n_fval=57.
65%|██████▌ | 13/20 [00:18<00:10, 1.48s/it]Executing task 13.
Final fval=0.0000, time=1.5494s, n_fval=81.
70%|███████ | 14/20 [00:19<00:09, 1.50s/it]Executing task 14.
Final fval=0.0000, time=1.8838s, n_fval=94.
75%|███████▌ | 15/20 [00:21<00:08, 1.62s/it]Executing task 15.
Final fval=0.0000, time=1.8472s, n_fval=84.
80%|████████ | 16/20 [00:23<00:06, 1.69s/it]Executing task 16.
Final fval=0.0000, time=1.6928s, n_fval=85.
85%|████████▌ | 17/20 [00:25<00:05, 1.69s/it]Executing task 17.
Final fval=0.0000, time=1.4911s, n_fval=83.
90%|█████████ | 18/20 [00:26<00:03, 1.63s/it]Executing task 18.
Final fval=0.0000, time=1.3229s, n_fval=74.
95%|█████████▌| 19/20 [00:27<00:01, 1.54s/it]Executing task 19.
Final fval=0.0000, time=1.5840s, n_fval=79.
100%|██████████| 20/20 [00:29<00:00, 1.47s/it]
Note that for this simple cost function, saving to CSV takes a considerable amount of time. This overhead decreases for more costly simulators, e.g. using ODE simulations via AMICI.
[6]:
print("History type: ", type(result.optimize_result.list[0].history))
# print("Function value trace of best run: ", result.optimize_result.list[0].history.get_fval_trace())
fig, ax = plt.subplots(1, 2)
visualize.waterfall(result, ax=ax[0])
visualize.optimizer_history(result, ax=ax[1])
fig.set_size_inches((15, 5))
History type: <class 'pypesto.objective.history.CsvHistory'>
HDF5 History¶
Just as in CSV, writing the history to HDF5 takes a considerable amount of time. If a user specifies a HDF5 output file named my_results.hdf5 and uses a parallelization engine, then: * a folder is created to contain partial results, named my_results/ (the stem of the output filename) * files are created to store the results of each start, named my_results/my_results_{START_INDEX}.hdf5 * a file is created to store the combined result from all starts, named my_results.hdf5. Note
that this file depends on the files in the my_results/ directory, so cease to function if my_results/ is deleted.
[7]:
# record the history and store to CSV
history_options = pypesto.HistoryOptions(trace_record=True, storage_file='history.hdf5')
# Run optimizaitons
result = optimize.minimize(
problem=problem, optimizer=optimizer,
n_starts=n_starts, history_options=history_options)
0%| | 0/20 [00:00<?, ?it/s]Executing task 0.
Final fval=0.0000, time=0.5606s, n_fval=322.
5%|▌ | 1/20 [00:00<00:10, 1.78it/s]Executing task 1.
Final fval=3.9866, time=0.3860s, n_fval=280.
10%|█ | 2/20 [00:00<00:08, 2.18it/s]Executing task 2.
Final fval=0.0000, time=0.5257s, n_fval=342.
15%|█▌ | 3/20 [00:01<00:08, 2.04it/s]Executing task 3.
Final fval=0.0000, time=0.4912s, n_fval=333.
20%|██ | 4/20 [00:01<00:07, 2.04it/s]Executing task 4.
Final fval=3.9866, time=0.3889s, n_fval=324.
25%|██▌ | 5/20 [00:02<00:06, 2.20it/s]Executing task 5.
Final fval=0.0000, time=0.4808s, n_fval=345.
30%|███ | 6/20 [00:02<00:06, 2.15it/s]Executing task 6.
Final fval=0.0000, time=0.4517s, n_fval=322.
35%|███▌ | 7/20 [00:03<00:05, 2.17it/s]Executing task 7.
Final fval=0.0000, time=0.5006s, n_fval=347.
40%|████ | 8/20 [00:03<00:05, 2.11it/s]Executing task 8.
Final fval=0.0000, time=0.4723s, n_fval=311.
45%|████▌ | 9/20 [00:04<00:05, 2.11it/s]Executing task 9.
Final fval=0.0000, time=0.3521s, n_fval=307.
50%|█████ | 10/20 [00:04<00:04, 2.29it/s]Executing task 10.
Final fval=3.9866, time=0.4401s, n_fval=283.
55%|█████▌ | 11/20 [00:05<00:03, 2.28it/s]Executing task 11.
Final fval=0.0000, time=0.4453s, n_fval=356.
60%|██████ | 12/20 [00:05<00:03, 2.27it/s]Executing task 12.
Final fval=0.0000, time=0.3788s, n_fval=335.
65%|██████▌ | 13/20 [00:05<00:02, 2.37it/s]Executing task 13.
Final fval=0.0000, time=0.4477s, n_fval=334.
70%|███████ | 14/20 [00:06<00:02, 2.32it/s]Executing task 14.
Final fval=0.0000, time=0.4339s, n_fval=319.
75%|███████▌ | 15/20 [00:06<00:02, 2.31it/s]Executing task 15.
Final fval=0.0000, time=0.4260s, n_fval=343.
80%|████████ | 16/20 [00:07<00:01, 2.32it/s]Executing task 16.
Final fval=3.9866, time=0.4394s, n_fval=313.
85%|████████▌ | 17/20 [00:07<00:01, 2.31it/s]Executing task 17.
Final fval=0.0000, time=0.2605s, n_fval=265.
90%|█████████ | 18/20 [00:07<00:00, 2.62it/s]Executing task 18.
Final fval=0.0000, time=0.4477s, n_fval=340.
95%|█████████▌| 19/20 [00:08<00:00, 2.49it/s]Executing task 19.
Final fval=3.9866, time=0.5053s, n_fval=337.
100%|██████████| 20/20 [00:08<00:00, 2.26it/s]
[8]:
print("History type: ", type(result.optimize_result.list[0].history))
# print("Function value trace of best run: ", result.optimize_result.list[0].history.get_fval_trace())
fig, ax = plt.subplots(1, 2)
visualize.waterfall(result, ax=ax[0])
visualize.optimizer_history(result, ax=ax[1])
fig.set_size_inches((15, 5))
History type: <class 'pypesto.objective.history.Hdf5History'>
Result storage¶
Result objects can be stored as HDF5 files. When applicable, this is preferable to just pickling results, which is not guaranteed to be reproducible in the future.
[9]:
# Run optimizaitons
result = optimize.minimize(
problem=problem, optimizer=optimizer,
n_starts=n_starts)
0%| | 0/20 [00:00<?, ?it/s]Executing task 0.
Final fval=3.9866, time=0.0118s, n_fval=48.
Executing task 1.
Final fval=3.9866, time=0.0201s, n_fval=90.
Executing task 2.
Final fval=0.0000, time=0.0210s, n_fval=100.
Executing task 3.
Final fval=0.0000, time=0.0164s, n_fval=73.
Executing task 4.
Final fval=0.0000, time=0.0174s, n_fval=76.
Executing task 5.
Final fval=0.0000, time=0.0155s, n_fval=71.
30%|███ | 6/20 [00:00<00:00, 55.46it/s]Executing task 6.
Final fval=0.0000, time=0.0190s, n_fval=87.
Executing task 7.
Final fval=0.0000, time=0.0195s, n_fval=88.
Executing task 8.
Final fval=0.0000, time=0.0177s, n_fval=79.
Executing task 9.
Final fval=3.9866, time=0.0179s, n_fval=83.
Executing task 10.
Final fval=0.0000, time=0.0188s, n_fval=86.
Executing task 11.
Final fval=3.9866, time=0.0202s, n_fval=84.
60%|██████ | 12/20 [00:00<00:00, 52.23it/s]Executing task 12.
Final fval=3.9866, time=0.0188s, n_fval=82.
Executing task 13.
Final fval=0.0000, time=0.0211s, n_fval=91.
Executing task 14.
Final fval=3.9866, time=0.0170s, n_fval=75.
Executing task 15.
Final fval=0.0000, time=0.0124s, n_fval=54.
Executing task 16.
Final fval=0.0000, time=0.0161s, n_fval=70.
Executing task 17.
Final fval=0.0000, time=0.0177s, n_fval=81.
90%|█████████ | 18/20 [00:00<00:00, 53.48it/s]Executing task 18.
Final fval=0.0000, time=0.0187s, n_fval=82.
Executing task 19.
Final fval=3.9866, time=0.0163s, n_fval=75.
100%|██████████| 20/20 [00:00<00:00, 53.45it/s]
[10]:
result.optimize_result.list[0:2]
[10]:
[{'id': '4',
'x': array([1.00000001, 1. , 1. , 0.99999999, 0.99999999,
1.00000001, 1.00000001, 1.00000004, 1.00000008, 1.00000014]),
'fval': 2.6045655152986313e-13,
'grad': array([ 7.38459033e-06, -4.78320167e-07, -6.50914679e-07, -1.47726642e-06,
-1.39575141e-05, 9.14793168e-06, -7.58437136e-06, 4.50055738e-07,
1.01219510e-05, -4.24214104e-06]),
'hess': None,
'res': None,
'sres': None,
'n_fval': 76,
'n_grad': 76,
'n_hess': 0,
'n_res': 0,
'n_sres': 0,
'x0': array([ 0.33383114, 2.09297901, -1.77381628, -1.60663808, -2.85350433,
0.71050093, -1.190691 , 0.91974885, -2.34344618, 1.21791823]),
'fval0': 18119.670540771178,
'history': <pypesto.objective.history.History at 0x7ffd399536a0>,
'exitflag': 0,
'time': 0.017375946044921875,
'message': 'CONVERGENCE: REL_REDUCTION_OF_F_<=_FACTR*EPSMCH'},
{'id': '16',
'x': array([1. , 1. , 1.00000001, 1. , 1.00000001,
1.00000003, 1.00000007, 1.00000009, 1.00000017, 1.00000039]),
'fval': 7.312572536347769e-13,
'grad': array([ 3.34432881e-06, -6.16413761e-06, 1.25983886e-05, -5.34613024e-06,
-7.50765648e-06, 1.11777438e-06, 1.94167105e-05, -5.91496342e-06,
-2.50337361e-05, 1.19659990e-05]),
'hess': None,
'res': None,
'sres': None,
'n_fval': 70,
'n_grad': 70,
'n_hess': 0,
'n_res': 0,
'n_sres': 0,
'x0': array([ 2.58291438, 2.48719491, 2.93132676, -0.75290073, 0.34568409,
0.60255167, -0.68200823, -1.01952663, -2.47953741, 2.14959561]),
'fval0': 14770.270006296314,
'history': <pypesto.objective.history.History at 0x7ffd496cea90>,
'exitflag': 0,
'time': 0.016092777252197266,
'message': 'CONVERGENCE: REL_REDUCTION_OF_F_<=_FACTR*EPSMCH'}]
As usual, having obtained our result, we can directly perform some plots:
[11]:
# plot waterfalls
visualize.waterfall(result, size=(15,6))
[11]:
<AxesSubplot:title={'center':'Waterfall plot'}, xlabel='Ordered optimizer run', ylabel='Offsetted function value (relative to best start)'>
Save optimization result as HDF5 file¶
The optimization result can be saved with pypesto.store.write_result(). This will write the problem and the optimization result, and the profiling and sampling results if available, to HDF5. All of them can be disabled with boolean flags (see the documentation)
[12]:
fn = tempfile.mktemp(".hdf5")
# Write result
save_to_hdf5.write_result(result, fn)
Warning: There is no sampling_result, which you tried to save to hdf5.
Read optimization result from HDF5 file¶
When reading in the stored result again, we recover the original optimization result:
[13]:
# Read result and problem
result = read_from_hdf5.read_result(fn)
WARNING: You are loading a problem.
This problem is not to be used without a separately created objective.
WARNING: You are loading a problem.
This problem is not to be used without a separately created objective.
WARNING: You are loading a problem.
This problem is not to be used without a separately created objective.
WARNING: You are loading a problem.
This problem is not to be used without a separately created objective.
Loading the sampling result failed. It is highly likely that no sampling result exists within /var/folders/2f/bnywv1ns2_9g8wtzlf_74yzh0000gn/T/tmpewjf65r6.hdf5.
[14]:
result.optimize_result.list[0:2]
[14]:
[{'id': '4',
'x': array([1.00000001, 1. , 1. , 0.99999999, 0.99999999,
1.00000001, 1.00000001, 1.00000004, 1.00000008, 1.00000014]),
'fval': 2.6045655152986313e-13,
'grad': array([ 7.38459033e-06, -4.78320167e-07, -6.50914679e-07, -1.47726642e-06,
-1.39575141e-05, 9.14793168e-06, -7.58437136e-06, 4.50055738e-07,
1.01219510e-05, -4.24214104e-06]),
'hess': None,
'res': None,
'sres': None,
'n_fval': 76,
'n_grad': 76,
'n_hess': 0,
'n_res': 0,
'n_sres': 0,
'x0': array([ 0.33383114, 2.09297901, -1.77381628, -1.60663808, -2.85350433,
0.71050093, -1.190691 , 0.91974885, -2.34344618, 1.21791823]),
'fval0': 18119.670540771178,
'history': None,
'exitflag': 0,
'time': 0.017375946044921875,
'message': 'CONVERGENCE: REL_REDUCTION_OF_F_<=_FACTR*EPSMCH'},
{'id': '16',
'x': array([1. , 1. , 1.00000001, 1. , 1.00000001,
1.00000003, 1.00000007, 1.00000009, 1.00000017, 1.00000039]),
'fval': 7.312572536347769e-13,
'grad': array([ 3.34432881e-06, -6.16413761e-06, 1.25983886e-05, -5.34613024e-06,
-7.50765648e-06, 1.11777438e-06, 1.94167105e-05, -5.91496342e-06,
-2.50337361e-05, 1.19659990e-05]),
'hess': None,
'res': None,
'sres': None,
'n_fval': 70,
'n_grad': 70,
'n_hess': 0,
'n_res': 0,
'n_sres': 0,
'x0': array([ 2.58291438, 2.48719491, 2.93132676, -0.75290073, 0.34568409,
0.60255167, -0.68200823, -1.01952663, -2.47953741, 2.14959561]),
'fval0': 14770.270006296314,
'history': None,
'exitflag': 0,
'time': 0.016092777252197266,
'message': 'CONVERGENCE: REL_REDUCTION_OF_F_<=_FACTR*EPSMCH'}]
[15]:
# plot waterfalls
pypesto.visualize.waterfall(result, size=(15,6))
[15]:
<AxesSubplot:title={'center':'Waterfall plot'}, xlabel='Ordered optimizer run', ylabel='Offsetted function value (relative to best start)'>
A sampler study¶
In this notebook, we perform a short study of how various samplers implemented in pyPESTO perform.
The pipeline¶
First, we show a typical workflow, fully integrating the samplers with a PEtab problem, using a toy example of a conversion reaction.
[1]:
import pypesto
import pypesto.petab
import pypesto.optimize as optimize
import pypesto.sample as sample
import pypesto.visualize as visualize
import petab
# import to petab
petab_problem = petab.Problem.from_yaml(
"conversion_reaction/conversion_reaction.yaml")
# import to pypesto
importer = pypesto.petab.PetabImporter(petab_problem)
# create problem
problem = importer.create_problem()
2021-03-15 08:50:22.614 - amici.petab_import - INFO - Importing model ...
2021-03-15 08:50:22.617 - amici.petab_import - INFO - Model name is 'conversion_reaction_0'.
Writing model code to '/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0'.
2021-03-15 08:50:22.619 - amici.petab_import - INFO - Species: 2
2021-03-15 08:50:22.619 - amici.petab_import - INFO - Global parameters: 2
2021-03-15 08:50:22.620 - amici.petab_import - INFO - Reactions: 2
2021-03-15 08:50:22.629 - amici.petab_import - INFO - Observables: 1
2021-03-15 08:50:22.632 - amici.petab_import - INFO - Sigmas: 1
2021-03-15 08:50:22.635 - amici.petab_import - DEBUG - Adding output parameters to model: OrderedDict()
2021-03-15 08:50:22.636 - amici.petab_import - DEBUG - Adding initial assignments for []
2021-03-15 08:50:22.637 - amici.petab_import - DEBUG - Condition table: (1, 0)
2021-03-15 08:50:22.637 - amici.petab_import - DEBUG - Fixed parameters are []
2021-03-15 08:50:22.638 - amici.petab_import - INFO - Overall fixed parameters: 0
2021-03-15 08:50:22.639 - amici.petab_import - INFO - Variable parameters: 2
2021-03-15 08:50:22.655 - amici.sbml_import - INFO - Finished gathering local SBML symbols ++ (3.76E-03s)
2021-03-15 08:50:22.660 - amici.sbml_import - INFO - Finished processing SBML parameters ++ (1.52E-04s)
2021-03-15 08:50:22.665 - amici.sbml_import - INFO - Finished processing SBML compartments ++ (2.55E-04s)
2021-03-15 08:50:22.674 - amici.sbml_import - INFO - Finished processing SBML species initials +++ (2.79E-04s)
2021-03-15 08:50:22.679 - amici.sbml_import - INFO - Finished processing SBML rate rules +++ (3.09E-05s)
2021-03-15 08:50:22.680 - amici.sbml_import - INFO - Finished processing SBML species ++ (9.89E-03s)
2021-03-15 08:50:22.688 - amici.sbml_import - INFO - Finished processing SBML reactions ++ (1.64E-03s)
2021-03-15 08:50:22.693 - amici.sbml_import - INFO - Finished processing SBML rules ++ (2.03E-04s)
2021-03-15 08:50:22.698 - amici.sbml_import - INFO - Finished processing SBML initial assignments++ (7.04E-05s)
2021-03-15 08:50:22.704 - amici.sbml_import - INFO - Finished processing SBML species references ++ (2.42E-04s)
2021-03-15 08:50:22.704 - amici.sbml_import - INFO - Finished importing SBML + (5.85E-02s)
2021-03-15 08:50:22.758 - amici.sbml_import - INFO - Finished processing SBML observables + (4.68E-02s)
2021-03-15 08:50:22.772 - amici.ode_export - INFO - Finished running smart_multiply ++ (1.29E-03s)
2021-03-15 08:50:22.785 - amici.ode_export - INFO - Finished simplifying w +++ (1.97E-03s)
2021-03-15 08:50:22.785 - amici.ode_export - INFO - Finished computing w ++ (7.49E-03s)
2021-03-15 08:50:22.788 - amici.ode_export - INFO - Finished importing SbmlImporter + (2.05E-02s)
2021-03-15 08:50:22.810 - amici.ode_export - INFO - Finished simplifying Jy ++++ (6.82E-03s)
2021-03-15 08:50:22.810 - amici.ode_export - INFO - Finished computing Jy +++ (1.05E-02s)
2021-03-15 08:50:22.832 - amici.ode_export - INFO - Finished writing Jy.cpp ++ (3.50E-02s)
2021-03-15 08:50:22.854 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (1.02E-02s)
2021-03-15 08:50:22.863 - amici.ode_export - INFO - Finished simplifying dJydsigmay ++++ (3.55E-03s)
2021-03-15 08:50:22.863 - amici.ode_export - INFO - Finished computing dJydsigmay +++ (2.29E-02s)
2021-03-15 08:50:22.867 - amici.ode_export - INFO - Finished writing dJydsigmay.cpp ++ (3.04E-02s)
2021-03-15 08:50:22.884 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (5.70E-03s)
2021-03-15 08:50:22.895 - amici.ode_export - INFO - Finished simplifying dJydy ++++ (5.63E-03s)
2021-03-15 08:50:22.897 - amici.ode_export - INFO - Finished computing dJydy +++ (2.16E-02s)
2021-03-15 08:50:22.904 - amici.ode_export - INFO - Finished writing dJydy.cpp ++ (3.23E-02s)
2021-03-15 08:50:22.921 - amici.ode_export - INFO - Finished simplifying root ++++ (7.09E-05s)
2021-03-15 08:50:22.922 - amici.ode_export - INFO - Finished computing root +++ (6.78E-03s)
2021-03-15 08:50:22.923 - amici.ode_export - INFO - Finished writing root.cpp ++ (1.28E-02s)
2021-03-15 08:50:22.944 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (3.90E-03s)
2021-03-15 08:50:22.953 - amici.ode_export - INFO - Finished simplifying dwdp ++++ (1.53E-03s)
2021-03-15 08:50:22.956 - amici.ode_export - INFO - Finished computing dwdp +++ (2.09E-02s)
2021-03-15 08:50:22.964 - amici.ode_export - INFO - Finished writing dwdp.cpp ++ (3.48E-02s)
2021-03-15 08:50:22.991 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (4.88E-03s)
2021-03-15 08:50:22.997 - amici.ode_export - INFO - Finished simplifying dwdx ++++ (1.64E-03s)
2021-03-15 08:50:23.000 - amici.ode_export - INFO - Finished computing dwdx +++ (2.08E-02s)
2021-03-15 08:50:23.006 - amici.ode_export - INFO - Finished writing dwdx.cpp ++ (3.27E-02s)
2021-03-15 08:50:23.022 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (1.28E-04s)
2021-03-15 08:50:23.028 - amici.ode_export - INFO - Finished simplifying dwdw ++++ (8.05E-05s)
2021-03-15 08:50:23.029 - amici.ode_export - INFO - Finished computing dwdw +++ (1.16E-02s)
2021-03-15 08:50:23.032 - amici.ode_export - INFO - Finished writing dwdw.cpp ++ (2.06E-02s)
2021-03-15 08:50:23.056 - amici.ode_export - INFO - Finished simplifying xdot ++++ (2.48E-03s)
2021-03-15 08:50:23.057 - amici.ode_export - INFO - Finished computing xdot +++ (1.02E-02s)
2021-03-15 08:50:23.066 - amici.ode_export - INFO - Finished writing dxdotdw.cpp ++ (2.14E-02s)
2021-03-15 08:50:23.089 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (2.54E-03s)
2021-03-15 08:50:23.100 - amici.ode_export - INFO - Finished simplifying dxdotdx_explicit ++++ (1.42E-04s)
2021-03-15 08:50:23.102 - amici.ode_export - INFO - Finished computing dxdotdx_explicit +++ (2.35E-02s)
2021-03-15 08:50:23.104 - amici.ode_export - INFO - Finished writing dxdotdx_explicit.cpp ++ (3.17E-02s)
2021-03-15 08:50:23.133 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (2.19E-04s)
2021-03-15 08:50:23.142 - amici.ode_export - INFO - Finished simplifying dxdotdp_explicit ++++ (1.24E-04s)
2021-03-15 08:50:23.143 - amici.ode_export - INFO - Finished computing dxdotdp_explicit +++ (1.97E-02s)
2021-03-15 08:50:23.146 - amici.ode_export - INFO - Finished writing dxdotdp_explicit.cpp ++ (3.14E-02s)
2021-03-15 08:50:23.179 - amici.ode_export - INFO - Finished simplifying y ++++++ (4.50E-05s)
2021-03-15 08:50:23.179 - amici.ode_export - INFO - Finished computing y +++++ (4.03E-03s)
2021-03-15 08:50:23.188 - amici.ode_export - INFO - Finished running smart_jacobian +++++ (8.90E-04s)
2021-03-15 08:50:23.194 - amici.ode_export - INFO - Finished simplifying dydx +++++ (6.74E-05s)
2021-03-15 08:50:23.195 - amici.ode_export - INFO - Finished computing dydx ++++ (2.33E-02s)
2021-03-15 08:50:23.211 - amici.ode_export - INFO - Finished running smart_jacobian +++++ (1.15E-04s)
2021-03-15 08:50:23.218 - amici.ode_export - INFO - Finished simplifying dydw +++++ (9.86E-05s)
2021-03-15 08:50:23.219 - amici.ode_export - INFO - Finished computing dydw ++++ (1.33E-02s)
2021-03-15 08:50:23.225 - amici.ode_export - INFO - Finished simplifying dydx ++++ (8.66E-05s)
2021-03-15 08:50:23.226 - amici.ode_export - INFO - Finished computing dydx +++ (5.92E-02s)
2021-03-15 08:50:23.230 - amici.ode_export - INFO - Finished writing dydx.cpp ++ (6.91E-02s)
2021-03-15 08:50:23.249 - amici.ode_export - INFO - Finished running smart_jacobian +++++ (1.44E-04s)
2021-03-15 08:50:23.256 - amici.ode_export - INFO - Finished simplifying dydp +++++ (6.76E-05s)
2021-03-15 08:50:23.257 - amici.ode_export - INFO - Finished computing dydp ++++ (1.17E-02s)
2021-03-15 08:50:23.262 - amici.ode_export - INFO - Finished simplifying dydp ++++ (6.56E-05s)
2021-03-15 08:50:23.262 - amici.ode_export - INFO - Finished computing dydp +++ (2.19E-02s)
2021-03-15 08:50:23.263 - amici.ode_export - INFO - Finished writing dydp.cpp ++ (2.69E-02s)
2021-03-15 08:50:23.278 - amici.ode_export - INFO - Finished simplifying sigmay +++++ (4.36E-05s)
2021-03-15 08:50:23.278 - amici.ode_export - INFO - Finished computing sigmay ++++ (3.84E-03s)
2021-03-15 08:50:23.283 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (2.24E-04s)
2021-03-15 08:50:23.288 - amici.ode_export - INFO - Finished simplifying dsigmaydp ++++ (6.41E-05s)
2021-03-15 08:50:23.289 - amici.ode_export - INFO - Finished computing dsigmaydp +++ (1.77E-02s)
2021-03-15 08:50:23.290 - amici.ode_export - INFO - Finished writing dsigmaydp.cpp ++ (2.23E-02s)
2021-03-15 08:50:23.299 - amici.ode_export - INFO - Finished writing sigmay.cpp ++ (1.19E-03s)
2021-03-15 08:50:23.308 - amici.ode_export - INFO - Finished computing stau +++ (1.14E-04s)
2021-03-15 08:50:23.309 - amici.ode_export - INFO - Finished writing stau.cpp ++ (4.80E-03s)
2021-03-15 08:50:23.317 - amici.ode_export - INFO - Finished computing deltasx +++ (1.12E-04s)
2021-03-15 08:50:23.318 - amici.ode_export - INFO - Finished writing deltasx.cpp ++ (4.36E-03s)
2021-03-15 08:50:23.324 - amici.ode_export - INFO - Finished writing w.cpp ++ (1.32E-03s)
2021-03-15 08:50:23.336 - amici.ode_export - INFO - Finished simplifying x0 ++++ (4.87E-05s)
2021-03-15 08:50:23.337 - amici.ode_export - INFO - Finished computing x0 +++ (4.14E-03s)
2021-03-15 08:50:23.339 - amici.ode_export - INFO - Finished writing x0.cpp ++ (9.07E-03s)
2021-03-15 08:50:23.351 - amici.ode_export - INFO - Finished simplifying x0_fixedParameters ++++ (3.09E-05s)
2021-03-15 08:50:23.352 - amici.ode_export - INFO - Finished computing x0_fixedParameters +++ (4.07E-03s)
2021-03-15 08:50:23.353 - amici.ode_export - INFO - Finished writing x0_fixedParameters.cpp ++ (9.17E-03s)
2021-03-15 08:50:23.364 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (2.02E-04s)
2021-03-15 08:50:23.369 - amici.ode_export - INFO - Finished simplifying sx0 ++++ (8.59E-05s)
2021-03-15 08:50:23.370 - amici.ode_export - INFO - Finished computing sx0 +++ (9.57E-03s)
2021-03-15 08:50:23.371 - amici.ode_export - INFO - Finished writing sx0.cpp ++ (1.38E-02s)
2021-03-15 08:50:23.383 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (4.07E-05s)
2021-03-15 08:50:23.390 - amici.ode_export - INFO - Finished running smart_jacobian ++++ (6.25E-05s)
2021-03-15 08:50:23.396 - amici.ode_export - INFO - Finished simplifying sx0_fixedParameters ++++ (4.51E-05s)
2021-03-15 08:50:23.397 - amici.ode_export - INFO - Finished computing sx0_fixedParameters +++ (1.78E-02s)
2021-03-15 08:50:23.398 - amici.ode_export - INFO - Finished writing sx0_fixedParameters.cpp ++ (2.25E-02s)
2021-03-15 08:50:23.407 - amici.ode_export - INFO - Finished writing xdot.cpp ++ (2.42E-03s)
2021-03-15 08:50:23.412 - amici.ode_export - INFO - Finished writing y.cpp ++ (5.83E-04s)
2021-03-15 08:50:23.425 - amici.ode_export - INFO - Finished simplifying x_rdata ++++ (6.01E-05s)
2021-03-15 08:50:23.425 - amici.ode_export - INFO - Finished computing x_rdata +++ (4.55E-03s)
2021-03-15 08:50:23.427 - amici.ode_export - INFO - Finished writing x_rdata.cpp ++ (9.85E-03s)
2021-03-15 08:50:23.442 - amici.ode_export - INFO - Finished simplifying total_cl ++++ (3.69E-05s)
2021-03-15 08:50:23.442 - amici.ode_export - INFO - Finished computing total_cl +++ (4.29E-03s)
2021-03-15 08:50:23.443 - amici.ode_export - INFO - Finished writing total_cl.cpp ++ (9.21E-03s)
2021-03-15 08:50:23.459 - amici.ode_export - INFO - Finished simplifying x_solver ++++ (7.44E-05s)
2021-03-15 08:50:23.460 - amici.ode_export - INFO - Finished computing x_solver +++ (5.19E-03s)
2021-03-15 08:50:23.462 - amici.ode_export - INFO - Finished writing x_solver.cpp ++ (1.14E-02s)
2021-03-15 08:50:23.472 - amici.ode_export - INFO - Finished generating cpp code + (6.78E-01s)
2021-03-15 08:50:55.810 - amici.ode_export - INFO - Finished compiling cpp code + (3.23E+01s)
2021-03-15 08:50:55.813 - amici.petab_import - INFO - Finished Importing PEtab model (3.32E+01s)
running build_ext
Changed extra_compile_args for unix to ['-fopenmp', '-std=c++14']
building 'conversion_reaction_0._conversion_reaction_0' extension
Testing SWIG executable swig4.0... FAILED.
Testing SWIG executable swig3.0... SUCCEEDED.
swigging swig/conversion_reaction_0.i to swig/conversion_reaction_0_wrap.cpp
swig3.0 -python -c++ -modern -outdir conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/swig -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -o swig/conversion_reaction_0_wrap.cpp swig/conversion_reaction_0.i
creating build
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/swig
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c swig/conversion_reaction_0_wrap.cpp -o build/temp.linux-x86_64-3.8/swig/conversion_reaction_0_wrap.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_Jy.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_Jy.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_deltasx.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_deltasx.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdp_explicit_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdp_explicit_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdw.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdw.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdp_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdp_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_w.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_w.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dydx.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dydx.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_stau.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_stau.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_x0.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_x0.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_total_cl.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_total_cl.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdw_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdw_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dJydsigmay.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydsigmay.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdx_explicit.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdx_explicit.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dydp.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dydp.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_sigmay.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_sigmay.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dJydy_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydy_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdx_explicit_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdx_explicit_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_xdot.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_xdot.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdx.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdx.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdp.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdp.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdw.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdw.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_y.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_y.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_x_solver.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_x_solver.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dJydy_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydy_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_sx0.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_sx0.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dsigmaydp.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dsigmaydp.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c wrapfunctions.cpp -o build/temp.linux-x86_64-3.8/wrapfunctions.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdx_explicit_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdx_explicit_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdw_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdw_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_x_rdata.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_x_rdata.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdp_explicit.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdp_explicit.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_sx0_fixedParameters.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_sx0_fixedParameters.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdp_explicit_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdp_explicit_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdx_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdx_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdp_colptrs.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdp_colptrs.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_x0_fixedParameters.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_x0_fixedParameters.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dxdotdw_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdw_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dJydy.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydy.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdx_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdx_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_root.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_root.o -fopenmp -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0 -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/gsl -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/sundials/include -I/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/usr/include/python3.8 -c conversion_reaction_0_dwdw_rowvals.cpp -o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdw_rowvals.o -fopenmp -std=c++14
x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/swig/conversion_reaction_0_wrap.o build/temp.linux-x86_64-3.8/conversion_reaction_0_Jy.o build/temp.linux-x86_64-3.8/conversion_reaction_0_deltasx.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdp_explicit_rowvals.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdw.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdp_rowvals.o build/temp.linux-x86_64-3.8/conversion_reaction_0_w.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dydx.o build/temp.linux-x86_64-3.8/conversion_reaction_0_stau.o build/temp.linux-x86_64-3.8/conversion_reaction_0_x0.o build/temp.linux-x86_64-3.8/conversion_reaction_0_total_cl.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdw_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydsigmay.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdx_explicit.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dydp.o build/temp.linux-x86_64-3.8/conversion_reaction_0_sigmay.o build/temp.linux-x86_64-3.8/conversion_reaction_0.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydy_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdx_explicit_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_xdot.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdx.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdp.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdw.o build/temp.linux-x86_64-3.8/conversion_reaction_0_y.o build/temp.linux-x86_64-3.8/conversion_reaction_0_x_solver.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydy_rowvals.o build/temp.linux-x86_64-3.8/conversion_reaction_0_sx0.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dsigmaydp.o build/temp.linux-x86_64-3.8/wrapfunctions.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdx_explicit_rowvals.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdw_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_x_rdata.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdp_explicit.o build/temp.linux-x86_64-3.8/conversion_reaction_0_sx0_fixedParameters.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdp_explicit_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdx_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdp_colptrs.o build/temp.linux-x86_64-3.8/conversion_reaction_0_x0_fixedParameters.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dxdotdw_rowvals.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dJydy.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdx_rowvals.o build/temp.linux-x86_64-3.8/conversion_reaction_0_root.o build/temp.linux-x86_64-3.8/conversion_reaction_0_dwdw_rowvals.o -L/usr/lib/x86_64-linux-gnu/hdf5/serial -L/usr/local/lib/python3.8/dist-packages/amici-0.11.13-py3.8-linux-x86_64.egg/amici/libs -lamici -lsundials -lsuitesparse -lcblas -lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5 -o /home/elba/Downloads/pyPESTO/doc/example/amici_models/conversion_reaction_0/conversion_reaction_0/_conversion_reaction_0.cpython-38-x86_64-linux-gnu.so -fopenmp
Commonly, as a first step, optimization is performed, in order to find good parameter point estimates.
[2]:
%%time
result = optimize.minimize(problem, n_starts=10)
Parameters obtained from history and optimizer do not match: [ -0.91617976 -10.39367452], [ -0.9161923 -10.39367204]
CPU times: user 2.21 s, sys: 406 ms, total: 2.62 s
Wall time: 2.06 s
[3]:
ax = visualize.waterfall(result, size=(4,4))
Next, we perform sampling. Here, we employ a pypesto.sample.AdaptiveParallelTemperingSampler sampler, which runs Markov Chain Monte Carlo (MCMC) chains on different temperatures. For each chain, we employ a pypesto.sample.AdaptiveMetropolisSampler. For more on the samplers see below or the API documentation.
[4]:
sampler = sample.AdaptiveParallelTemperingSampler(
internal_sampler=sample.AdaptiveMetropolisSampler(),
n_chains=3)
For the actual sampling, we call the pypesto.sample.sample function. By passing the result object to the function, the previously found global optimum is used as starting point for the MCMC sampling.
[5]:
%%time
result = sample.sample(problem, n_samples=10000, sampler=sampler, result=result)
100%|██████████| 10000/10000 [00:55<00:00, 179.06it/s]
CPU times: user 1min, sys: 9.35 s, total: 1min 9s
Wall time: 55.9 s
When the sampling is finished, we can analyse our results. A first thing to do is to analyze the sampling burn-in:
[6]:
sample.geweke_test(result)
[6]:
0
pyPESTO provides functions to analyse both the sampling process as well as the obtained sampling result. Visualizing the traces e.g. allows to detect burn-in phases, or fine-tune hyperparameters. First, the parameter trajectories can be visualized:
[7]:
sample.geweke_test(result)
ax = visualize.sampling_parameter_traces(result, use_problem_bounds=False)
Next, also the log posterior trace can be visualized:
[8]:
ax = visualize.sampling_fval_traces(result)
To visualize the result, there are various options. The scatter plot shows histograms of 1-dim parameter marginals and scatter plots of 2-dimensional parameter combinations:
[9]:
ax = visualize.sampling_scatter(result, size=[13,6])
sampling_1d_marginals allows to plot e.g. kernel density estimates or histograms (internally using seaborn):
[10]:
for i_chain in range(len(result.sample_result.betas)):
visualize.sampling_1d_marginals(
result, i_chain=i_chain, suptitle=f"Chain: {i_chain}")
That’s it for the moment on using the sampling pipeline.
1-dim test problem¶
To compare and test the various implemented samplers, we first study a 1-dimensional test problem of a gaussian mixture density, together with a flat prior.
[1]:
import numpy as np
from scipy.stats import multivariate_normal
import seaborn as sns
import pypesto
import pypesto.sample as sample
import pypesto.visualize as visualize
def density(x):
return 0.3*multivariate_normal.pdf(x, mean=-1.5, cov=0.1) + \
0.7*multivariate_normal.pdf(x, mean=2.5, cov=0.2)
def nllh(x):
return - np.log(density(x))
objective = pypesto.Objective(fun=nllh)
problem = pypesto.Problem(
objective=objective, lb=-4, ub=5, x_names=['x'])
The likelihood has two separate modes:
[2]:
xs = np.linspace(-4, 5, 100)
ys = [density(x) for x in xs]
ax = sns.lineplot(xs, ys, color='C1')
Metropolis sampler¶
For this problem, let us try out the simplest sampler, the pypesto.sample.MetropolisSampler.
[13]:
%%time
sampler = sample.MetropolisSampler({'std': 0.5})
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
100%|██████████| 10000/10000 [00:03<00:00, 2774.43it/s]
CPU times: user 3.65 s, sys: 194 ms, total: 3.84 s
Wall time: 3.62 s
[14]:
sample.geweke_test(result)
ax = visualize.sampling_1d_marginals(result)
ax[0][0].plot(xs, ys)
[14]:
[<matplotlib.lines.Line2D at 0x7f8466613f40>]
The obtained posterior does not accurately represent the distribution, often only capturing one mode. This is because it is hard for the Markov chain to jump between the distribution’s two modes. This can be fixed by choosing a higher proposal variation std:
[15]:
%%time
sampler = sample.MetropolisSampler({'std': 1})
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
100%|██████████| 10000/10000 [00:03<00:00, 2849.08it/s]
CPU times: user 3.55 s, sys: 190 ms, total: 3.74 s
Wall time: 3.52 s
[16]:
sample.geweke_test(result)
ax = visualize.sampling_1d_marginals(result)
ax[0][0].plot(xs, ys)
[16]:
[<matplotlib.lines.Line2D at 0x7f844fffcdf0>]
In general, MCMC have difficulties exploring multimodel landscapes. One way to overcome this is to used parallel tempering. There, various chains are run, lifting the densities to different temperatures. At high temperatures, proposed steps are more likely to get accepted and thus jumps between modes more likely.
Parallel tempering sampler¶
In pyPESTO, the most basic parallel tempering algorithm is the pypesto.sample.ParallelTemperingSampler. It takes an internal_sampler parameter, to specify what sampler to use for performing sampling the different chains. Further, we can directly specify what inverse temperatures betas to use. When not specifying the betas explicitly but just the number of chains n_chains, an established near-exponential decay scheme is used.
[17]:
%%time
sampler = sample.ParallelTemperingSampler(
internal_sampler=sample.MetropolisSampler(),
betas=[1, 1e-1, 1e-2])
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
100%|██████████| 10000/10000 [00:11<00:00, 863.05it/s]
CPU times: user 11.8 s, sys: 621 ms, total: 12.4 s
Wall time: 11.6 s
[18]:
sample.geweke_test(result)
for i_chain in range(len(result.sample_result.betas)):
visualize.sampling_1d_marginals(
result, i_chain=i_chain, suptitle=f"Chain: {i_chain}")
Of interest is here finally the first chain at index i_chain=0, which approximates the posterior well.
Adaptive Metropolis sampler¶
The problem of having to specify the proposal step variation manually can be overcome by using the pypesto.sample.AdaptiveMetropolisSampler, which iteratively adjusts the proposal steps to the function landscape.
[19]:
%%time
sampler = sample.AdaptiveMetropolisSampler()
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
100%|██████████| 10000/10000 [00:04<00:00, 2337.47it/s]
CPU times: user 4.35 s, sys: 55.4 ms, total: 4.41 s
Wall time: 4.3 s
[20]:
sample.geweke_test(result)
ax = visualize.sampling_1d_marginals(result)
Adaptive parallel tempering sampler¶
The pypesto.sample.AdaptiveParallelTemperingSampler iteratively adjusts the temperatures to obtain good swapping rates between chains.
[21]:
%%time
sampler = sample.AdaptiveParallelTemperingSampler(
internal_sampler=sample.AdaptiveMetropolisSampler(), n_chains=3)
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
100%|██████████| 10000/10000 [00:13<00:00, 752.49it/s]
CPU times: user 13.3 s, sys: 91 ms, total: 13.4 s
Wall time: 13.3 s
[22]:
sample.geweke_test(result)
for i_chain in range(len(result.sample_result.betas)):
visualize.sampling_1d_marginals(
result, i_chain=i_chain, suptitle=f"Chain: {i_chain}")
[23]:
result.sample_result.betas
[23]:
array([1.0000000e+00, 2.1503801e-01, 2.0000000e-05])
Pymc3 sampler¶
[24]:
%%time
sampler = sample.Pymc3Sampler()
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
Auto-assigning NUTS sampler...
Initializing NUTS using jitter+adapt_diag...
Initializing NUTS failed. Falling back to elementwise auto-assignment.
Sequential sampling (1 chains in 1 job)
Slice: [x]
Sampling chain 0, 0 divergences: 100%|██████████| 10500/10500 [00:25<00:00, 407.36it/s]
Only one chain was sampled, this makes it impossible to run some convergence checks
CPU times: user 29.2 s, sys: 860 ms, total: 30.1 s
Wall time: 30.8 s
[25]:
sample.geweke_test(result)
for i_chain in range(len(result.sample_result.betas)):
visualize.sampling_1d_marginals(
result, i_chain=i_chain, suptitle=f"Chain: {i_chain}")
If not specified, pymc3 chooses an adequate sampler automatically.
Emcee sampler¶
[4]:
%%time
sampler = sample.EmceeSampler(nwalkers=10, run_args={'progress': True})
result = sample.sample(problem, 1e4, sampler, x0=np.array([0.5]))
100%|██████████| 10000/10000 [00:35<00:00, 278.38it/s]
CPU times: user 35.8 s, sys: 344 ms, total: 36.2 s
Wall time: 35.9 s
[5]:
sample.geweke_test(result)
for i_chain in range(len(result.sample_result.betas)):
visualize.sampling_1d_marginals(
result, i_chain=i_chain, suptitle=f"Chain: {i_chain}")
2-dim test problem: Rosenbrock banana¶
The adaptive parallel tempering sampler with chains running adaptive Metropolis samplers is also able to sample from more challenging posterior distributions. To illustrates this shortly, we use the Rosenbrock function.
[26]:
import scipy.optimize as so
import pypesto
# first type of objective
objective = pypesto.Objective(fun=so.rosen)
dim_full = 4
lb = -5 * np.ones((dim_full, 1))
ub = 5 * np.ones((dim_full, 1))
problem = pypesto.Problem(objective=objective, lb=lb, ub=ub)
[27]:
%%time
sampler = sample.AdaptiveParallelTemperingSampler(
internal_sampler=sample.AdaptiveMetropolisSampler(), n_chains=10)
result =sample.sample(problem, 1e4, sampler, x0=np.zeros(dim_full))
100%|██████████| 10000/10000 [00:35<00:00, 279.44it/s]
CPU times: user 35.6 s, sys: 47.5 ms, total: 35.7 s
Wall time: 35.9 s
[28]:
sample.geweke_test(result)
ax = visualize.sampling_scatter(result)
ax = visualize.sampling_1d_marginals(result)
MCMC sampling diagnostics¶
In this notebook, we illustrate how to assess the quality of your MCMC samples, e.g. convergence and auto-correlation, in pyPESTO.
The pipeline¶
First, we load the model and data to generate the MCMC samples from. In this example we show a toy example of a conversion reaction, loaded as a PEtab problem.
[1]:
import pypesto
import pypesto.petab
import pypesto.optimize as optimize
import pypesto.sample as sample
import pypesto.visualize as visualize
import petab
import numpy as np
import logging
import matplotlib.pyplot as plt
# log diagnostics
logger = logging.getLogger("pypesto.sample.diagnostics")
logger.setLevel(logging.INFO)
logger.addHandler(logging.StreamHandler())
# import to petab
petab_problem = petab.Problem.from_yaml(
"conversion_reaction/multiple_conditions/conversion_reaction.yaml")
# import to pypesto
importer = pypesto.petab.PetabImporter(petab_problem)
# create problem
problem = importer.create_problem()
Create the sampler object, in this case we will use adaptive parallel tempering with 3 temperatures.
[2]:
sampler = sample.AdaptiveParallelTemperingSampler(
internal_sampler=sample.AdaptiveMetropolisSampler(),
n_chains=3)
First, we will initiate the MCMC chain at a “random” point in parameter space, e.g. \(\theta_{start} = [3, -4]\)
[3]:
result = sample.sample(problem, n_samples=10000, sampler=sampler, x0=np.array([3,-4]))
elapsed_time = result.sample_result.time
print(f'Elapsed time: {round(elapsed_time,2)}')
100%|██████████| 10000/10000 [00:44<00:00, 225.23it/s]
Elapsed time: 54.85
[4]:
ax = visualize.sampling_parameter_traces(result, use_problem_bounds=False, size=(12,5))
By visualizing the chains, we can see a warm up phase occurring until convergence of the chain is reached. This is commonly known as “burn in” phase and should be discarded. An automatic way to evaluate and find the index of the chain in which the warm up is finished can be done by using the Geweke test.
[5]:
sample.geweke_test(result=result)
ax = visualize.sampling_parameter_traces(result, use_problem_bounds=False, size=(12,5))
Geweke burn-in index: 500
[6]:
ax = visualize.sampling_parameter_traces(result, use_problem_bounds=False, full_trace=True, size=(12,5))
Calculate the effective sample size per computation time. We save the results in a variable as we will compare them later.
[7]:
sample.effective_sample_size(result=result)
ess = result.sample_result.effective_sample_size
print(f'Effective sample size per computation time: {round(ess/elapsed_time,2)}')
Estimated chain autocorrelation: 8.482536903793251
Estimated effective sample size: 1001.947062942551
Effective sample size per computation time: 18.27
[8]:
alpha = [99, 95, 90]
ax = visualize.sampling_parameter_cis(result, alpha=alpha, size=(10,5))
Predictions can be performed by creating a parameter ensemble from the sample, then applying a predictor to the ensemble. The predictor requires a simulation tool. Here, AMICI is used. First, the predictor is setup.
[9]:
from pypesto.predict.constants import AMICI_STATUS, AMICI_T, AMICI_X, AMICI_Y
from pypesto.predict import AmiciPredictor
# This post_processor will transform the output of the simulation tool
# such that the output is compatible with the next steps.
def post_processor(amici_outputs, output_type, output_ids):
outputs = [
amici_output[output_type] if amici_output[AMICI_STATUS] == 0
else np.full((len(amici_output[AMICI_T]), len(output_ids)), np.nan)
for amici_output in amici_outputs
]
return outputs
# Setup post-processors for both states and observables.
from functools import partial
amici_objective = result.problem.objective
state_ids = amici_objective.amici_model.getStateIds()
observable_ids = amici_objective.amici_model.getObservableIds()
post_processor_x = partial(
post_processor,
output_type=AMICI_X,
output_ids=state_ids,
)
post_processor_y = partial(
post_processor,
output_type=AMICI_Y,
output_ids=observable_ids,
)
# Create pyPESTO predictors for states and observables
predictor_x = AmiciPredictor(
amici_objective,
post_processor=post_processor_x,
output_ids=state_ids,
)
predictor_y = AmiciPredictor(
amici_objective,
post_processor=post_processor_y,
output_ids=observable_ids,
)
Next, the ensemble is created.
[10]:
from pypesto.ensemble import Ensemble, EnsembleType
# corresponds to only the estimated parameters
x_names = result.problem.get_reduced_vector(result.problem.x_names)
# Create the ensemble with the MCMC chain from parallel tempering with the real temperature.
ensemble = Ensemble.from_sample(
result,
chain_slice=slice(None, None, 2), # Optional argument: only use every second vector in the chain.
x_names=x_names,
ensemble_type=EnsembleType.sample,
lower_bound=result.problem.lb,
upper_bound=result.problem.ub
)
The predictor is then applied to the ensemble to generate predictions.
[11]:
from pypesto.engine import MultiProcessEngine
# Currently, parallelization of predictions is supported with the
# `pypesto.engine.MultiProcessEngine` and `pypesto.engine.MultiThreadEngine`
# engines. If no engine is specified, the `pypesto.engine.SingleCoreEngine`
# engine is used.
engine = MultiProcessEngine()
ensemble_prediction = ensemble.predict(predictor_x, prediction_id=AMICI_X, engine=engine)
Engine set up to use up to 8 processes in total. The number was automatically determined and might not be appropriate on some systems.
100%|██████████| 8/8 [00:00<00:00, 641.55it/s]
[12]:
from pypesto.predict.constants import CONDITION, OUTPUT
credibility_interval_levels = [90, 95, 99]
ax = visualize.sampling_prediction_trajectories(
ensemble_prediction,
levels=credibility_interval_levels,
size=(10,5),
labels={'A': 'state_A', 'condition_0': 'cond_0'},
axis_label_padding=60,
groupby=CONDITION,
condition_ids=['condition_0', 'condition_1'], # `None` for all conditions
output_ids=['A', 'B'], # `None` for all outputs
)
[13]:
ax = visualize.sampling_prediction_trajectories(
ensemble_prediction,
levels=credibility_interval_levels,
size=(10,5),
labels={'A': 'obs_A', 'condition_0': 'cond_0'},
axis_label_padding=60,
groupby=OUTPUT,
)
Predictions are stored in ensemble_prediction.prediction_summary.
Commonly, as a first step, optimization is performed, in order to find good parameter point estimates.¶
[14]:
res = optimize.minimize(problem, n_starts=10)
100%|██████████| 10/10 [00:02<00:00, 4.72it/s]
By passing the result object to the function, the previously found global optimum is used as starting point for the MCMC sampling.
[15]:
res = sample.sample(problem, n_samples=10000, sampler=sampler, result=res)
elapsed_time = res.sample_result.time
print('Elapsed time: '+str(round(elapsed_time,2)))
100%|██████████| 10000/10000 [00:42<00:00, 237.21it/s]
Elapsed time: 52.21
When the sampling is finished, we can analyse our results. pyPESTO provides functions to analyse both the sampling process as well as the obtained sampling result. Visualizing the traces e.g. allows to detect burn-in phases, or fine-tune hyperparameters. First, the parameter trajectories can be visualized:
[16]:
ax = visualize.sampling_parameter_traces(res, use_problem_bounds=False, size=(12,5))
By visual inspection one can see that the chain is already converged from the start. This is already showing the benefit of initiating the chain at the optimal parameter vector. However, this may not be always the case.
[17]:
sample.geweke_test(result=res)
ax = visualize.sampling_parameter_traces(res, use_problem_bounds=False, size=(12,5))
Geweke burn-in index: 0
[18]:
sample.effective_sample_size(result=res)
ess = res.sample_result.effective_sample_size
print(f'Effective sample size per computation time: {round(ess/elapsed_time,2)}')
Estimated chain autocorrelation: 7.213987603646274
Estimated effective sample size: 1217.5572307365612
Effective sample size per computation time: 23.32
[19]:
percentiles = [99, 95, 90]
ax = visualize.sampling_parameter_cis(res, alpha=percentiles, size=(10,5))
[20]:
# Create the ensemble with the MCMC chain from parallel tempering with the real temperature.
ensemble = Ensemble.from_sample(
res,
x_names=x_names,
ensemble_type=EnsembleType.sample,
lower_bound=res.problem.lb,
upper_bound=res.problem.ub
)
ensemble_prediction = ensemble.predict(predictor_y, prediction_id=AMICI_Y, engine=engine)
100%|██████████| 8/8 [00:00<00:00, 2219.21it/s]
[21]:
ax = visualize.sampling_prediction_trajectories(
ensemble_prediction,
levels=credibility_interval_levels,
size=(10,5),
labels={'A': 'obs_A', 'condition_0': 'cond_0'},
axis_label_padding=60,
groupby=CONDITION,
)
[22]:
ax = visualize.sampling_prediction_trajectories(
ensemble_prediction,
levels=credibility_interval_levels,
size=(10,5),
labels={'A': 'obs_A', 'condition_0': 'cond_0'},
axis_label_padding=60,
groupby=OUTPUT,
)
Custom timepoints can also be specified, either for each condition - amici_objective.set_custom_timepoints(..., timepoints=...)
or for all conditions - amici_objective.set_custom_timepoints(..., timepoints_global=...).
[23]:
# Create a custom objective with new output timepoints.
timepoints = [np.linspace(0, 10, 100), np.linspace(0, 20, 200)]
amici_objective_custom = amici_objective.set_custom_timepoints(timepoints=timepoints)
# Create an observable predictor with the custom objective.
predictor_y_custom = AmiciPredictor(
amici_objective_custom,
post_processor=post_processor_y,
output_ids=observable_ids,
)
# Predict then plot.
ensemble_prediction = ensemble.predict(predictor_y_custom, prediction_id=AMICI_Y, engine=engine)
ax = visualize.sampling_prediction_trajectories(
ensemble_prediction,
levels=credibility_interval_levels,
groupby=CONDITION,
)
100%|██████████| 8/8 [00:00<00:00, 1193.09it/s]
Optimization with Synthetic Data¶
In this notebook, optimization is performed with an SBML model and PEtab parameter estimation problem, which includes some measurements.
Next, optimization is performed with synthetic data as measurements, which is generated using PEtab and AMICI. The ability to recover the parameter vector that was used to generate the synthetic data is demonstrated.
Requirements¶
Additional requirements for this notebook can be installed with pip install amici petab.
1. Load required packages. PEtab provides a base class that is designed to be easily extended to support simulation with different tools. Here, the AMICI implementation of this base class is used.
[1]:
import amici.petab_simulate
import matplotlib.pyplot as plt
import petab
import pypesto.optimize
import pypesto.petab
import pypesto.visualize
# Helper function to get the maximum likelihood estimate as a dictionary from a pyPESTO optimization result.
def get_x_mle(optimize_result, pypesto_problem, petab_problem, scaled=True):
if not scaled:
scaling = petab.parameters.get_optimization_parameter_scaling(petab_problem.parameter_df)
return {
x_id: (petab.parameters.unscale(x_value, scaling[x_id]) if not scaled else x_value)
for x_id, x_value in zip(pypesto_problem.x_names, optimize_result.list[0]['x'])
#if x_id in scaling
}
Standard Optimization¶
The PEtab problem is used to generate a pyPESTO problem, which is used to estimate model parameters.
2. Load a PEtab problem. The synthetic data returned by the PEtab-derived synthetic data generator (later, an instance of amici.petab_simulate.PetabSimulator) will be equivalent to switching the measurements in the PEtab problem’s measurements table with simulated values.
[2]:
petab_yaml_filename = 'conversion_reaction/conversion_reaction.yaml'
petab_problem_original = petab.Problem.from_yaml(petab_yaml_filename)
3. Create a pyPESTO problem from the PEtab problem. Here, the original PEtab problem is used for parameter estimation (no synthetic data is generated).
[3]:
pypesto_importer_original = pypesto.petab.PetabImporter(petab_problem_original)
pypesto_problem_original = pypesto_importer_original.create_problem()
4. Estimate parameters. Multi-start local optimization with 100 starts is used, with the default pyPESTO optimizer.
[4]:
pypesto_result_original = pypesto.optimize.minimize(pypesto_problem_original, n_starts=100)
Parameters obtained from history and optimizer do not match: [-0.25418068 -0.60837086], [-0.25416788 -0.60834112]
5. Visualize parameter estimation. Here, estimated values for k1 and k2 are shown, then a waterfall plot to indicate optimization quality, then a plot of the estimated parameters from the different starts to indicate identifiability.
Here, parameter estimation appears to have been successful. In the case of problematic parameter estimation, synthetic data can be used to determine whether parameter estimation can be used to identify known parameter values.
[5]:
x_mle_unscaled_original = get_x_mle(pypesto_result_original.optimize_result,
pypesto_problem_original,
petab_problem_original,
scaled=False)
print('Parameters are estimated to be (linear scale):')
print('\n'.join([f'{x_id}: {x_value}' for x_id, x_value in x_mle_unscaled_original.items()]))
pypesto.visualize.waterfall(pypesto_result_original);
pypesto.visualize.parameters(pypesto_result_original);
Parameters are estimated to be (linear scale):
k1: 0.7755615818811391
k2: 0.5442529577589637
Synthetic Optimization¶
Similar to the standard optimization, except the PEtab measurements table is replaced with synthetic data that is generated from specified parameters, with noise, and then used for optimization.
Here, parameters are specified with a dictionary that is used to update the original PEtab parameters table. An alternative is use a second PEtab YAML file that is identical to the original, except for the parameters table, which would now contain the parameter values to be used for synthetic data generation.
Noise¶
Noise is added to the simulated data according to the: - noise distribution in the PEtab observables table; - noise formula in the PEtab observables table, which is used to calculate the scale of the noise distribution; and - noise parameters in the PEtab measurements table, which are substituted into the noise formula for measurement-specific noise distribution scales.
6. As before, load a PEtab problem. This time, the parameters table is edited to contain parameters values that will be used for synthetic data generation (synthetic_parameters). Then, the simulator is used to generate synthetic data, which replaces the measurements table of the PEtab problem for parameter estimation in the next step.
Here, synthetic data also has noise added (noise=True), which is defined by the PEtab problem as described above. A noise scaling factor can also be specified (here, a small value - noise_scaling_factor=0.01 - is used, to reduce noise such that the synthetic parameters are more likely to be recovered with parameter estimation).
The simulator working directory is then deleted along with its contents.
[6]:
petab_problem_synthetic = petab.Problem.from_yaml(petab_yaml_filename)
synthetic_parameters = {'k1': 1.5, 'k2': 2.5}
petab_problem_synthetic.parameter_df[petab.C.NOMINAL_VALUE].update(synthetic_parameters)
simulator = amici.petab_simulate.PetabSimulator(petab_problem_synthetic)
# Optional: the AMICI simulator is provided a model, to avoid recompilation
petab_problem_synthetic.measurement_df = simulator.simulate(
noise=True,
noise_scaling_factor=0.01,
amici_model=pypesto_problem_original.objective.amici_model,
)
simulator.remove_working_dir()
7. Create a pyPESTO problem from the edited PEtab problem, and estimate parameters.
[7]:
pypesto_importer_synthetic = pypesto.petab.PetabImporter(petab_problem_synthetic)
pypesto_problem_synthetic = pypesto_importer_synthetic.create_problem()
pypesto_result_synthetic = pypesto.optimize.minimize(pypesto_problem_synthetic, n_starts=100)
Function values from history and optimizer do not match: -24.31965832797165, 1439.3853896684805
Parameters obtained from history and optimizer do not match: [0.10235171 0.50828654], [-10.9022877 11.51292546]
8. Visualize parameter estimation. Here, the estimates for k1 and k2 are similar to the synthetic parameters, suggesting that parameter estimation works well with this PEtab problem and can be used to identify parameter values successfully (caveat: noise is reduced here; parameter estimation can be expected to perform worse with more realistically noisy data).
[8]:
x_mle_unscaled_synthetic = get_x_mle(pypesto_result_synthetic.optimize_result,
pypesto_problem_synthetic,
petab_problem_synthetic,
scaled=False)
print('Parameters are estimated to be (linear scale):')
print('\n'.join([f'{x_id}: {x_value}' for x_id, x_value in x_mle_unscaled_synthetic.items()]))
pypesto.visualize.waterfall(pypesto_result_synthetic);
pypesto.visualize.parameters(pypesto_result_synthetic);
Parameters are estimated to be (linear scale):
k1: 1.4969201262521281
k2: 2.494299196042553
Definition of Priors:¶
In this notebook we demonstrate how to include prior knowledge into a parameter inference problem, in particular how to define (log-)priors for parameters. If you want to maximize your posterior distribution, you need to define
A (negative log-)likelihood
A (log-)prior
The posterior is then built as an AggregatedObjective. If you import a problem via PEtab and the priors are contained in the parameter table, the definition of priors is done automatically.
CAUTION: The user needs to specify the negative log-likelihood, while the log-prior is internally mulitplied by -1.
[1]:
import numpy as np
import scipy as sp
import pypesto
Example: Rosenbrock Banana¶
We will use the Rosenbrock Banana
as an example. Here we interpret the first term as the negative log-likelihood and the second term as Gaussian log-prior with mean \(1\) and standard deviation \(1/\sqrt{2}\).
Note that the second term is only equivalent to the negative log-distribution of a Gaussian up to a constant.
Define the negative log-likelihood¶
[2]:
n_x = 5
def rosenbrock_part_1(x):
"""
Calculate obj. fct + gradient of the "likelihood" part.
"""
obj = sum(100.0*(x[1:] - x[:-1]**2.0)**2.0)
grad = np.zeros_like(x)
grad[:-1] += -400 * (x[1:] - x[:-1]**2.0) * x[:-1]
grad[1:] += 200 * (x[1:] - x[:-1]**2.0)
return (obj, grad)
neg_log_likelihood = pypesto.Objective(fun=rosenbrock_part_1, grad=True)
Define the log-prior¶
A prior on an individual paramater is defined in a prior_dict, which contains the following key-value pairs:
index: Index of the parameterdensity_fun: (Log-)posterior. (Scalar function!)density_dx: d/dx (Log-)posterior (optional)density_ddx: d2/dx2 (Log-)posterior (optional)
A prior_dict can be either obtained by get_parameter_prior_dict for several common priors, or defined by the user.
[3]:
from pypesto.objective.priors import get_parameter_prior_dict
# create a list of prior dicts...
prior_list = []
mean = 1
std_dev = 1 / np.sqrt(2)
for i in range(n_x-1):
prior_list.append(get_parameter_prior_dict(i, 'normal', [mean, std_dev]))
# create the prior
neg_log_prior = pypesto.objective.NegLogParameterPriors(prior_list)
Define the negative log-posterior and the problem¶
The negative log-posterior is defined as an AggregatedObjective. Since optimization/visualization is not the main focus of this notebook, the reader is referred to other examples for a more in-depth presentation of these.
[4]:
neg_log_posterior = pypesto.objective.AggregatedObjective([neg_log_likelihood, neg_log_prior])
lb = -5 * np.ones((n_x, 1))
ub = 5 * np.ones((n_x, 1))
problem = pypesto.Problem(objective=neg_log_posterior,
lb=lb,
ub=ub)
Optimize¶
[5]:
import pypesto.optimize as optimize
result = optimize.minimize(problem=problem, n_starts=10)
Some basic visualizations¶
[6]:
import pypesto.visualize as visualize
visualize.waterfall(result, size=(15,6))
# parallel coordinates plot for best 5 fits
visualize.parameters(result, start_indices=5)
[6]:
<matplotlib.axes._subplots.AxesSubplot at 0x12faa1908>
[ ]:
Save and load results as HDF5 files¶
[24]:
import pypesto
import numpy as np
import scipy as sp
import pypesto.optimize as optimize
import matplotlib.pyplot as plt
import pypesto.store as store
import pypesto.profile as profile
import pypesto.sample as sample
import tempfile
%matplotlib inline
In this notebook, we will demonstrate how to save and (re-)load optimization results, profile results and sampling results to an .hdf5 file. The use case of this notebook is to generate visualizations from reloaded result objects.
Define the objective and problem¶
[25]:
objective = pypesto.Objective(fun=sp.optimize.rosen,
grad=sp.optimize.rosen_der,
hess=sp.optimize.rosen_hess)
dim_full = 20
lb = -5 * np.ones((dim_full, 1))
ub = 5 * np.ones((dim_full, 1))
problem = pypesto.Problem(objective=objective, lb=lb, ub=ub)
Fill result object with profile, sample, optimization¶
[26]:
# create optimizers
optimizer = optimize.ScipyOptimizer()
# set number of starts
n_starts = 10
# Optimization
result = pypesto.optimize.minimize(
problem=problem, optimizer=optimizer,
n_starts=n_starts)
# Profiling
result = profile.parameter_profile(
problem=problem, result=result,
optimizer=optimizer)
# Sampling
sampler = sample.AdaptiveMetropolisSampler()
result = sample.sample(problem=problem,
sampler=sampler,
n_samples=100000,
result=result)
100%|██████████| 100000/100000 [00:29<00:00, 3431.32it/s]
Plot results¶
We now want to plot the results (before saving).
[27]:
import pypesto.visualize
# plot waterfalls
pypesto.visualize.waterfall(result, size=(15,6))
[27]:
<AxesSubplot:title={'center':'Waterfall plot'}, xlabel='Ordered optimizer run', ylabel='Offsetted function value (relative to best start)'>
[28]:
# plot profiles
pypesto.visualize.profiles(result)
[28]:
[<AxesSubplot:xlabel='x0', ylabel='Log-posterior ratio'>,
<AxesSubplot:xlabel='x1'>,
<AxesSubplot:xlabel='x2'>,
<AxesSubplot:xlabel='x3'>,
<AxesSubplot:xlabel='x4'>,
<AxesSubplot:xlabel='x5', ylabel='Log-posterior ratio'>,
<AxesSubplot:xlabel='x6'>,
<AxesSubplot:xlabel='x7'>,
<AxesSubplot:xlabel='x8'>,
<AxesSubplot:xlabel='x9'>,
<AxesSubplot:xlabel='x10', ylabel='Log-posterior ratio'>,
<AxesSubplot:xlabel='x11'>,
<AxesSubplot:xlabel='x12'>,
<AxesSubplot:xlabel='x13'>,
<AxesSubplot:xlabel='x14'>,
<AxesSubplot:xlabel='x15', ylabel='Log-posterior ratio'>,
<AxesSubplot:xlabel='x16'>,
<AxesSubplot:xlabel='x17'>,
<AxesSubplot:xlabel='x18'>,
<AxesSubplot:xlabel='x19'>]
[29]:
# plot samples
pypesto.visualize.sampling_fval_traces(result)
[29]:
<AxesSubplot:xlabel='iteration index', ylabel='log-posterior'>
Save result object in HDF5 File¶
[30]:
# create temporary file
fn = tempfile.mktemp(".hdf5")
# write result with write_result function.
# Choose which parts of the result object to save with
# corresponding booleans.
store.write_result(result=result,
filename=fn,
problem=True,
optimize=True,
profile=True,
sample=True)
Reload results¶
[31]:
# Read result
result2 = store.read_result(fn)
Plot (reloaded) results¶
[32]:
# plot waterfalls
pypesto.visualize.waterfall(result2, size=(15,6))
[32]:
<AxesSubplot:title={'center':'Waterfall plot'}, xlabel='Ordered optimizer run', ylabel='Offsetted function value (relative to best start)'>
[33]:
# plot profiles
pypesto.visualize.profiles(result2)
[33]:
[<AxesSubplot:xlabel='x0', ylabel='Log-posterior ratio'>,
<AxesSubplot:xlabel='x1'>,
<AxesSubplot:xlabel='x2'>,
<AxesSubplot:xlabel='x3'>,
<AxesSubplot:xlabel='x4'>,
<AxesSubplot:xlabel='x5', ylabel='Log-posterior ratio'>,
<AxesSubplot:xlabel='x6'>,
<AxesSubplot:xlabel='x7'>,
<AxesSubplot:xlabel='x8'>,
<AxesSubplot:xlabel='x9'>,
<AxesSubplot:xlabel='x10', ylabel='Log-posterior ratio'>,
<AxesSubplot:xlabel='x11'>,
<AxesSubplot:xlabel='x12'>,
<AxesSubplot:xlabel='x13'>,
<AxesSubplot:xlabel='x14'>,
<AxesSubplot:xlabel='x15', ylabel='Log-posterior ratio'>,
<AxesSubplot:xlabel='x16'>,
<AxesSubplot:xlabel='x17'>,
<AxesSubplot:xlabel='x18'>,
<AxesSubplot:xlabel='x19'>]
[34]:
# plot samples
pypesto.visualize.sampling_fval_traces(result2)
[34]:
<AxesSubplot:xlabel='iteration index', ylabel='log-posterior'>
For the saving of optimization history, we refer to store.ipynb.
Storage¶
It is important to be able to store analysis results efficiently, easily accessible, and portable across systems. For this aim, pyPESTO allows to store results in efficient, portable HDF5 files. Further, optimization trajectories can be stored using various backends, including HDF5 and CSV.
In the following, describe the file formats.
For detailed information on usage, consult the doc/example/hdf5_storage.ipynb
and doc/example/store.ipynb notebook, and the API documentation for the
pypesto.objective.history and pypesto.storage modules.
pyPESTO Problem¶
+ /problem/
- Attributes:
- filled by objective.get_config()
- ...
- lb [float n_par]
- ub [float n_par]
- lb_full [float n_par_full]
- ub_full [float n_par_full]
- dim [int]
- dim_full [int]
- x_fixed_values [float (n_par_full-n_par)]
- x_fixed_indices [int (n_par_full-n_par)]
- x_free_indices [int n_par]
- x_names [str n_par_full]
Parameter estimation¶
Parameter estimation settings¶
Parameter estimation settings are saved in /optimization/settings.
Parameter estimation results¶
Parameter estimation results are saved in /optimization/results/.
Results per local optimization¶
Results of the $n’th multistart a saved in the format
+ /optimization/results/$n/
- fval: [float]
Objective function value of best iteration
- x: [float n_par_full]
Parameter set of best iteration
- grad: [float n_par_full]
Gradient of objective function at point x
- hess: [float n_par_full x n_par_full]
Hessian matrix of objective function at point x
- n_fval: [int]
Total number of objective function evaluations
- n_grad: [int]
Number of gradient evaluations
- n_hess: [int]
Number of Hessian evaluations
- x0: [float n_par_full]
Initial parameter set
- fval0: [float]
Objective function value at starting parameters
- exitflag: [str] Some exit flag
- time: [float] Execution time
- message: [str] Some exit message
Trace per local optimization¶
When objective function call histories are saved to HDF5, they are under
/optimization/results/$n/trace/.
+ /optimization/results/$n/trace/
- fval: [float n_iter]
Objective function value of best iteration
- x: [float n_iter x n_par_full]
Parameter set of best iteration
- grad: [float n_iter x n_par_full]
Gradient of objective function at point x
- hess: [float n_iter x n_par_full x n_par_full]
Hessian matrix of objective function at point x
- time: [float n_iter] Executition time
- chi2: [float n_iter x ...]
- schi2: [float n_iter x ...]
Sampling¶
Sampling results¶
Sampling results are saved in /sampling/results/.
+ /sampling/results/
- betas [float n_chains]
- trace_neglogpost [float n_chains x (n_samples+1)]
- trace_neglogprior [float n_chains x (n_samples+1)]
- trace_x [float n_chains x (n_samples+1) x n_par]
- Attributes:
- time
Profiling¶
Profiling results¶
Profiling results are saved in /profiling/$profiling_id/, where profiling_id indicates the number of profilings done.
+/profiling/profiling_id/
- $parameter_index/
- exitflag_path [float n_iter]
- fval_path [float n_iter]
- gradnorm_path [float n_iter]
- ratio_path [float n_iter]
- time_path [float n_iter]
- x_path [float n_par x n_iter]
- Attributes:
- time_total
- IsNone
- n_fval
- n_grad
- n_hess
API reference¶
pyPESTO¶
Parameter Estimation TOolbox for python.
-
class
pypesto.AmiciObjective(amici_model: Union[amici.Model, amici.ModelPtr], amici_solver: Union[amici.Solver, amici.SolverPtr], edatas: Union[Sequence[amici.ExpData], amici.ExpData], max_sensi_order: int = None, x_ids: Sequence[str] = None, x_names: Sequence[str] = None, parameter_mapping: ParameterMapping = None, guess_steadystate: Optional[bool] = None, n_threads: int = 1, fim_for_hess: bool = True, amici_object_builder: pypesto.objective.amici.AmiciObjectBuilder = None, calculator: pypesto.objective.amici_calculator.AmiciCalculator = None)[source]¶ Bases:
pypesto.objective.base.ObjectiveBaseThis class allows to create an objective directly from an amici model.
-
__init__(amici_model: Union[amici.Model, amici.ModelPtr], amici_solver: Union[amici.Solver, amici.SolverPtr], edatas: Union[Sequence[amici.ExpData], amici.ExpData], max_sensi_order: int = None, x_ids: Sequence[str] = None, x_names: Sequence[str] = None, parameter_mapping: ParameterMapping = None, guess_steadystate: Optional[bool] = None, n_threads: int = 1, fim_for_hess: bool = True, amici_object_builder: pypesto.objective.amici.AmiciObjectBuilder = None, calculator: pypesto.objective.amici_calculator.AmiciCalculator = None)[source]¶ Constructor.
- Parameters
amici_model – The amici model.
amici_solver – The solver to use for the numeric integration of the model.
edatas – The experimental data. If a list is passed, its entries correspond to multiple experimental conditions.
max_sensi_order – Maximum sensitivity order supported by the model. Defaults to 2 if the model was compiled with o2mode, otherwise 1.
x_ids – Ids of optimization parameters. In the simplest case, this will be the AMICI model parameters (default).
x_names – Names of optimization parameters.
parameter_mapping – Mapping of optimization parameters to model parameters. Format as created by amici.petab_objective.create_parameter_mapping. The default is just to assume that optimization and simulation parameters coincide.
guess_steadystate – Whether to guess steadystates based on previous steadystates and respective derivatives. This option may lead to unexpected results for models with conservation laws and should accordingly be deactivated for those models.
n_threads – Number of threads that are used for parallelization over experimental conditions. If amici was not installed with openMP support this option will have no effect.
fim_for_hess – Whether to use the FIM whenever the Hessian is requested. This only applies with forward sensitivities. With adjoint sensitivities, the true Hessian will be used, if available. FIM or Hessian will only be exposed if max_sensi_order>1.
amici_object_builder – AMICI object builder. Allows recreating the objective for pickling, required in some parallelization schemes.
calculator – Performs the actual calculation of the function values and derivatives.
-
apply_custom_timepoints() → None[source]¶ Apply custom timepoints, if applicable.
See the set_custom_timepoints method for more information.
-
apply_steadystate_guess(condition_ix: int, x_dct: Dict) → None[source]¶ Use the stored steadystate as well as the respective sensitivity ( if available) and parameter value to approximate the steadystate at the current parameters using a zeroth or first order taylor approximation: x_ss(x’) = x_ss(x) [+ dx_ss/dx(x)*(x’-x)]
-
call_unprocessed(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, edatas: Sequence[amici.ExpData] = None, parameter_mapping: ParameterMapping = None)[source]¶ Call objective function without pre- or post-processing and formatting.
- Parameters
x – The parameters for which to evaluate the objective function.
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
A dict containing the results.
- Return type
result
-
check_gradients_match_finite_differences(x: Optional[numpy.ndarray] = None, *args, **kwargs) → bool[source]¶ Check if gradients match finite differences (FDs)
- Parameters
x (The parameters for which to evaluate the gradient.) –
- Returns
Indicates whether gradients match (True) FDs or not (False)
- Return type
-
check_mode(mode: str) → bool[source]¶ Check if the objective is able to compute in the requested mode.
Either check_mode or the fun_… functions must be overwritten in derived classes.
- Parameters
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether mode is supported
- Return type
flag
-
check_sensi_orders(sensi_orders: Tuple[int, …], mode: str) → bool[source]¶ Check if the objective is able to compute the requested sensitivities.
Either check_sensi_orders or the fun_… functions must be overwritten in derived classes.
- Parameters
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether combination of sensi_orders and mode is supported
- Return type
flag
-
get_config() → dict[source]¶ Get the configuration information of the objective function and return it as a dictonary.
-
initialize()[source]¶ Initialize the objective function. This function is used at the beginning of an analysis, e.g. optimization, and can e.g. reset the objective memory. By default does nothing.
-
set_custom_timepoints(timepoints: Optional[Sequence[Sequence[Union[float, int]]]] = None, timepoints_global: Optional[Sequence[Union[float, int]]] = None) → pypesto.objective.amici.AmiciObjective[source]¶ Create a copy of this objective that will be evaluated at custom timepoints.
The intended use is to aid in predictions at unmeasured timepoints.
- Parameters
timepoints – The outer sequence should contain a sequence of timepoints for each experimental condition.
timepoints_global – A sequence of timepoints that will be used for all experimental conditions.
- Returns
- Return type
The customized copy of this objective.
-
-
class
pypesto.CsvHistory(file: str, x_names: Optional[Sequence[str]] = None, options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None, load_from_file: bool = False)[source]¶ Bases:
pypesto.objective.history.HistoryStores a representation of the history in a CSV file.
- Parameters
file – CSV file name.
x_names – Parameter names.
options – History options.
load_from_file – If True, history will be initialized from data in the specified file
-
__init__(file: str, x_names: Optional[Sequence[str]] = None, options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None, load_from_file: bool = False)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
get_chi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Chi2 values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_fval_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Function values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_grad_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Gradients.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_hess_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Hessians.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_res_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Residuals.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_schi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Chi2 sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_sres_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Residual sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_time_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Cumulative execution times.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_x_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Parameters.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
update(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, result: Dict[str, Union[float, numpy.ndarray]]) → None[source]¶ Update history after a function evaluation.
- Parameters
x – The parameter vector.
sensi_orders – The sensitivity orders computed.
mode – The objective function mode computed (function value or residuals).
result – The objective function values for parameters x, sensitivities sensi_orders and mode mode.
-
class
pypesto.FD(obj: pypesto.objective.base.ObjectiveBase, grad: Optional[bool] = None, hess: Optional[bool] = None, sres: Optional[bool] = None, hess_via_fval: bool = True, delta_fun: Union[pypesto.objective.finite_difference.FDDelta, numpy.ndarray, float, str] = 1e-06, delta_grad: Union[pypesto.objective.finite_difference.FDDelta, numpy.ndarray, float, str] = 1e-06, delta_res: Union[pypesto.objective.finite_difference.FDDelta, float, numpy.ndarray, str] = 1e-06, method: str = 'central', x_names: Optional[List[str]] = None)[source]¶ Bases:
pypesto.objective.base.ObjectiveBaseFinite differences (FDs) for derivatives.
Given an objective that gives function values and/or residuals, this class allows to flexibly obtain all derivatives calculated via FDs.
For the parameters grad, hess, sres, a value of None means that the objective derivative is used if available, otherwise resorting to FDs. True means that FDs are used in any case, False means that the derivative is not exported.
Note that the step sizes should be carefully chosen. They should be small enough to provide an accurate linear approximation, but large enough to be robust against numerical inaccuracies, in particular if the objective relies on numerical approximations, such as an ODE.
- Parameters
grad – Derivative method for the gradient (see above).
hess – Derivative method for the Hessian (see above).
sres – Derivative method for the residual sensitivities (see above).
hess_via_fval – If the Hessian is to be calculated via finite differences: whether to employ 2nd order FDs via fval even if the objective can provide a gradient.
delta_fun – FD step sizes for function values. Can be either a float, or a
np.ndarrayof shape (n_par,) for different step sizes for different coordinates.delta_grad – FD step sizes for gradients, if the Hessian is calculated via 1st order sensitivities from the gradients. Similar to delta_fun.
delta_res – FD step sizes for residuals. Similar to delta_fun.
method – Method to calculate FDs. Can be any of FD.METHODS: central, forward or backward differences. The latter two require only roughly half as many function evaluations, are however less accurate than central (O(x) vs O(x**2)).
x_names – Parameter names that can be optionally used in, e.g., history or gradient checks.
Examples
Define residuals and objective function, and obtain all derivatives via FDs:
>>> from pypesto import Objective, FD >>> import numpy as np >>> x_obs = np.array([11, 12, 13]) >>> res = lambda x: x - x_obs >>> fun = lambda x: 0.5 * sum(res(x)**2) >>> obj = FD(Objective(fun=fun, res=res))
-
BACKWARD= 'backward'¶
-
CENTRAL= 'central'¶
-
FORWARD= 'forward'¶
-
METHODS= ['central', 'forward', 'backward']¶
-
__init__(obj: pypesto.objective.base.ObjectiveBase, grad: Optional[bool] = None, hess: Optional[bool] = None, sres: Optional[bool] = None, hess_via_fval: bool = True, delta_fun: Union[pypesto.objective.finite_difference.FDDelta, numpy.ndarray, float, str] = 1e-06, delta_grad: Union[pypesto.objective.finite_difference.FDDelta, numpy.ndarray, float, str] = 1e-06, delta_res: Union[pypesto.objective.finite_difference.FDDelta, float, numpy.ndarray, str] = 1e-06, method: str = 'central', x_names: Optional[List[str]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
call_unprocessed(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, **kwargs) → Dict[str, Union[float, numpy.ndarray, Dict]][source]¶ Call objective function without pre- or post-processing and formatting.
- Parameters
x – The parameters for which to evaluate the objective function.
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
A dict containing the results.
- Return type
result
-
property
has_fun¶
-
property
has_grad¶
-
property
has_hess¶
-
property
has_res¶
-
property
has_sres¶
-
class
pypesto.FDDelta(delta: Optional[Union[numpy.ndarray, float]] = None, test_deltas: Optional[numpy.ndarray] = None, update_condition: str = 'constant', max_distance: float = 0.5, max_steps: int = 30)[source]¶ Bases:
objectFinite difference step size with automatic updating.
Reference implementation: https://github.com/ICB-DCM/PESTO/blob/master/private/getStepSizeFD.m
- Parameters
delta – (Initial) step size, either a float, or a vector of size (n_par,). If not None, this is used as initial step size.
test_deltas – Step sizes to try out in step size selection. If None, a range [1e-1, 1e-2, …, 1e-8] is considered.
update_condition – A “good” step size may be a local property. Thus, this class allows updating the step size if certain criteria are met, in the
pypesto.objective.finite_difference.FDDelta.update()function. FDDelta.CONSTANT means that the step size is only initially selected. FDDelta.DISTANCE means that the step size is updated if the current evaluation point is sufficiently far away from the last training point. FDDelta.STEPS means that the step size is updated max_steps evaluations after the last update.max_distance – Coefficient on the distance between current and reference point beyond which to update, in the FDDelta.DISTANCE update condition.
max_steps – Number of steps after which to update in the FDDelta.STEPS update condition.
-
CONSTANT= 'constant'¶
-
DISTANCE= 'distance'¶
-
STEPS= 'steps'¶
-
UPDATE_CONDITIONS= ['constant', 'distance', 'steps']¶
-
__init__(delta: Optional[Union[numpy.ndarray, float]] = None, test_deltas: Optional[numpy.ndarray] = None, update_condition: str = 'constant', max_distance: float = 0.5, max_steps: int = 30)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
get() → numpy.ndarray[source]¶ Get delta vector.
-
update(x: numpy.ndarray, fval: Optional[Union[float, numpy.ndarray]], fun: Callable, fd_method: str) → None[source]¶ Update delta if update conditions are met.
- Parameters
x – Current parameter vector, shape (n_par,).
fval – fun(x), to avoid re-evaluation. Scalar- or vector-valued.
fun – Function whose 1st-order derivative to approximate. Scalar- or vector-valued.
fd_method – FD method employed by
pypesto.objective.finite_difference.FD, see there.
-
class
pypesto.Hdf5History(id: str, file: str, options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None)[source]¶ Bases:
pypesto.objective.history.HistoryStores a representation of the history in an HDF5 file.
- Parameters
id – Id of the history
file – HDF5 file name.
options – History options.
-
__init__(id: str, file: str, options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
get_chi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Chi2 values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_fval_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Function values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_grad_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Gradients.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_hess_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Hessians.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_res_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Residuals.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_schi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Chi2 sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_sres_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Residual sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_time_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Cumulative execution times.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_x_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Parameters.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
property
n_fval¶ Number of function evaluations.
-
property
n_grad¶ Number of gradient evaluations.
-
property
n_hess¶ Number of Hessian evaluations.
-
property
n_res¶ Number of residual evaluations.
-
property
n_sres¶ Number or residual sensitivity evaluations.
-
property
trace_save_iter¶
-
update(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, result: Dict[str, Union[float, numpy.ndarray]]) → None[source]¶ Update history after a function evaluation.
- Parameters
x – The parameter vector.
sensi_orders – The sensitivity orders computed.
mode – The objective function mode computed (function value or residuals).
result – The objective function values for parameters x, sensitivities sensi_orders and mode mode.
-
class
pypesto.History(options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None)[source]¶ Bases:
pypesto.objective.history.HistoryBaseTracks numbers of function evaluations only, no trace.
- Parameters
options – History options.
-
__init__(options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
property
n_fval¶ Number of function evaluations.
-
property
n_grad¶ Number of gradient evaluations.
-
property
n_hess¶ Number of Hessian evaluations.
-
property
n_res¶ Number of residual evaluations.
-
property
n_sres¶ Number or residual sensitivity evaluations.
-
property
start_time¶ Start time.
-
update(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, result: Dict[str, Union[float, numpy.ndarray]]) → None[source]¶ Update history after a function evaluation.
- Parameters
x – The parameter vector.
sensi_orders – The sensitivity orders computed.
mode – The objective function mode computed (function value or residuals).
result – The objective function values for parameters x, sensitivities sensi_orders and mode mode.
-
class
pypesto.HistoryBase[source]¶ Bases:
abc.ABCAbstract base class for history objects.
Can be used as a dummy history, but does not implement any history functionality.
-
get_chi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[float], float][source]¶ Chi2 values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_fval_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[float], float][source]¶ Function values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_grad_trace(ix: Optional[Union[int, Sequence[int]]] = None, trim: bool = False) → Union[Sequence[Union[numpy.ndarray, np.nan]], numpy.ndarray, np.nan][source]¶ Gradients.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_hess_trace(ix: Optional[Union[int, Sequence[int]]] = None, trim: bool = False) → Union[Sequence[Union[numpy.ndarray, np.nan]], numpy.ndarray, np.nan][source]¶ Hessians.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_res_trace(ix: Optional[Union[int, Sequence[int]]] = None, trim: bool = False) → Union[Sequence[Union[numpy.ndarray, np.nan]], numpy.ndarray, np.nan][source]¶ Residuals.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_schi2_trace(ix: Optional[Union[int, Sequence[int]]] = None, trim: bool = False) → Union[Sequence[Union[numpy.ndarray, np.nan]], numpy.ndarray, np.nan][source]¶ Chi2 sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_sres_trace(ix: Optional[Union[int, Sequence[int]]] = None, trim: bool = False) → Union[Sequence[Union[numpy.ndarray, np.nan]], numpy.ndarray, np.nan][source]¶ Residual sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_time_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[float], float][source]¶ Cumulative execution times.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_trimmed_indices()[source]¶ Returns indices of the history to get a monotonically decreasing history.
-
get_x_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[numpy.ndarray], numpy.ndarray][source]¶ Parameters.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
property
n_fval¶ Number of function evaluations.
-
property
n_grad¶ Number of gradient evaluations.
-
property
n_hess¶ Number of Hessian evaluations.
-
property
n_res¶ Number of residual evaluations.
-
property
n_sres¶ Number or residual sensitivity evaluations.
-
property
start_time¶ Start time.
-
update(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, result: Dict[str, Union[float, numpy.ndarray]]) → None[source]¶ Update history after a function evaluation.
- Parameters
x – The parameter vector.
sensi_orders – The sensitivity orders computed.
mode – The objective function mode computed (function value or residuals).
result – The objective function values for parameters x, sensitivities sensi_orders and mode mode.
-
-
class
pypesto.HistoryOptions(trace_record: bool = False, trace_record_grad: bool = True, trace_record_hess: bool = True, trace_record_res: bool = True, trace_record_sres: bool = True, trace_record_chi2: bool = True, trace_record_schi2: bool = True, trace_save_iter: int = 10, storage_file: Optional[str] = None)[source]¶ Bases:
dictOptions for the objective that are used in optimization, profiling and sampling.
In addition implements a factory pattern to generate history objects.
- Parameters
trace_record – Flag indicating whether to record the trace of function calls. The trace_record_* flags only become effective if trace_record is True.
trace_record_grad – Flag indicating whether to record the gradient in the trace.
trace_record_hess – Flag indicating whether to record the Hessian in the trace.
trace_record_res – Flag indicating whether to record the residual in the trace.
trace_record_sres – Flag indicating whether to record the residual sensitivities in the trace.
trace_record_chi2 – Flag indicating whether to record the chi2 in the trace.
trace_record_schi2 – Flag indicating whether to record the chi2 sensitivities in the trace.
trace_save_iter – After how many iterations to store the trace.
storage_file – File to save the history to. Can be any of None, a “{filename}.csv”, or a “{filename}.hdf5” file. Depending on the values, the create_history method creates the appropriate object. Occurrences of “{id}” in the file name are replaced by the id upon creation of a history, if applicable.
-
__init__(trace_record: bool = False, trace_record_grad: bool = True, trace_record_hess: bool = True, trace_record_res: bool = True, trace_record_sres: bool = True, trace_record_chi2: bool = True, trace_record_schi2: bool = True, trace_save_iter: int = 10, storage_file: Optional[str] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
static
assert_instance(maybe_options: Union[pypesto.objective.history.HistoryOptions, Dict]) → pypesto.objective.history.HistoryOptions[source]¶ Returns a valid options object.
- Parameters
maybe_options (HistoryOptions or dict) –
-
class
pypesto.MemoryHistory(options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None)[source]¶ Bases:
pypesto.objective.history.HistoryTracks numbers of function evaluations and keeps an in-memory trace of function evaluations.
- Parameters
options – History options.
-
__init__(options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
get_chi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Chi2 values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_fval_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Function values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_grad_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Gradients.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_hess_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Hessians.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_res_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Residuals.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_schi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Chi2 sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_sres_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Residual sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_time_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Cumulative execution times.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_x_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Parameters.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
update(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, result: Dict[str, Union[float, numpy.ndarray]]) → None[source]¶ Update history after a function evaluation.
- Parameters
x – The parameter vector.
sensi_orders – The sensitivity orders computed.
mode – The objective function mode computed (function value or residuals).
result – The objective function values for parameters x, sensitivities sensi_orders and mode mode.
-
class
pypesto.NegLogPriors(objectives: Sequence[pypesto.objective.base.ObjectiveBase], x_names: Optional[Sequence[str]] = None)[source]¶ Bases:
pypesto.objective.aggregated.AggregatedObjectiveAggregates different forms of negative log-prior distributions.
Allows to distinguish priors from the likelihood by testing the type of an objective.
Consists basically of a list of individual negative log-priors, given in self.objectives.
-
class
pypesto.Objective(fun: Optional[Callable] = None, grad: Optional[Union[Callable, bool]] = None, hess: Optional[Callable] = None, hessp: Optional[Callable] = None, res: Optional[Callable] = None, sres: Optional[Union[Callable, bool]] = None, x_names: Optional[Sequence[str]] = None)[source]¶ Bases:
pypesto.objective.base.ObjectiveBaseThe objective class allows the user explicitly specify functions that compute the function value and/or residuals as well as respective derivatives.
Denote dimensions n = parameters, m = residuals.
- Parameters
fun –
The objective function to be minimized. If it only computes the objective function value, it should be of the form
fun(x) -> floatwhere x is an 1-D array with shape (n,), and n is the parameter space dimension.
grad –
Method for computing the gradient vector. If it is a callable, it should be of the form
grad(x) -> array_like, shape (n,).If its value is True, then fun should return the gradient as a second output.
hess –
Method for computing the Hessian matrix. If it is a callable, it should be of the form
hess(x) -> array, shape (n, n).If its value is True, then fun should return the gradient as a second, and the Hessian as a third output, and grad should be True as well.
hessp –
Method for computing the Hessian vector product, i.e.
hessp(x, v) -> array_like, shape (n,)computes the product H*v of the Hessian of fun at x with v.
res –
Method for computing residuals, i.e.
res(x) -> array_like, shape(m,).sres –
Method for computing residual sensitivities. If it is a callable, it should be of the form
sres(x) -> array, shape (m, n).If its value is True, then res should return the residual sensitivities as a second output.
x_names – Parameter names. None if no names provided, otherwise a list of str, length dim_full (as in the Problem class). Can be read by the problem.
-
__init__(fun: Optional[Callable] = None, grad: Optional[Union[Callable, bool]] = None, hess: Optional[Callable] = None, hessp: Optional[Callable] = None, res: Optional[Callable] = None, sres: Optional[Union[Callable, bool]] = None, x_names: Optional[Sequence[str]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
call_unprocessed(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, **kwargs) → Dict[str, Union[float, numpy.ndarray, Dict]][source]¶ Call objective function without pre- or post-processing and formatting.
- Returns
A dict containing the results.
- Return type
result
-
get_config() → dict[source]¶ Get the configuration information of the objective function and return it as a dictonary.
-
property
has_fun¶
-
property
has_grad¶
-
property
has_hess¶
-
property
has_hessp¶
-
property
has_res¶
-
property
has_sres¶
-
class
pypesto.ObjectiveBase(x_names: Optional[Sequence[str]] = None)[source]¶ Bases:
abc.ABCThe objective class is a simple wrapper around the objective function, giving a standardized way of calling. Apart from that, it manages several things including fixing of parameters and history.
The objective function is assumed to be in the format of a cost function, log-likelihood function, or log-posterior function. These functions are subject to minimization. For profiling and sampling, the sign is internally flipped, all returned and stored values are however given as returned by this objective function. If maximization is to be performed, the sign should be flipped before creating the objective function.
- Parameters
x_names – Parameter names that can be optionally used in, e.g., history or gradient checks.
-
history¶ For storing the call history. Initialized by the methods, e.g. the optimizer, in initialize_history().
-
pre_post_processor¶ Preprocess input values to and postprocess output values from __call__. Configured in update_from_problem().
-
__call__(x: numpy.ndarray, sensi_orders: Tuple[int, …] = (0), mode: str = 'mode_fun', return_dict: bool = False, **kwargs) → Union[float, numpy.ndarray, Tuple, Dict[str, Union[float, numpy.ndarray, Dict]]][source]¶ Method to obtain arbitrary sensitivities. This is the central method which is always called, also by the get_* methods.
There are different ways in which an optimizer calls the objective function, and in how the objective function provides information (e.g. derivatives via separate functions or along with the function values). The different calling modes increase efficiency in space and time and make the objective flexible.
- Parameters
x – The parameters for which to evaluate the objective function.
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
return_dict – If False (default), the result is a Tuple of the requested values in the requested order. Tuples of length one are flattened. If True, instead a dict is returned which can carry further information.
- Returns
By default, this is a tuple of the requested function values and derivatives in the requested order (if only 1 value, the tuple is flattened). If return_dict, then instead a dict is returned with function values and derivatives indicated by ids.
- Return type
result
-
__init__(x_names: Optional[Sequence[str]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
abstract
call_unprocessed(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, **kwargs) → Dict[str, Union[float, numpy.ndarray, Dict]][source]¶ Call objective function without pre- or post-processing and formatting.
- Parameters
x – The parameters for which to evaluate the objective function.
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
A dict containing the results.
- Return type
result
-
check_grad(x: numpy.ndarray, x_indices: Optional[Sequence[int]] = None, eps: float = 1e-05, verbosity: int = 1, mode: str = 'mode_fun', detailed: bool = False) → pandas.core.frame.DataFrame[source]¶ Compare gradient evaluation: Firstly approximate via finite differences, and secondly use the objective gradient.
- Parameters
x – The parameters for which to evaluate the gradient.
x_indices – Indices for which to compute gradients. Default: all.
eps – Finite differences step size.
verbosity – Level of verbosity for function output. 0: no output, 1: summary for all parameters, 2: summary for individual parameters.
mode – Residual (MODE_RES) or objective function value (MODE_FUN) computation mode.
detailed – Toggle whether additional values are returned. Additional values are function values, and the central difference weighted by the difference in output from all methods (standard deviation and mean).
- Returns
gradient, finite difference approximations and error estimates.
- Return type
result
-
check_grad_multi_eps(*args, multi_eps: Optional[Iterable] = None, label: str = 'rel_err', **kwargs)[source]¶ Equivalent to the ObjectiveBase.check_grad method, except multiple finite difference step sizes are tested. The result contains the lowest finite difference for each parameter, and the corresponding finite difference step size.
- Parameters
ObjectiveBase.check_grad method parameters. (All) –
multi_eps – The finite difference step sizes to be tested.
label – The label of the column that will be minimized for each parameter. Valid options are the column labels of the dataframe returned by the ObjectiveBase.check_grad method.
-
check_gradients_match_finite_differences(*args, x: Optional[numpy.ndarray] = None, x_free: Optional[Sequence[int]] = None, rtol: float = 0.01, atol: float = 0.001, mode: Optional[str] = None, multi_eps=None, **kwargs) → bool[source]¶ Check if gradients match finite differences (FDs)
- Parameters
rtol (relative error tolerance) –
x (The parameters for which to evaluate the gradient) –
x_free (Indices for which to compute gradients) –
rtol –
atol (absolute error tolerance) –
mode (function values or residuals) –
multi_eps (multiple test step width for FDs) –
- Returns
Indicates whether gradients match (True) FDs or not (False)
- Return type
-
check_mode(mode: str) → bool[source]¶ Check if the objective is able to compute in the requested mode.
Either check_mode or the fun_… functions must be overwritten in derived classes.
- Parameters
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether mode is supported
- Return type
flag
-
check_sensi_orders(sensi_orders: Tuple[int, …], mode: str) → bool[source]¶ Check if the objective is able to compute the requested sensitivities.
Either check_sensi_orders or the fun_… functions must be overwritten in derived classes.
- Parameters
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether combination of sensi_orders and mode is supported
- Return type
flag
-
get_config() → dict[source]¶ Get the configuration information of the objective function and return it as a dictonary.
-
get_fval(x: numpy.ndarray) → float[source]¶ Get the function value at x.
-
get_grad(x: numpy.ndarray) → numpy.ndarray[source]¶ Get the gradient at x.
-
get_hess(x: numpy.ndarray) → numpy.ndarray[source]¶ Get the Hessian at x.
-
get_res(x: numpy.ndarray) → numpy.ndarray[source]¶ Get the residuals at x.
-
get_sres(x: numpy.ndarray) → numpy.ndarray[source]¶ Get the residual sensitivities at x.
-
property
has_fun¶
-
property
has_grad¶
-
property
has_hess¶
-
property
has_hessp¶
-
property
has_res¶
-
property
has_sres¶
-
initialize()[source]¶ Initialize the objective function. This function is used at the beginning of an analysis, e.g. optimization, and can e.g. reset the objective memory. By default does nothing.
-
static
output_to_tuple(sensi_orders: Tuple[int, …], mode: str, **kwargs: Union[float, numpy.ndarray]) → Tuple[source]¶ Return values as requested by the caller, since usually only a subset is demanded. One output is returned as-is, more than one output are returned as a tuple in order (fval, grad, hess).
-
update_from_problem(dim_full: int, x_free_indices: Sequence[int], x_fixed_indices: Sequence[int], x_fixed_vals: Sequence[float])[source]¶ Handle fixed parameters. Later, the objective will be given parameter vectors x of dimension dim, which have to be filled up with fixed parameter values to form a vector of dimension dim_full >= dim. This vector is then used to compute function value and derivatives. The derivatives must later be reduced again to dimension dim.
This is so as to make the fixing of parameters transparent to the caller.
The methods preprocess, postprocess are overwritten for the above functionality, respectively.
- Parameters
dim_full – Dimension of the full vector including fixed parameters.
x_free_indices – Vector containing the indices (zero-based) of free parameters (complimentary to x_fixed_indices).
x_fixed_indices – Vector containing the indices (zero-based) of parameter components that are not to be optimized.
x_fixed_vals – Vector of the same length as x_fixed_indices, containing the values of the fixed parameters.
-
class
pypesto.OptimizeResult[source]¶ Bases:
objectResult of the minimize() function.
-
append(optimizer_result: optimize.OptimizerResult)[source]¶ Append an optimizer result to the result object.
- Parameters
optimizer_result – The result of one (local) optimizer run.
-
as_dataframe(keys=None) → pandas.core.frame.DataFrame[source]¶ Get as pandas DataFrame. If keys is a list, return only the specified values.
-
-
class
pypesto.OptimizerHistory(history: pypesto.objective.history.History, x0: numpy.ndarray, generate_from_history: bool = False)[source]¶ Bases:
objectObjective call history. Container around a History object, which keeps track of optimal values.
-
fval0, fval_min Initial and best function value found.
-
chi20, chi2_min Initial and best chi2 value found.
-
x0, x_min Initial and best parameters found.
-
grad_min¶ gradient for best parameters
-
hess_min¶ hessian (approximation) for best parameters
-
res_min¶ residuals for best parameters
-
sres_min¶ residual sensitivities for best parameters
- Parameters
history – History object to attach to this container. This history object implements the storage of the actual history.
x0 – Initial values for optimization
generate_from_history – If set to true, this function will try to fill attributes of this function based on the provided history
-
__init__(history: pypesto.objective.history.History, x0: numpy.ndarray, generate_from_history: bool = False) → None[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
update(x: numpy.ndarray, sensi_orders: Tuple[int], mode: str, result: Dict[str, Union[float, numpy.ndarray]]) → None[source]¶ Update history and best found value.
-
-
class
pypesto.Problem(objective: pypesto.objective.base.ObjectiveBase, lb: Union[numpy.ndarray, List[float]], ub: Union[numpy.ndarray, List[float]], dim_full: Optional[int] = None, x_fixed_indices: Optional[Union[Iterable[SupportsInt], SupportsInt]] = None, x_fixed_vals: Optional[Union[Iterable[SupportsFloat], SupportsFloat]] = None, x_guesses: Optional[Iterable[float]] = None, startpoint_method: Optional[Callable] = None, x_names: Optional[Iterable[str]] = None, x_scales: Optional[Iterable[str]] = None, x_priors_defs: Optional[pypesto.objective.priors.NegLogPriors] = None, lb_init: Optional[Union[numpy.ndarray, List[float]]] = None, ub_init: Optional[Union[numpy.ndarray, List[float]]] = None)[source]¶ Bases:
objectThe problem formulation. A problem specifies the objective function, boundaries and constraints, parameter guesses as well as the parameters which are to be optimized.
- Parameters
objective – The objective function for minimization. Note that a shallow copy is created.
lb – The lower and upper bounds for optimization. For unbounded directions set to +-inf.
ub – The lower and upper bounds for optimization. For unbounded directions set to +-inf.
lb_init – The lower and upper bounds for initialization, typically for defining search start points. If not set, set to lb, ub.
ub_init – The lower and upper bounds for initialization, typically for defining search start points. If not set, set to lb, ub.
dim_full – The full dimension of the problem, including fixed parameters.
x_fixed_indices – Vector containing the indices (zero-based) of parameter components that are not to be optimized.
x_fixed_vals – Vector of the same length as x_fixed_indices, containing the values of the fixed parameters.
x_guesses – Guesses for the parameter values, shape (g, dim), where g denotes the number of guesses. These are used as start points in the optimization.
startpoint_method – Callable. startpoint_method(n_starts) returns a n_starts x n_free_indices array of initial values for the optimization.
x_names – Parameter names that can be optionally used e.g. in visualizations. If objective.get_x_names() is not None, those values are used, else the values specified here are used if not None, otherwise the variable names are set to [‘x0’, … ‘x{dim_full}’]. The list must always be of length dim_full.
x_scales – Parameter scales can be optionally given and are used e.g. in visualisation and prior generation. Currently the scales ‘lin’, ‘log`and ‘log10’ are supported.
x_priors_defs – Definitions of priors for parameters. Types of priors, and their required and optional parameters, are described in the Prior class.
Notes
On the fixing of parameter values:
The number of parameters dim_full the objective takes as input must be known, so it must be either lb a vector of that size, or dim_full specified as a parameter.
All vectors are mapped to the reduced space of dimension dim in __init__, regardless of whether they were in dimension dim or dim_full before. If the full representation is needed, the methods get_full_vector() and get_full_matrix() can be used.
-
__init__(objective: pypesto.objective.base.ObjectiveBase, lb: Union[numpy.ndarray, List[float]], ub: Union[numpy.ndarray, List[float]], dim_full: Optional[int] = None, x_fixed_indices: Optional[Union[Iterable[SupportsInt], SupportsInt]] = None, x_fixed_vals: Optional[Union[Iterable[SupportsFloat], SupportsFloat]] = None, x_guesses: Optional[Iterable[float]] = None, startpoint_method: Optional[Callable] = None, x_names: Optional[Iterable[str]] = None, x_scales: Optional[Iterable[str]] = None, x_priors_defs: Optional[pypesto.objective.priors.NegLogPriors] = None, lb_init: Optional[Union[numpy.ndarray, List[float]]] = None, ub_init: Optional[Union[numpy.ndarray, List[float]]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
property
dim¶
-
fix_parameters(parameter_indices: Union[Iterable[SupportsInt], SupportsInt], parameter_vals: Union[Iterable[SupportsFloat], SupportsFloat]) → None[source]¶ Fix specified parameters to specified values
-
full_index_to_free_index(full_index: int)[source]¶ Calculate index in reduced vector from index in full vector.
- Parameters
full_index (The index in the full vector.) –
- Returns
free_index
- Return type
The index in the free vector.
-
get_full_matrix(x: Optional[numpy.ndarray]) → Optional[numpy.ndarray][source]¶ Map matrix from dim to dim_full. Usually used for hessian.
- Parameters
x (array_like, shape=(dim, dim)) – The matrix in dimension dim.
-
get_full_vector(x: Optional[numpy.ndarray], x_fixed_vals: Optional[Iterable[float]] = None) → Optional[numpy.ndarray][source]¶ Map vector from dim to dim_full. Usually used for x, grad.
- Parameters
x (array_like, shape=(dim,)) – The vector in dimension dim.
x_fixed_vals (array_like, ndim=1, optional) – The values to be used for the fixed indices. If None, then nans are inserted. Usually, None will be used for grad and problem.x_fixed_vals for x.
-
get_reduced_matrix(x_full: Optional[numpy.ndarray]) → Optional[numpy.ndarray][source]¶ Map matrix from dim_full to dim, i.e. delete fixed indices.
- Parameters
x_full (array_like, ndim=2) – The matrix in dimension dim_full.
-
get_reduced_vector(x_full: Optional[numpy.ndarray], x_indices: Optional[List[int]] = None) → Optional[numpy.ndarray][source]¶ Keep only those elements, which indices are specified in x_indices If x_indices is not provided, delete fixed indices.
- Parameters
x_full (array_like, ndim=1) – The vector in dimension dim_full.
x_indices – indices of x_full that should remain
-
property
lb¶
-
property
lb_init¶
-
normalize() → None[source]¶ Reduce all vectors to dimension dim and have the objective accept vectors of dimension dim.
-
print_parameter_summary() → None[source]¶ Prints a summary of what parameters are being optimized and parameter boundaries.
-
set_x_guesses(x_guesses: Iterable[float])[source]¶ Sets the x_guesses of a problem.
- Parameters
x_guesses –
-
property
ub¶
-
property
ub_init¶
-
unfix_parameters(parameter_indices: Union[Iterable[SupportsInt], SupportsInt]) → None[source]¶ Free specified parameters
-
property
x_free_indices¶
-
property
x_guesses¶
-
class
pypesto.ProfileResult[source]¶ Bases:
objectResult of the profile() function.
It holds a list of profile lists. Each profile list consists of a list of ProfilerResult objects, one for each parameter.
-
append_empty_profile_list() → int[source]¶ Append an empty profile list to the list of profile lists.
- Returns
The index of the created profile list.
- Return type
index
-
append_profiler_result(profiler_result: profile.ProfilerResult = None, profile_list: int = None) → None[source]¶ Append the profiler result to the profile list.
- Parameters
profiler_result – The result of one profiler run for a parameter, or None if to be left empty.
profile_list – Index specifying the profile list to which we want to append. Defaults to the last list.
-
get_profiler_result(i_par: int, profile_list: Optional[int] = None)[source]¶ Get theprofiler result at parameter index i_par of profile list profile_list.
- Parameters
i_par – Integer specifying the profile index.
profile_list – Index specifying the profile list. Defaults to the last list.
-
set_profiler_result(profiler_result: profile.ProfilerResult, i_par: int, profile_list: int = None) → None[source]¶ Write a profiler result to the result object at i_par of profile list profile_list.
- Parameters
profiler_result – The result of one (local) profiler run.
i_par – Integer specifying the parameter index.
profile_list – Index specifying the profile list. Defaults to the last list.
-
-
class
pypesto.Result(problem=None)[source]¶ Bases:
objectUniversal result object for pypesto. The algorithms like optimize, profile, sample fill different parts of it.
-
problem¶ The problem underlying the results.
- Type
-
optimize_result¶ The results of the optimizer runs.
-
profile_result¶ The results of the profiler run.
-
sample_result¶ The results of the sampler run.
-
Objective¶
-
class
pypesto.objective.AggregatedObjective(objectives: Sequence[pypesto.objective.base.ObjectiveBase], x_names: Optional[Sequence[str]] = None)[source]¶ Bases:
pypesto.objective.base.ObjectiveBaseThis class aggregates multiple objectives into one objective.
-
__init__(objectives: Sequence[pypesto.objective.base.ObjectiveBase], x_names: Optional[Sequence[str]] = None)[source]¶ Constructor.
- Parameters
objectives – Sequence of pypesto.ObjectiveBase instances
x_names – Sequence of names of the (optimized) parameters. (Details see documentation of x_names in
pypesto.ObjectiveBase)
-
call_unprocessed(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, **kwargs) → Dict[str, Union[float, numpy.ndarray, Dict]][source]¶ Call objective function without pre- or post-processing and formatting.
- Parameters
x – The parameters for which to evaluate the objective function.
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
A dict containing the results.
- Return type
result
-
check_mode(mode: str) → bool[source]¶ Check if the objective is able to compute in the requested mode.
Either check_mode or the fun_… functions must be overwritten in derived classes.
- Parameters
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether mode is supported
- Return type
flag
-
check_sensi_orders(sensi_orders: Tuple[int, …], mode: str) → bool[source]¶ Check if the objective is able to compute the requested sensitivities.
Either check_sensi_orders or the fun_… functions must be overwritten in derived classes.
- Parameters
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether combination of sensi_orders and mode is supported
- Return type
flag
-
-
class
pypesto.objective.AmiciCalculator[source]¶ Bases:
objectClass to perform the actual call to AMICI and obtain requested objective function values.
-
__call__(x_dct: Dict, sensi_order: int, mode: str, amici_model: Union[amici.Model, amici.ModelPtr], amici_solver: Union[amici.Solver, amici.SolverPtr], edatas: List[amici.ExpData], n_threads: int, x_ids: Sequence[str], parameter_mapping: ParameterMapping, fim_for_hess: bool)[source]¶ Perform the actual AMICI call.
Called within the
AmiciObjective.__call__()method.- Parameters
x_dct – Parameters for which to compute function value and derivatives.
sensi_order – Maximum sensitivity order.
mode – Call mode (function value or residual based).
amici_model – The AMICI model.
amici_solver – The AMICI solver.
edatas – The experimental data.
n_threads – Number of threads for AMICI call.
x_ids – Ids of optimization parameters.
parameter_mapping – Mapping of optimization to simulation parameters.
fim_for_hess – Whether to use the FIM (if available) instead of the Hessian (if requested).
-
-
class
pypesto.objective.AmiciObjectBuilder[source]¶ Bases:
abc.ABCAllows to build AMICI model, solver, and edatas.
This class is useful for pickling an
pypesto.AmiciObjective, which is required in some parallelization schemes. Therefore, this class itself must be picklable.
-
class
pypesto.objective.AmiciObjective(amici_model: Union[amici.Model, amici.ModelPtr], amici_solver: Union[amici.Solver, amici.SolverPtr], edatas: Union[Sequence[amici.ExpData], amici.ExpData], max_sensi_order: int = None, x_ids: Sequence[str] = None, x_names: Sequence[str] = None, parameter_mapping: ParameterMapping = None, guess_steadystate: Optional[bool] = None, n_threads: int = 1, fim_for_hess: bool = True, amici_object_builder: pypesto.objective.amici.AmiciObjectBuilder = None, calculator: pypesto.objective.amici_calculator.AmiciCalculator = None)[source]¶ Bases:
pypesto.objective.base.ObjectiveBaseThis class allows to create an objective directly from an amici model.
-
__init__(amici_model: Union[amici.Model, amici.ModelPtr], amici_solver: Union[amici.Solver, amici.SolverPtr], edatas: Union[Sequence[amici.ExpData], amici.ExpData], max_sensi_order: int = None, x_ids: Sequence[str] = None, x_names: Sequence[str] = None, parameter_mapping: ParameterMapping = None, guess_steadystate: Optional[bool] = None, n_threads: int = 1, fim_for_hess: bool = True, amici_object_builder: pypesto.objective.amici.AmiciObjectBuilder = None, calculator: pypesto.objective.amici_calculator.AmiciCalculator = None)[source]¶ Constructor.
- Parameters
amici_model – The amici model.
amici_solver – The solver to use for the numeric integration of the model.
edatas – The experimental data. If a list is passed, its entries correspond to multiple experimental conditions.
max_sensi_order – Maximum sensitivity order supported by the model. Defaults to 2 if the model was compiled with o2mode, otherwise 1.
x_ids – Ids of optimization parameters. In the simplest case, this will be the AMICI model parameters (default).
x_names – Names of optimization parameters.
parameter_mapping – Mapping of optimization parameters to model parameters. Format as created by amici.petab_objective.create_parameter_mapping. The default is just to assume that optimization and simulation parameters coincide.
guess_steadystate – Whether to guess steadystates based on previous steadystates and respective derivatives. This option may lead to unexpected results for models with conservation laws and should accordingly be deactivated for those models.
n_threads – Number of threads that are used for parallelization over experimental conditions. If amici was not installed with openMP support this option will have no effect.
fim_for_hess – Whether to use the FIM whenever the Hessian is requested. This only applies with forward sensitivities. With adjoint sensitivities, the true Hessian will be used, if available. FIM or Hessian will only be exposed if max_sensi_order>1.
amici_object_builder – AMICI object builder. Allows recreating the objective for pickling, required in some parallelization schemes.
calculator – Performs the actual calculation of the function values and derivatives.
-
apply_custom_timepoints() → None[source]¶ Apply custom timepoints, if applicable.
See the set_custom_timepoints method for more information.
-
apply_steadystate_guess(condition_ix: int, x_dct: Dict) → None[source]¶ Use the stored steadystate as well as the respective sensitivity ( if available) and parameter value to approximate the steadystate at the current parameters using a zeroth or first order taylor approximation: x_ss(x’) = x_ss(x) [+ dx_ss/dx(x)*(x’-x)]
-
call_unprocessed(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, edatas: Sequence[amici.ExpData] = None, parameter_mapping: ParameterMapping = None)[source]¶ Call objective function without pre- or post-processing and formatting.
- Parameters
x – The parameters for which to evaluate the objective function.
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
A dict containing the results.
- Return type
result
-
check_gradients_match_finite_differences(x: Optional[numpy.ndarray] = None, *args, **kwargs) → bool[source]¶ Check if gradients match finite differences (FDs)
- Parameters
x (The parameters for which to evaluate the gradient.) –
- Returns
Indicates whether gradients match (True) FDs or not (False)
- Return type
-
check_mode(mode: str) → bool[source]¶ Check if the objective is able to compute in the requested mode.
Either check_mode or the fun_… functions must be overwritten in derived classes.
- Parameters
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether mode is supported
- Return type
flag
-
check_sensi_orders(sensi_orders: Tuple[int, …], mode: str) → bool[source]¶ Check if the objective is able to compute the requested sensitivities.
Either check_sensi_orders or the fun_… functions must be overwritten in derived classes.
- Parameters
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether combination of sensi_orders and mode is supported
- Return type
flag
-
get_config() → dict[source]¶ Get the configuration information of the objective function and return it as a dictonary.
-
initialize()[source]¶ Initialize the objective function. This function is used at the beginning of an analysis, e.g. optimization, and can e.g. reset the objective memory. By default does nothing.
-
set_custom_timepoints(timepoints: Optional[Sequence[Sequence[Union[float, int]]]] = None, timepoints_global: Optional[Sequence[Union[float, int]]] = None) → pypesto.objective.amici.AmiciObjective[source]¶ Create a copy of this objective that will be evaluated at custom timepoints.
The intended use is to aid in predictions at unmeasured timepoints.
- Parameters
timepoints – The outer sequence should contain a sequence of timepoints for each experimental condition.
timepoints_global – A sequence of timepoints that will be used for all experimental conditions.
- Returns
- Return type
The customized copy of this objective.
-
-
class
pypesto.objective.CsvHistory(file: str, x_names: Optional[Sequence[str]] = None, options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None, load_from_file: bool = False)[source]¶ Bases:
pypesto.objective.history.HistoryStores a representation of the history in a CSV file.
- Parameters
file – CSV file name.
x_names – Parameter names.
options – History options.
load_from_file – If True, history will be initialized from data in the specified file
-
__init__(file: str, x_names: Optional[Sequence[str]] = None, options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None, load_from_file: bool = False)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
get_chi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Chi2 values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_fval_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Function values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_grad_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Gradients.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_hess_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Hessians.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_res_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Residuals.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_schi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Chi2 sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_sres_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Residual sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_time_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Cumulative execution times.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_x_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Parameters.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
update(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, result: Dict[str, Union[float, numpy.ndarray]]) → None[source]¶ Update history after a function evaluation.
- Parameters
x – The parameter vector.
sensi_orders – The sensitivity orders computed.
mode – The objective function mode computed (function value or residuals).
result – The objective function values for parameters x, sensitivities sensi_orders and mode mode.
-
class
pypesto.objective.FD(obj: pypesto.objective.base.ObjectiveBase, grad: Optional[bool] = None, hess: Optional[bool] = None, sres: Optional[bool] = None, hess_via_fval: bool = True, delta_fun: Union[pypesto.objective.finite_difference.FDDelta, numpy.ndarray, float, str] = 1e-06, delta_grad: Union[pypesto.objective.finite_difference.FDDelta, numpy.ndarray, float, str] = 1e-06, delta_res: Union[pypesto.objective.finite_difference.FDDelta, float, numpy.ndarray, str] = 1e-06, method: str = 'central', x_names: Optional[List[str]] = None)[source]¶ Bases:
pypesto.objective.base.ObjectiveBaseFinite differences (FDs) for derivatives.
Given an objective that gives function values and/or residuals, this class allows to flexibly obtain all derivatives calculated via FDs.
For the parameters grad, hess, sres, a value of None means that the objective derivative is used if available, otherwise resorting to FDs. True means that FDs are used in any case, False means that the derivative is not exported.
Note that the step sizes should be carefully chosen. They should be small enough to provide an accurate linear approximation, but large enough to be robust against numerical inaccuracies, in particular if the objective relies on numerical approximations, such as an ODE.
- Parameters
grad (Optional[bool]) – Derivative method for the gradient (see above).
hess (Optional[bool]) – Derivative method for the Hessian (see above).
sres (Optional[bool]) – Derivative method for the residual sensitivities (see above).
hess_via_fval (bool) – If the Hessian is to be calculated via finite differences: whether to employ 2nd order FDs via fval even if the objective can provide a gradient.
delta_fun (pypesto.objective.finite_difference.FDDelta) – FD step sizes for function values. Can be either a float, or a
np.ndarrayof shape (n_par,) for different step sizes for different coordinates.delta_grad (pypesto.objective.finite_difference.FDDelta) – FD step sizes for gradients, if the Hessian is calculated via 1st order sensitivities from the gradients. Similar to delta_fun.
delta_res (pypesto.objective.finite_difference.FDDelta) – FD step sizes for residuals. Similar to delta_fun.
method (str) – Method to calculate FDs. Can be any of FD.METHODS: central, forward or backward differences. The latter two require only roughly half as many function evaluations, are however less accurate than central (O(x) vs O(x**2)).
x_names – Parameter names that can be optionally used in, e.g., history or gradient checks.
Examples
Define residuals and objective function, and obtain all derivatives via FDs:
>>> from pypesto import Objective, FD >>> import numpy as np >>> x_obs = np.array([11, 12, 13]) >>> res = lambda x: x - x_obs >>> fun = lambda x: 0.5 * sum(res(x)**2) >>> obj = FD(Objective(fun=fun, res=res))
-
BACKWARD= 'backward'¶
-
CENTRAL= 'central'¶
-
FORWARD= 'forward'¶
-
METHODS= ['central', 'forward', 'backward']¶
-
__init__(obj: pypesto.objective.base.ObjectiveBase, grad: Optional[bool] = None, hess: Optional[bool] = None, sres: Optional[bool] = None, hess_via_fval: bool = True, delta_fun: Union[pypesto.objective.finite_difference.FDDelta, numpy.ndarray, float, str] = 1e-06, delta_grad: Union[pypesto.objective.finite_difference.FDDelta, numpy.ndarray, float, str] = 1e-06, delta_res: Union[pypesto.objective.finite_difference.FDDelta, float, numpy.ndarray, str] = 1e-06, method: str = 'central', x_names: Optional[List[str]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
call_unprocessed(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, **kwargs) → Dict[str, Union[float, numpy.ndarray, Dict]][source]¶ Call objective function without pre- or post-processing and formatting.
- Parameters
x – The parameters for which to evaluate the objective function.
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
A dict containing the results.
- Return type
result
-
delta_fun: pypesto.objective.finite_difference.FDDelta¶
-
delta_grad: pypesto.objective.finite_difference.FDDelta¶
-
delta_res: pypesto.objective.finite_difference.FDDelta¶
-
property
has_fun¶
-
property
has_grad¶
-
property
has_hess¶
-
property
has_res¶
-
property
has_sres¶
-
obj: pypesto.objective.base.ObjectiveBase¶
-
class
pypesto.objective.FDDelta(delta: Optional[Union[numpy.ndarray, float]] = None, test_deltas: Optional[numpy.ndarray] = None, update_condition: str = 'constant', max_distance: float = 0.5, max_steps: int = 30)[source]¶ Bases:
objectFinite difference step size with automatic updating.
Reference implementation: https://github.com/ICB-DCM/PESTO/blob/master/private/getStepSizeFD.m
- Parameters
delta (Optional[Union[numpy.ndarray, float]]) – (Initial) step size, either a float, or a vector of size (n_par,). If not None, this is used as initial step size.
test_deltas (numpy.ndarray) – Step sizes to try out in step size selection. If None, a range [1e-1, 1e-2, …, 1e-8] is considered.
update_condition (str) – A “good” step size may be a local property. Thus, this class allows updating the step size if certain criteria are met, in the
pypesto.objective.finite_difference.FDDelta.update()function. FDDelta.CONSTANT means that the step size is only initially selected. FDDelta.DISTANCE means that the step size is updated if the current evaluation point is sufficiently far away from the last training point. FDDelta.STEPS means that the step size is updated max_steps evaluations after the last update.max_distance (float) – Coefficient on the distance between current and reference point beyond which to update, in the FDDelta.DISTANCE update condition.
max_steps (int) – Number of steps after which to update in the FDDelta.STEPS update condition.
-
CONSTANT= 'constant'¶
-
DISTANCE= 'distance'¶
-
STEPS= 'steps'¶
-
UPDATE_CONDITIONS= ['constant', 'distance', 'steps']¶
-
__init__(delta: Optional[Union[numpy.ndarray, float]] = None, test_deltas: Optional[numpy.ndarray] = None, update_condition: str = 'constant', max_distance: float = 0.5, max_steps: int = 30)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
delta: Optional[Union[numpy.ndarray, float]]¶
-
get() → numpy.ndarray[source]¶ Get delta vector.
-
test_deltas: numpy.ndarray¶
-
update(x: numpy.ndarray, fval: Optional[Union[float, numpy.ndarray]], fun: Callable, fd_method: str) → None[source]¶ Update delta if update conditions are met.
- Parameters
x – Current parameter vector, shape (n_par,).
fval – fun(x), to avoid re-evaluation. Scalar- or vector-valued.
fun – Function whose 1st-order derivative to approximate. Scalar- or vector-valued.
fd_method – FD method employed by
pypesto.objective.finite_difference.FD, see there.
-
x0: Optional[numpy.ndarray]¶
-
class
pypesto.objective.Hdf5History(id: str, file: str, options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None)[source]¶ Bases:
pypesto.objective.history.HistoryStores a representation of the history in an HDF5 file.
- Parameters
id – Id of the history
file – HDF5 file name.
options – History options.
-
__init__(id: str, file: str, options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
get_chi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Chi2 values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_fval_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Function values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_grad_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Gradients.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_hess_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Hessians.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_res_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Residuals.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_schi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Chi2 sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_sres_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Residual sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_time_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Cumulative execution times.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_x_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Parameters.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
property
n_fval¶ Number of function evaluations.
-
property
n_grad¶ Number of gradient evaluations.
-
property
n_hess¶ Number of Hessian evaluations.
-
property
n_res¶ Number of residual evaluations.
-
property
n_sres¶ Number or residual sensitivity evaluations.
-
property
trace_save_iter¶
-
update(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, result: Dict[str, Union[float, numpy.ndarray]]) → None[source]¶ Update history after a function evaluation.
- Parameters
x – The parameter vector.
sensi_orders – The sensitivity orders computed.
mode – The objective function mode computed (function value or residuals).
result – The objective function values for parameters x, sensitivities sensi_orders and mode mode.
-
class
pypesto.objective.History(options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None)[source]¶ Bases:
pypesto.objective.history.HistoryBaseTracks numbers of function evaluations only, no trace.
- Parameters
options – History options.
-
__init__(options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
property
n_fval¶ Number of function evaluations.
-
property
n_grad¶ Number of gradient evaluations.
-
property
n_hess¶ Number of Hessian evaluations.
-
property
n_res¶ Number of residual evaluations.
-
property
n_sres¶ Number or residual sensitivity evaluations.
-
property
start_time¶ Start time.
-
update(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, result: Dict[str, Union[float, numpy.ndarray]]) → None[source]¶ Update history after a function evaluation.
- Parameters
x – The parameter vector.
sensi_orders – The sensitivity orders computed.
mode – The objective function mode computed (function value or residuals).
result – The objective function values for parameters x, sensitivities sensi_orders and mode mode.
-
class
pypesto.objective.HistoryBase[source]¶ Bases:
abc.ABCAbstract base class for history objects.
Can be used as a dummy history, but does not implement any history functionality.
-
get_chi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[float], float][source]¶ Chi2 values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_fval_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[float], float][source]¶ Function values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_grad_trace(ix: Optional[Union[int, Sequence[int]]] = None, trim: bool = False) → Union[Sequence[Union[numpy.ndarray, np.nan]], numpy.ndarray, np.nan][source]¶ Gradients.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_hess_trace(ix: Optional[Union[int, Sequence[int]]] = None, trim: bool = False) → Union[Sequence[Union[numpy.ndarray, np.nan]], numpy.ndarray, np.nan][source]¶ Hessians.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_res_trace(ix: Optional[Union[int, Sequence[int]]] = None, trim: bool = False) → Union[Sequence[Union[numpy.ndarray, np.nan]], numpy.ndarray, np.nan][source]¶ Residuals.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_schi2_trace(ix: Optional[Union[int, Sequence[int]]] = None, trim: bool = False) → Union[Sequence[Union[numpy.ndarray, np.nan]], numpy.ndarray, np.nan][source]¶ Chi2 sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_sres_trace(ix: Optional[Union[int, Sequence[int]]] = None, trim: bool = False) → Union[Sequence[Union[numpy.ndarray, np.nan]], numpy.ndarray, np.nan][source]¶ Residual sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_time_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[float], float][source]¶ Cumulative execution times.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_trimmed_indices()[source]¶ Returns indices of the history to get a monotonically decreasing history.
-
get_x_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[numpy.ndarray], numpy.ndarray][source]¶ Parameters.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
property
n_fval¶ Number of function evaluations.
-
property
n_grad¶ Number of gradient evaluations.
-
property
n_hess¶ Number of Hessian evaluations.
-
property
n_res¶ Number of residual evaluations.
-
property
n_sres¶ Number or residual sensitivity evaluations.
-
property
start_time¶ Start time.
-
update(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, result: Dict[str, Union[float, numpy.ndarray]]) → None[source]¶ Update history after a function evaluation.
- Parameters
x – The parameter vector.
sensi_orders – The sensitivity orders computed.
mode – The objective function mode computed (function value or residuals).
result – The objective function values for parameters x, sensitivities sensi_orders and mode mode.
-
-
class
pypesto.objective.HistoryOptions(trace_record: bool = False, trace_record_grad: bool = True, trace_record_hess: bool = True, trace_record_res: bool = True, trace_record_sres: bool = True, trace_record_chi2: bool = True, trace_record_schi2: bool = True, trace_save_iter: int = 10, storage_file: Optional[str] = None)[source]¶ Bases:
dictOptions for the objective that are used in optimization, profiling and sampling.
In addition implements a factory pattern to generate history objects.
- Parameters
trace_record – Flag indicating whether to record the trace of function calls. The trace_record_* flags only become effective if trace_record is True.
trace_record_grad – Flag indicating whether to record the gradient in the trace.
trace_record_hess – Flag indicating whether to record the Hessian in the trace.
trace_record_res – Flag indicating whether to record the residual in the trace.
trace_record_sres – Flag indicating whether to record the residual sensitivities in the trace.
trace_record_chi2 – Flag indicating whether to record the chi2 in the trace.
trace_record_schi2 – Flag indicating whether to record the chi2 sensitivities in the trace.
trace_save_iter – After how many iterations to store the trace.
storage_file – File to save the history to. Can be any of None, a “{filename}.csv”, or a “{filename}.hdf5” file. Depending on the values, the create_history method creates the appropriate object. Occurrences of “{id}” in the file name are replaced by the id upon creation of a history, if applicable.
-
__init__(trace_record: bool = False, trace_record_grad: bool = True, trace_record_hess: bool = True, trace_record_res: bool = True, trace_record_sres: bool = True, trace_record_chi2: bool = True, trace_record_schi2: bool = True, trace_save_iter: int = 10, storage_file: Optional[str] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
static
assert_instance(maybe_options: Union[pypesto.objective.history.HistoryOptions, Dict]) → pypesto.objective.history.HistoryOptions[source]¶ Returns a valid options object.
- Parameters
maybe_options (HistoryOptions or dict) –
-
class
pypesto.objective.MemoryHistory(options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None)[source]¶ Bases:
pypesto.objective.history.HistoryTracks numbers of function evaluations and keeps an in-memory trace of function evaluations.
- Parameters
options – History options.
-
__init__(options: Optional[Union[pypesto.objective.history.HistoryOptions, Dict]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
get_chi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Chi2 values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_fval_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Function values.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_grad_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Gradients.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_hess_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Hessians.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_res_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Residuals.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_schi2_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Chi2 sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_sres_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Residual sensitivities.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_time_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Cumulative execution times.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
get_x_trace(ix: Optional[Union[Sequence[int], int]] = None, trim: bool = False) → Union[Sequence[Union[float, numpy.ndarray, np.nan]], float, numpy.ndarray, np.nan][source]¶ Parameters.
Takes as parameter an index or indices and returns corresponding trace values. If only a single value is requested, the list is flattened.
-
update(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, result: Dict[str, Union[float, numpy.ndarray]]) → None[source]¶ Update history after a function evaluation.
- Parameters
x – The parameter vector.
sensi_orders – The sensitivity orders computed.
mode – The objective function mode computed (function value or residuals).
result – The objective function values for parameters x, sensitivities sensi_orders and mode mode.
-
class
pypesto.objective.NegLogParameterPriors(prior_list: List[Dict], x_names: Optional[Sequence[str]] = None)[source]¶ Bases:
pypesto.objective.base.ObjectiveBaseThis class implements Negative Log Priors on Parameters.
Contains a list of prior dictionaries for the individual parameters of the format
{‘index’: [int], ‘density_fun’: [Callable], ‘density_dx’: [Callable], ‘density_ddx’: [Callable]}
A prior instance can be added to e.g. an objective, that gives the likelihood, by an AggregatedObjective.
Notes
All callables should correspond to log-densities. That is, they return log-densities and their corresponding derivatives. Internally, values are multiplied by -1, since pyPESTO expects the Objective function to be of a negative log-density type.
-
__init__(prior_list: List[Dict], x_names: Optional[Sequence[str]] = None)[source]¶ Constructor
- Parameters
prior_list – List of dicts containing the individual parameter priors. Format see above.
x_names – Sequence of parameter names (optional).
-
call_unprocessed(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str) → Dict[str, Union[float, numpy.ndarray, Dict]][source]¶ Call objective function without pre- or post-processing and formatting.
- Parameters
x – The parameters for which to evaluate the objective function.
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
A dict containing the results.
- Return type
result
-
check_mode(mode) → bool[source]¶ Check if the objective is able to compute in the requested mode.
Either check_mode or the fun_… functions must be overwritten in derived classes.
- Parameters
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether mode is supported
- Return type
flag
-
check_sensi_orders(sensi_orders: Tuple[int, …], mode: str) → bool[source]¶ Check if the objective is able to compute the requested sensitivities.
Either check_sensi_orders or the fun_… functions must be overwritten in derived classes.
- Parameters
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether combination of sensi_orders and mode is supported
- Return type
flag
-
gradient_neg_log_density(x)[source]¶ Computes the gradient of the negative log-density for a parameter vector x.
-
hessian_neg_log_density(x)[source]¶ Computes the hessian of the negative log-density for a parameter vector x.
-
-
class
pypesto.objective.NegLogPriors(objectives: Sequence[pypesto.objective.base.ObjectiveBase], x_names: Optional[Sequence[str]] = None)[source]¶ Bases:
pypesto.objective.aggregated.AggregatedObjectiveAggregates different forms of negative log-prior distributions.
Allows to distinguish priors from the likelihood by testing the type of an objective.
Consists basically of a list of individual negative log-priors, given in self.objectives.
-
class
pypesto.objective.Objective(fun: Optional[Callable] = None, grad: Optional[Union[Callable, bool]] = None, hess: Optional[Callable] = None, hessp: Optional[Callable] = None, res: Optional[Callable] = None, sres: Optional[Union[Callable, bool]] = None, x_names: Optional[Sequence[str]] = None)[source]¶ Bases:
pypesto.objective.base.ObjectiveBaseThe objective class allows the user explicitly specify functions that compute the function value and/or residuals as well as respective derivatives.
Denote dimensions n = parameters, m = residuals.
- Parameters
fun –
The objective function to be minimized. If it only computes the objective function value, it should be of the form
fun(x) -> floatwhere x is an 1-D array with shape (n,), and n is the parameter space dimension.
grad –
Method for computing the gradient vector. If it is a callable, it should be of the form
grad(x) -> array_like, shape (n,).If its value is True, then fun should return the gradient as a second output.
hess –
Method for computing the Hessian matrix. If it is a callable, it should be of the form
hess(x) -> array, shape (n, n).If its value is True, then fun should return the gradient as a second, and the Hessian as a third output, and grad should be True as well.
hessp –
Method for computing the Hessian vector product, i.e.
hessp(x, v) -> array_like, shape (n,)computes the product H*v of the Hessian of fun at x with v.
res –
Method for computing residuals, i.e.
res(x) -> array_like, shape(m,).sres –
Method for computing residual sensitivities. If it is a callable, it should be of the form
sres(x) -> array, shape (m, n).If its value is True, then res should return the residual sensitivities as a second output.
x_names – Parameter names. None if no names provided, otherwise a list of str, length dim_full (as in the Problem class). Can be read by the problem.
-
__init__(fun: Optional[Callable] = None, grad: Optional[Union[Callable, bool]] = None, hess: Optional[Callable] = None, hessp: Optional[Callable] = None, res: Optional[Callable] = None, sres: Optional[Union[Callable, bool]] = None, x_names: Optional[Sequence[str]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
call_unprocessed(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, **kwargs) → Dict[str, Union[float, numpy.ndarray, Dict]][source]¶ Call objective function without pre- or post-processing and formatting.
- Returns
A dict containing the results.
- Return type
result
-
get_config() → dict[source]¶ Get the configuration information of the objective function and return it as a dictonary.
-
property
has_fun¶
-
property
has_grad¶
-
property
has_hess¶
-
property
has_hessp¶
-
property
has_res¶
-
property
has_sres¶
-
class
pypesto.objective.ObjectiveBase(x_names: Optional[Sequence[str]] = None)[source]¶ Bases:
abc.ABCThe objective class is a simple wrapper around the objective function, giving a standardized way of calling. Apart from that, it manages several things including fixing of parameters and history.
The objective function is assumed to be in the format of a cost function, log-likelihood function, or log-posterior function. These functions are subject to minimization. For profiling and sampling, the sign is internally flipped, all returned and stored values are however given as returned by this objective function. If maximization is to be performed, the sign should be flipped before creating the objective function.
- Parameters
x_names – Parameter names that can be optionally used in, e.g., history or gradient checks.
-
history¶ For storing the call history. Initialized by the methods, e.g. the optimizer, in initialize_history().
-
pre_post_processor¶ Preprocess input values to and postprocess output values from __call__. Configured in update_from_problem().
-
__call__(x: numpy.ndarray, sensi_orders: Tuple[int, …] = (0), mode: str = 'mode_fun', return_dict: bool = False, **kwargs) → Union[float, numpy.ndarray, Tuple, Dict[str, Union[float, numpy.ndarray, Dict]]][source]¶ Method to obtain arbitrary sensitivities. This is the central method which is always called, also by the get_* methods.
There are different ways in which an optimizer calls the objective function, and in how the objective function provides information (e.g. derivatives via separate functions or along with the function values). The different calling modes increase efficiency in space and time and make the objective flexible.
- Parameters
x – The parameters for which to evaluate the objective function.
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
return_dict – If False (default), the result is a Tuple of the requested values in the requested order. Tuples of length one are flattened. If True, instead a dict is returned which can carry further information.
- Returns
By default, this is a tuple of the requested function values and derivatives in the requested order (if only 1 value, the tuple is flattened). If return_dict, then instead a dict is returned with function values and derivatives indicated by ids.
- Return type
result
-
__init__(x_names: Optional[Sequence[str]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
abstract
call_unprocessed(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, **kwargs) → Dict[str, Union[float, numpy.ndarray, Dict]][source]¶ Call objective function without pre- or post-processing and formatting.
- Parameters
x – The parameters for which to evaluate the objective function.
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
A dict containing the results.
- Return type
result
-
check_grad(x: numpy.ndarray, x_indices: Optional[Sequence[int]] = None, eps: float = 1e-05, verbosity: int = 1, mode: str = 'mode_fun', detailed: bool = False) → pandas.core.frame.DataFrame[source]¶ Compare gradient evaluation: Firstly approximate via finite differences, and secondly use the objective gradient.
- Parameters
x – The parameters for which to evaluate the gradient.
x_indices – Indices for which to compute gradients. Default: all.
eps – Finite differences step size.
verbosity – Level of verbosity for function output. 0: no output, 1: summary for all parameters, 2: summary for individual parameters.
mode – Residual (MODE_RES) or objective function value (MODE_FUN) computation mode.
detailed – Toggle whether additional values are returned. Additional values are function values, and the central difference weighted by the difference in output from all methods (standard deviation and mean).
- Returns
gradient, finite difference approximations and error estimates.
- Return type
result
-
check_grad_multi_eps(*args, multi_eps: Optional[Iterable] = None, label: str = 'rel_err', **kwargs)[source]¶ Equivalent to the ObjectiveBase.check_grad method, except multiple finite difference step sizes are tested. The result contains the lowest finite difference for each parameter, and the corresponding finite difference step size.
- Parameters
ObjectiveBase.check_grad method parameters. (All) –
multi_eps – The finite difference step sizes to be tested.
label – The label of the column that will be minimized for each parameter. Valid options are the column labels of the dataframe returned by the ObjectiveBase.check_grad method.
-
check_gradients_match_finite_differences(*args, x: Optional[numpy.ndarray] = None, x_free: Optional[Sequence[int]] = None, rtol: float = 0.01, atol: float = 0.001, mode: Optional[str] = None, multi_eps=None, **kwargs) → bool[source]¶ Check if gradients match finite differences (FDs)
- Parameters
rtol (relative error tolerance) –
x (The parameters for which to evaluate the gradient) –
x_free (Indices for which to compute gradients) –
rtol –
atol (absolute error tolerance) –
mode (function values or residuals) –
multi_eps (multiple test step width for FDs) –
- Returns
Indicates whether gradients match (True) FDs or not (False)
- Return type
-
check_mode(mode: str) → bool[source]¶ Check if the objective is able to compute in the requested mode.
Either check_mode or the fun_… functions must be overwritten in derived classes.
- Parameters
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether mode is supported
- Return type
flag
-
check_sensi_orders(sensi_orders: Tuple[int, …], mode: str) → bool[source]¶ Check if the objective is able to compute the requested sensitivities.
Either check_sensi_orders or the fun_… functions must be overwritten in derived classes.
- Parameters
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether combination of sensi_orders and mode is supported
- Return type
flag
-
get_config() → dict[source]¶ Get the configuration information of the objective function and return it as a dictonary.
-
get_fval(x: numpy.ndarray) → float[source]¶ Get the function value at x.
-
get_grad(x: numpy.ndarray) → numpy.ndarray[source]¶ Get the gradient at x.
-
get_hess(x: numpy.ndarray) → numpy.ndarray[source]¶ Get the Hessian at x.
-
get_res(x: numpy.ndarray) → numpy.ndarray[source]¶ Get the residuals at x.
-
get_sres(x: numpy.ndarray) → numpy.ndarray[source]¶ Get the residual sensitivities at x.
-
property
has_fun¶
-
property
has_grad¶
-
property
has_hess¶
-
property
has_hessp¶
-
property
has_res¶
-
property
has_sres¶
-
initialize()[source]¶ Initialize the objective function. This function is used at the beginning of an analysis, e.g. optimization, and can e.g. reset the objective memory. By default does nothing.
-
static
output_to_tuple(sensi_orders: Tuple[int, …], mode: str, **kwargs: Union[float, numpy.ndarray]) → Tuple[source]¶ Return values as requested by the caller, since usually only a subset is demanded. One output is returned as-is, more than one output are returned as a tuple in order (fval, grad, hess).
-
update_from_problem(dim_full: int, x_free_indices: Sequence[int], x_fixed_indices: Sequence[int], x_fixed_vals: Sequence[float])[source]¶ Handle fixed parameters. Later, the objective will be given parameter vectors x of dimension dim, which have to be filled up with fixed parameter values to form a vector of dimension dim_full >= dim. This vector is then used to compute function value and derivatives. The derivatives must later be reduced again to dimension dim.
This is so as to make the fixing of parameters transparent to the caller.
The methods preprocess, postprocess are overwritten for the above functionality, respectively.
- Parameters
dim_full – Dimension of the full vector including fixed parameters.
x_free_indices – Vector containing the indices (zero-based) of free parameters (complimentary to x_fixed_indices).
x_fixed_indices – Vector containing the indices (zero-based) of parameter components that are not to be optimized.
x_fixed_vals – Vector of the same length as x_fixed_indices, containing the values of the fixed parameters.
-
class
pypesto.objective.OptimizerHistory(history: pypesto.objective.history.History, x0: numpy.ndarray, generate_from_history: bool = False)[source]¶ Bases:
objectObjective call history. Container around a History object, which keeps track of optimal values.
-
fval0, fval_min Initial and best function value found.
-
chi20, chi2_min Initial and best chi2 value found.
-
x0, x_min Initial and best parameters found.
-
grad_min¶ gradient for best parameters
-
hess_min¶ hessian (approximation) for best parameters
-
res_min¶ residuals for best parameters
-
sres_min¶ residual sensitivities for best parameters
- Parameters
history – History object to attach to this container. This history object implements the storage of the actual history.
x0 – Initial values for optimization
generate_from_history – If set to true, this function will try to fill attributes of this function based on the provided history
-
__init__(history: pypesto.objective.history.History, x0: numpy.ndarray, generate_from_history: bool = False) → None[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
update(x: numpy.ndarray, sensi_orders: Tuple[int], mode: str, result: Dict[str, Union[float, numpy.ndarray]]) → None[source]¶ Update history and best found value.
-
Problem¶
A problem contains the objective as well as all information like prior describing the problem to be solved.
-
class
pypesto.problem.NegLogPriors(objectives: Sequence[pypesto.objective.base.ObjectiveBase], x_names: Optional[Sequence[str]] = None)[source]¶ Bases:
pypesto.objective.aggregated.AggregatedObjectiveAggregates different forms of negative log-prior distributions.
Allows to distinguish priors from the likelihood by testing the type of an objective.
Consists basically of a list of individual negative log-priors, given in self.objectives.
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class
pypesto.problem.ObjectiveBase(x_names: Optional[Sequence[str]] = None)[source]¶ Bases:
abc.ABCThe objective class is a simple wrapper around the objective function, giving a standardized way of calling. Apart from that, it manages several things including fixing of parameters and history.
The objective function is assumed to be in the format of a cost function, log-likelihood function, or log-posterior function. These functions are subject to minimization. For profiling and sampling, the sign is internally flipped, all returned and stored values are however given as returned by this objective function. If maximization is to be performed, the sign should be flipped before creating the objective function.
- Parameters
x_names – Parameter names that can be optionally used in, e.g., history or gradient checks.
-
history¶ For storing the call history. Initialized by the methods, e.g. the optimizer, in initialize_history().
-
pre_post_processor¶ Preprocess input values to and postprocess output values from __call__. Configured in update_from_problem().
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__call__(x: numpy.ndarray, sensi_orders: Tuple[int, …] = (0), mode: str = 'mode_fun', return_dict: bool = False, **kwargs) → Union[float, numpy.ndarray, Tuple, Dict[str, Union[float, numpy.ndarray, Dict]]][source]¶ Method to obtain arbitrary sensitivities. This is the central method which is always called, also by the get_* methods.
There are different ways in which an optimizer calls the objective function, and in how the objective function provides information (e.g. derivatives via separate functions or along with the function values). The different calling modes increase efficiency in space and time and make the objective flexible.
- Parameters
x – The parameters for which to evaluate the objective function.
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
return_dict – If False (default), the result is a Tuple of the requested values in the requested order. Tuples of length one are flattened. If True, instead a dict is returned which can carry further information.
- Returns
By default, this is a tuple of the requested function values and derivatives in the requested order (if only 1 value, the tuple is flattened). If return_dict, then instead a dict is returned with function values and derivatives indicated by ids.
- Return type
result
-
__init__(x_names: Optional[Sequence[str]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
abstract
call_unprocessed(x: numpy.ndarray, sensi_orders: Tuple[int, …], mode: str, **kwargs) → Dict[str, Union[float, numpy.ndarray, Dict]][source]¶ Call objective function without pre- or post-processing and formatting.
- Parameters
x – The parameters for which to evaluate the objective function.
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
A dict containing the results.
- Return type
result
-
check_grad(x: numpy.ndarray, x_indices: Optional[Sequence[int]] = None, eps: float = 1e-05, verbosity: int = 1, mode: str = 'mode_fun', detailed: bool = False) → pandas.core.frame.DataFrame[source]¶ Compare gradient evaluation: Firstly approximate via finite differences, and secondly use the objective gradient.
- Parameters
x – The parameters for which to evaluate the gradient.
x_indices – Indices for which to compute gradients. Default: all.
eps – Finite differences step size.
verbosity – Level of verbosity for function output. 0: no output, 1: summary for all parameters, 2: summary for individual parameters.
mode – Residual (MODE_RES) or objective function value (MODE_FUN) computation mode.
detailed – Toggle whether additional values are returned. Additional values are function values, and the central difference weighted by the difference in output from all methods (standard deviation and mean).
- Returns
gradient, finite difference approximations and error estimates.
- Return type
result
-
check_grad_multi_eps(*args, multi_eps: Optional[Iterable] = None, label: str = 'rel_err', **kwargs)[source]¶ Equivalent to the ObjectiveBase.check_grad method, except multiple finite difference step sizes are tested. The result contains the lowest finite difference for each parameter, and the corresponding finite difference step size.
- Parameters
ObjectiveBase.check_grad method parameters. (All) –
multi_eps – The finite difference step sizes to be tested.
label – The label of the column that will be minimized for each parameter. Valid options are the column labels of the dataframe returned by the ObjectiveBase.check_grad method.
-
check_gradients_match_finite_differences(*args, x: Optional[numpy.ndarray] = None, x_free: Optional[Sequence[int]] = None, rtol: float = 0.01, atol: float = 0.001, mode: Optional[str] = None, multi_eps=None, **kwargs) → bool[source]¶ Check if gradients match finite differences (FDs)
- Parameters
rtol (relative error tolerance) –
x (The parameters for which to evaluate the gradient) –
x_free (Indices for which to compute gradients) –
rtol –
atol (absolute error tolerance) –
mode (function values or residuals) –
multi_eps (multiple test step width for FDs) –
- Returns
Indicates whether gradients match (True) FDs or not (False)
- Return type
-
check_mode(mode: str) → bool[source]¶ Check if the objective is able to compute in the requested mode.
Either check_mode or the fun_… functions must be overwritten in derived classes.
- Parameters
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether mode is supported
- Return type
flag
-
check_sensi_orders(sensi_orders: Tuple[int, …], mode: str) → bool[source]¶ Check if the objective is able to compute the requested sensitivities.
Either check_sensi_orders or the fun_… functions must be overwritten in derived classes.
- Parameters
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
- Returns
Boolean indicating whether combination of sensi_orders and mode is supported
- Return type
flag
-
get_config() → dict[source]¶ Get the configuration information of the objective function and return it as a dictonary.
-
get_fval(x: numpy.ndarray) → float[source]¶ Get the function value at x.
-
get_grad(x: numpy.ndarray) → numpy.ndarray[source]¶ Get the gradient at x.
-
get_hess(x: numpy.ndarray) → numpy.ndarray[source]¶ Get the Hessian at x.
-
get_res(x: numpy.ndarray) → numpy.ndarray[source]¶ Get the residuals at x.
-
get_sres(x: numpy.ndarray) → numpy.ndarray[source]¶ Get the residual sensitivities at x.
-
property
has_fun¶
-
property
has_grad¶
-
property
has_hess¶
-
property
has_hessp¶
-
property
has_res¶
-
property
has_sres¶
-
initialize()[source]¶ Initialize the objective function. This function is used at the beginning of an analysis, e.g. optimization, and can e.g. reset the objective memory. By default does nothing.
-
static
output_to_tuple(sensi_orders: Tuple[int, …], mode: str, **kwargs: Union[float, numpy.ndarray]) → Tuple[source]¶ Return values as requested by the caller, since usually only a subset is demanded. One output is returned as-is, more than one output are returned as a tuple in order (fval, grad, hess).
-
update_from_problem(dim_full: int, x_free_indices: Sequence[int], x_fixed_indices: Sequence[int], x_fixed_vals: Sequence[float])[source]¶ Handle fixed parameters. Later, the objective will be given parameter vectors x of dimension dim, which have to be filled up with fixed parameter values to form a vector of dimension dim_full >= dim. This vector is then used to compute function value and derivatives. The derivatives must later be reduced again to dimension dim.
This is so as to make the fixing of parameters transparent to the caller.
The methods preprocess, postprocess are overwritten for the above functionality, respectively.
- Parameters
dim_full – Dimension of the full vector including fixed parameters.
x_free_indices – Vector containing the indices (zero-based) of free parameters (complimentary to x_fixed_indices).
x_fixed_indices – Vector containing the indices (zero-based) of parameter components that are not to be optimized.
x_fixed_vals – Vector of the same length as x_fixed_indices, containing the values of the fixed parameters.
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class
pypesto.problem.Problem(objective: pypesto.objective.base.ObjectiveBase, lb: Union[numpy.ndarray, List[float]], ub: Union[numpy.ndarray, List[float]], dim_full: Optional[int] = None, x_fixed_indices: Optional[Union[Iterable[SupportsInt], SupportsInt]] = None, x_fixed_vals: Optional[Union[Iterable[SupportsFloat], SupportsFloat]] = None, x_guesses: Optional[Iterable[float]] = None, startpoint_method: Optional[Callable] = None, x_names: Optional[Iterable[str]] = None, x_scales: Optional[Iterable[str]] = None, x_priors_defs: Optional[pypesto.objective.priors.NegLogPriors] = None, lb_init: Optional[Union[numpy.ndarray, List[float]]] = None, ub_init: Optional[Union[numpy.ndarray, List[float]]] = None)[source]¶ Bases:
objectThe problem formulation. A problem specifies the objective function, boundaries and constraints, parameter guesses as well as the parameters which are to be optimized.
- Parameters
objective – The objective function for minimization. Note that a shallow copy is created.
lb – The lower and upper bounds for optimization. For unbounded directions set to +-inf.
ub – The lower and upper bounds for optimization. For unbounded directions set to +-inf.
lb_init – The lower and upper bounds for initialization, typically for defining search start points. If not set, set to lb, ub.
ub_init – The lower and upper bounds for initialization, typically for defining search start points. If not set, set to lb, ub.
dim_full – The full dimension of the problem, including fixed parameters.
x_fixed_indices – Vector containing the indices (zero-based) of parameter components that are not to be optimized.
x_fixed_vals – Vector of the same length as x_fixed_indices, containing the values of the fixed parameters.
x_guesses – Guesses for the parameter values, shape (g, dim), where g denotes the number of guesses. These are used as start points in the optimization.
startpoint_method – Callable. startpoint_method(n_starts) returns a n_starts x n_free_indices array of initial values for the optimization.
x_names – Parameter names that can be optionally used e.g. in visualizations. If objective.get_x_names() is not None, those values are used, else the values specified here are used if not None, otherwise the variable names are set to [‘x0’, … ‘x{dim_full}’]. The list must always be of length dim_full.
x_scales – Parameter scales can be optionally given and are used e.g. in visualisation and prior generation. Currently the scales ‘lin’, ‘log`and ‘log10’ are supported.
x_priors_defs – Definitions of priors for parameters. Types of priors, and their required and optional parameters, are described in the Prior class.
Notes
On the fixing of parameter values:
The number of parameters dim_full the objective takes as input must be known, so it must be either lb a vector of that size, or dim_full specified as a parameter.
All vectors are mapped to the reduced space of dimension dim in __init__, regardless of whether they were in dimension dim or dim_full before. If the full representation is needed, the methods get_full_vector() and get_full_matrix() can be used.
-
__init__(objective: pypesto.objective.base.ObjectiveBase, lb: Union[numpy.ndarray, List[float]], ub: Union[numpy.ndarray, List[float]], dim_full: Optional[int] = None, x_fixed_indices: Optional[Union[Iterable[SupportsInt], SupportsInt]] = None, x_fixed_vals: Optional[Union[Iterable[SupportsFloat], SupportsFloat]] = None, x_guesses: Optional[Iterable[float]] = None, startpoint_method: Optional[Callable] = None, x_names: Optional[Iterable[str]] = None, x_scales: Optional[Iterable[str]] = None, x_priors_defs: Optional[pypesto.objective.priors.NegLogPriors] = None, lb_init: Optional[Union[numpy.ndarray, List[float]]] = None, ub_init: Optional[Union[numpy.ndarray, List[float]]] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
property
dim¶
-
fix_parameters(parameter_indices: Union[Iterable[SupportsInt], SupportsInt], parameter_vals: Union[Iterable[SupportsFloat], SupportsFloat]) → None[source]¶ Fix specified parameters to specified values
-
full_index_to_free_index(full_index: int)[source]¶ Calculate index in reduced vector from index in full vector.
- Parameters
full_index (The index in the full vector.) –
- Returns
free_index
- Return type
The index in the free vector.
-
get_full_matrix(x: Optional[numpy.ndarray]) → Optional[numpy.ndarray][source]¶ Map matrix from dim to dim_full. Usually used for hessian.
- Parameters
x (array_like, shape=(dim, dim)) – The matrix in dimension dim.
-
get_full_vector(x: Optional[numpy.ndarray], x_fixed_vals: Optional[Iterable[float]] = None) → Optional[numpy.ndarray][source]¶ Map vector from dim to dim_full. Usually used for x, grad.
- Parameters
x (array_like, shape=(dim,)) – The vector in dimension dim.
x_fixed_vals (array_like, ndim=1, optional) – The values to be used for the fixed indices. If None, then nans are inserted. Usually, None will be used for grad and problem.x_fixed_vals for x.
-
get_reduced_matrix(x_full: Optional[numpy.ndarray]) → Optional[numpy.ndarray][source]¶ Map matrix from dim_full to dim, i.e. delete fixed indices.
- Parameters
x_full (array_like, ndim=2) – The matrix in dimension dim_full.
-
get_reduced_vector(x_full: Optional[numpy.ndarray], x_indices: Optional[List[int]] = None) → Optional[numpy.ndarray][source]¶ Keep only those elements, which indices are specified in x_indices If x_indices is not provided, delete fixed indices.
- Parameters
x_full (array_like, ndim=1) – The vector in dimension dim_full.
x_indices – indices of x_full that should remain
-
property
lb¶
-
property
lb_init¶
-
normalize() → None[source]¶ Reduce all vectors to dimension dim and have the objective accept vectors of dimension dim.
-
print_parameter_summary() → None[source]¶ Prints a summary of what parameters are being optimized and parameter boundaries.
-
set_x_guesses(x_guesses: Iterable[float])[source]¶ Sets the x_guesses of a problem.
- Parameters
x_guesses –
-
property
ub¶
-
property
ub_init¶
-
unfix_parameters(parameter_indices: Union[Iterable[SupportsInt], SupportsInt]) → None[source]¶ Free specified parameters
-
property
x_free_indices¶
-
property
x_guesses¶
Prediction¶
Generate predictions from simulations with specified parameter vectors, with optional post-processing.
-
class
pypesto.predict.AmiciPredictor(amici_objective: pypesto.objective.amici.AmiciObjective, amici_output_fields: Optional[Sequence[str]] = None, post_processor: Optional[Callable] = None, post_processor_sensi: Optional[Callable] = None, post_processor_time: Optional[Callable] = None, max_chunk_size: Optional[int] = None, output_ids: Optional[Sequence[str]] = None, condition_ids: Optional[Sequence[str]] = None)[source]¶ Bases:
objectDo forward simulations (predictions) with parameter vectors, for an AMICI model. The user may supply post-processing methods. If post-processing methods are supplied, and a gradient of the prediction is requested, then the sensitivities of the AMICI model must also be post-processed. There are no checks here to ensure that the sensitivities are correctly post-processed, this is explicitly left to the user. There are also no safeguards if the postprocessor routines fail. This may happen if, e.g., a call to Amici fails, and no timepoints, states or observables are returned. As the AmiciPredictor is agnostic about the dimension of the postprocessor and also the dimension of the postprocessed output, these checks are also left to the user. An example for such a check is provided in the default output (see _default_output()).
-
__call__(x: numpy.ndarray, sensi_orders: Tuple[int, …] = (0), mode: str = 'mode_fun', output_file: str = '', output_format: str = 'csv') → pypesto.predict.result.PredictionResult[source]¶ Simulate a model for a certain prediction function. This method relies on the AmiciObjective, which is underlying, but allows the user to apply any post-processing of the results, the sensitivities, and the timepoints.
- Parameters
x – The parameters for which to evaluate the prediction function.
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
mode – Whether to compute function values or residuals.
output_file – Path to an output file.
output_format – Either ‘csv’, ‘h5’. If an output file is specified, this routine will return a csv file, created from a DataFrame, or an h5 file, created from a dict.
- Returns
PredictionResult object containing timepoints, outputs, and output_sensitivities if requested
- Return type
results
-
__init__(amici_objective: pypesto.objective.amici.AmiciObjective, amici_output_fields: Optional[Sequence[str]] = None, post_processor: Optional[Callable] = None, post_processor_sensi: Optional[Callable] = None, post_processor_time: Optional[Callable] = None, max_chunk_size: Optional[int] = None, output_ids: Optional[Sequence[str]] = None, condition_ids: Optional[Sequence[str]] = None)[source]¶ Constructor.
- Parameters
amici_objective – An objective object, which will be used to get model simulations
amici_output_fields – keys that exist in the return data object from AMICI, which should be available for the post-processors
post_processor – A callable function which applies postprocessing to the simulation results and possibly defines different outputs than those of the amici model. Default are the observables (pypesto.predict.constants.AMICI_Y) of the AMICI model. This method takes a list of dicts (with the returned fields pypesto.predict.constants.AMICI_T, pypesto.predict.constants.AMICI_X, and pypesto.predict.constants.AMICI_Y of the AMICI ReturnData objects) as input. Safeguards for, e.g., failure of AMICI are left to the user.
post_processor_sensi – A callable function which applies postprocessing to the sensitivities of the simulation results. Defaults to the observable sensitivities of the AMICI model. This method takes a list of dicts (with the returned fields pypesto.predict.constants.AMICI_T, pypesto.predict.constants.AMICI_X, pypesto.predict.constants.AMICI_Y, pypesto.predict.constants.AMICI_SX, and pypesto.predict.constants.AMICI_SY of the AMICI ReturnData objects) as input. Safeguards for, e.g., failure of AMICI are left to the user.
post_processor_time – A callable function which applies postprocessing to the timepoints of the simulations. Defaults to the timepoints of the amici model. This method takes a list of dicts (with the returned field pypesto.predict.constants.AMICI_T of the amici ReturnData objects) as input. Safeguards for, e.g., failure of AMICI are left to the user.
max_chunk_size – In some cases, we don’t want to compute all predictions at once when calling the prediction function, as this might not fit into the memory for large datasets and models. Here, the user can specify a maximum chunk size of conditions, which should be simulated at a time. Defaults to None, meaning that all conditions will be simulated.
output_ids – IDs of outputs, as post-processing allows the creation of customizable outputs, which may not coincide with those from the AMICI model (defaults to AMICI observables).
condition_ids – List of identifiers for the conditions of the edata objects of the amici objective, will be passed to the PredictionResult at call.
-
-
class
pypesto.predict.PredictionConditionResult(timepoints: numpy.ndarray, output_ids: Sequence[str], output: Optional[numpy.ndarray] = None, output_sensi: Optional[numpy.ndarray] = None, x_names: Optional[Sequence[str]] = None)[source]¶ Bases:
objectThis class is a light-weight wrapper for the prediction of one simulation condition of an amici model. It should provide a common api how amici predictions should look like in pyPESTO.
-
__init__(timepoints: numpy.ndarray, output_ids: Sequence[str], output: Optional[numpy.ndarray] = None, output_sensi: Optional[numpy.ndarray] = None, x_names: Optional[Sequence[str]] = None)[source]¶ Constructor.
- Parameters
timepoints – Output timepoints for this simulation condition
output_ids – IDs of outputs for this simulation condition
outputs – Postprocessed outputs (ndarray)
outputs_sensi – Sensitivities of postprocessed outputs (ndarray)
x_names – IDs of model parameter w.r.t to which sensitivities were computed
-
-
class
pypesto.predict.PredictionResult(conditions: Sequence[Union[pypesto.predict.result.PredictionConditionResult, Dict]], condition_ids: Optional[Sequence[str]] = None, comment: Optional[str] = None)[source]¶ Bases:
objectThis class is a light-weight wrapper around predictions from pyPESTO made via an amici model. It’s only purpose is to have fixed format/api, how prediction results should be stored, read, and handled: as predictions are a very flexible format anyway, they should at least have a common definition, which allows to work with them in a reasonable way.
-
__init__(conditions: Sequence[Union[pypesto.predict.result.PredictionConditionResult, Dict]], condition_ids: Optional[Sequence[str]] = None, comment: Optional[str] = None)[source]¶ Constructor.
- Parameters
conditions – A list of PredictionConditionResult objects or dicts
condition_ids – IDs or names of the simulation conditions, which belong to this prediction (e.g., PEtab uses tuples of preequilibration condition and simulation conditions)
comment – An additional note, which can be attached to this prediction
-
-
class
pypesto.predict.PredictorTask(predictor: pypesto.predict.Predictor, x: Sequence[float], sensi_orders: Tuple[int, …], mode: str, id: str)[source]¶ Bases:
pypesto.engine.task.TaskPerform a single prediction with
pypesto.engine.Task.Designed for use with
pypesto.ensemble.Ensemble.-
predictor¶ The predictor to use.
-
x¶ The parameter vector to compute predictions with.
-
sensi_orders¶ Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad.
-
mode¶ Whether to compute function values or residuals.
-
id¶ The input ID.
-
__init__(predictor: pypesto.predict.Predictor, x: Sequence[float], sensi_orders: Tuple[int, …], mode: str, id: str)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
execute() → pypesto.predict.PredictionResult[source]¶ Execute the task and return its results.
-
PEtab¶
pyPESTO support for the PEtab data format.
-
class
pypesto.petab.PetabImporter(petab_problem: petab.Problem, output_folder: str = None, model_name: str = None, validate_petab: bool = True)[source]¶ Bases:
pypesto.objective.amici.AmiciObjectBuilder-
MODEL_BASE_DIR= 'amici_models'¶
-
__init__(petab_problem: petab.Problem, output_folder: str = None, model_name: str = None, validate_petab: bool = True)[source]¶ - petab_problem:
Managing access to the model and data.
- output_folder:
Folder to contain the amici model. Defaults to ‘./amici_models/{model_name}’.
- model_name:
Name of the model, which will in particular be the name of the compiled model python module.
- validate_petab:
Flag indicating if the PEtab problem shall be validated.
-
check_gradients(*args, rtol: float = 0.01, atol: float = 0.001, mode: Literal = None, multi_eps=None, **kwargs) → bool[source]¶ Check if gradients match finite differences (FDs)
- Parameters
rtol (relative error tolerance) –
atol (absolute error tolerance) –
mode (function values or residuals) –
objAbsoluteTolerance (absolute tolerance in sensitivity calculation) –
objRelativeTolerance (relative tolerance in sensitivity calculation) –
multi_eps (multiple test step width for FDs) –
- Returns
Indicates whether gradients match (True) FDs or not (False)
- Return type
-
compile_model(**kwargs)[source]¶ Compile the model. If the output folder exists already, it is first deleted.
- Parameters
kwargs (Extra arguments passed to amici.SbmlImporter.sbml2amici.) –
-
create_edatas(model: amici.Model = None, simulation_conditions=None) → List[amici.ExpData][source]¶ Create list of amici.ExpData objects.
-
create_model(force_compile: bool = False, **kwargs) → amici.Model[source]¶ Import amici model. If necessary or force_compile is True, compile first.
- Parameters
force_compile –
If False, the model is compiled only if the output folder does not exist yet. If True, the output folder is deleted and the model (re-)compiled in either case.
Warning
If force_compile, then an existing folder of that name will be deleted.
kwargs (Extra arguments passed to amici.SbmlImporter.sbml2amici) –
-
create_objective(model: amici.Model = None, solver: amici.Solver = None, edatas: Sequence[amici.ExpData] = None, force_compile: bool = False, **kwargs) → pypesto.objective.amici.AmiciObjective[source]¶ Create a
pypesto.AmiciObjective.- Parameters
model – The AMICI model.
solver – The AMICI solver.
edatas – The experimental data in AMICI format.
force_compile – Whether to force-compile the model if not passed.
**kwargs – Additional arguments passed on to the objective.
- Returns
A
pypesto.AmiciObjectivefor the model and the data.- Return type
objective
-
create_predictor(objective: Optional[pypesto.objective.amici.AmiciObjective] = None, amici_output_fields: Optional[Sequence[str]] = None, post_processor: Optional[Callable] = None, post_processor_sensi: Optional[Callable] = None, post_processor_time: Optional[Callable] = None, max_chunk_size: Optional[int] = None, output_ids: Optional[Sequence[str]] = None, condition_ids: Optional[Sequence[str]] = None) → pypesto.predict.amici_predictor.AmiciPredictor[source]¶ Create a
pypesto.predict.AmiciPredictor.The AmiciPredictor facilitates generation of predictions from parameter vectors.
- Parameters
objective – An objective object, which will be used to get model simulations
amici_output_fields – keys that exist in the return data object from AMICI, which should be available for the post-processors
post_processor – A callable function which applies postprocessing to the simulation results. Default are the observables of the AMICI model. This method takes a list of ndarrays (as returned in the field [‘y’] of amici ReturnData objects) as input.
post_processor_sensi – A callable function which applies postprocessing to the sensitivities of the simulation results. Default are the observable sensitivities of the AMICI model. This method takes two lists of ndarrays (as returned in the fields [‘y’] and [‘sy’] of amici ReturnData objects) as input.
post_processor_time – A callable function which applies postprocessing to the timepoints of the simulations. Default are the timepoints of the amici model. This method takes a list of ndarrays (as returned in the field [‘t’] of amici ReturnData objects) as input.
max_chunk_size – In some cases, we don’t want to compute all predictions at once when calling the prediction function, as this might not fit into the memory for large datasets and models. Here, the user can specify a maximum number of conditions, which should be simulated at a time. Default is 0 meaning that all conditions will be simulated. Other values are only applicable, if an output file is specified.
output_ids – IDs of outputs, if post-processing is used
condition_ids – IDs of conditions, if post-processing is used
- Returns
A
pypesto.predict.AmiciPredictorfor the model, using the outputs of the AMICI model and the timepoints from the PEtab data- Return type
predictor
-
create_prior() → pypesto.objective.priors.NegLogParameterPriors[source]¶ Creates a prior from the parameter table. Returns None, if no priors are defined.
-
create_problem(objective: Optional[pypesto.objective.amici.AmiciObjective] = None, x_guesses: Optional[Iterable[float]] = None, **kwargs) → pypesto.problem.Problem[source]¶ Create a
pypesto.Problem.- Parameters
objective – Objective as created by create_objective.
x_guesses – Guesses for the parameter values, shape (g, dim), where g denotes the number of guesses. These are used as start points in the optimization.
**kwargs – Additional key word arguments passed on to the objective, if not provided.
- Returns
A
pypesto.Problemfor the objective.- Return type
problem
-
create_startpoint_method()[source]¶ Creates a startpoint method, if the PEtab problem specifies an initializationPrior. Returns None, if no initializationPrior is specified.
-
static
from_yaml(yaml_config: Union[dict, str], output_folder: Optional[str] = None, model_name: Optional[str] = None) → pypesto.petab.importer.PetabImporter[source]¶ Simplified constructor using a petab yaml file.
-
prediction_to_petab_measurement_df(prediction: pypesto.predict.result.PredictionResult, predictor: Optional[pypesto.predict.amici_predictor.AmiciPredictor] = None) → pandas.core.frame.DataFrame[source]¶ If a PEtab problem is simulated without post-processing, then the result can be cast into a PEtab measurement or simulation dataframe
- Parameters
prediction – A prediction result as produced by an AmiciPredictor
predictor – The AmiciPredictor function
- Returns
A dataframe built from the rdatas in the format as in self.petab_problem.measurement_df.
- Return type
measurement_df
-
prediction_to_petab_simulation_df(prediction: pypesto.predict.result.PredictionResult, predictor: Optional[pypesto.predict.amici_predictor.AmiciPredictor] = None) → pandas.core.frame.DataFrame[source]¶ Same as prediction_to_petab_measurement_df, except a PEtab simulation dataframe is created, i.e. the measurement column label is adjusted.
-
rdatas_to_measurement_df(rdatas: Sequence[amici.ReturnData], model: amici.Model = None) → pandas.core.frame.DataFrame[source]¶ Create a measurement dataframe in the petab format from the passed rdatas and own information.
- Parameters
rdatas – A list of rdatas as produced by pypesto.AmiciObjective.__call__(x, return_dict=True)[‘rdatas’].
model – The amici model.
- Returns
A dataframe built from the rdatas in the format as in self.petab_problem.measurement_df.
- Return type
measurement_df
-
-
class
pypesto.petab.PetabImporterPysb(petab_problem: amici.petab_import_pysb.PysbPetabProblem, output_folder: str = None)[source]¶ Bases:
pypesto.petab.importer.PetabImporterImport for experimental PySB-based PEtab problems
-
__init__(petab_problem: amici.petab_import_pysb.PysbPetabProblem, output_folder: str = None)[source]¶ - petab_problem:
Managing access to the model and data.
- output_folder:
Folder to contain the amici model.
-
Optimize¶
Multistart optimization with support for various optimizers.
-
class
pypesto.optimize.CmaesOptimizer(par_sigma0: float = 0.25, options: Optional[Dict] = None)[source]¶ Bases:
pypesto.optimize.optimizer.OptimizerGlobal optimization using cma-es. Package homepage: https://pypi.org/project/cma-es/
-
__init__(par_sigma0: float = 0.25, options: Optional[Dict] = None)[source]¶ - Parameters
par_sigma0 – scalar, initial standard deviation in each coordinate. par_sigma0 should be about 1/4th of the search domain width (where the optimum is to be expected)
options – Optimizer options that are directly passed on to cma.
-
-
class
pypesto.optimize.DlibOptimizer(options: Optional[Dict] = None)[source]¶ Bases:
pypesto.optimize.optimizer.OptimizerUse the Dlib toolbox for optimization.
-
class
pypesto.optimize.FidesOptimizer(hessian_update: Optional[fides.HessianApproximation] = 'Hybrid', options: Optional[Dict] = None, verbose: Optional[int] = 20)[source]¶ Bases:
pypesto.optimize.optimizer.OptimizerGlobal/Local optimization using the trust region optimizer fides. Package Homepage: https://fides-optimizer.readthedocs.io/en/latest
-
__init__(hessian_update: Optional[fides.HessianApproximation] = 'Hybrid', options: Optional[Dict] = None, verbose: Optional[int] = 20)[source]¶ - Parameters
options – Optimizer options.
hessian_update – Hessian update strategy. If this is None, Hessian (approximation) computed by problem.objective will be used.
-
-
class
pypesto.optimize.IpoptOptimizer(options: Optional[Dict] = None)[source]¶ Bases:
pypesto.optimize.optimizer.OptimizerUse IpOpt (https://pypi.org/project/ipopt/) for optimization.
-
class
pypesto.optimize.NLoptOptimizer(method=None, local_method=None, options: Optional[Dict] = None, local_options: Optional[Dict] = None)[source]¶ Bases:
pypesto.optimize.optimizer.OptimizerGlobal/Local optimization using NLopt. Package homepage: https://nlopt.readthedocs.io/en/latest/
-
__init__(method=None, local_method=None, options: Optional[Dict] = None, local_options: Optional[Dict] = None)[source]¶ - Parameters
method – Local or global Optimizer to use for minimization.
local_method – Local method to use in combination with the global optimizer ( for the MLSL family of solvers) or to solve a subproblem (for the AUGLAG family of solvers)
options – Optimizer options. scipy option maxiter is automatically transformed into maxeval and takes precedence.
local_options – Optimizer options for the local method
-
-
class
pypesto.optimize.OptimizeOptions(startpoint_resample: bool = False, allow_failed_starts: bool = True)[source]¶ Bases:
dictOptions for the multistart optimization.
- Parameters
startpoint_resample – Flag indicating whether initial points are supposed to be resampled if function evaluation fails at the initial point
allow_failed_starts – Flag indicating whether we tolerate that exceptions are thrown during the minimization process.
-
__init__(startpoint_resample: bool = False, allow_failed_starts: bool = True)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
static
assert_instance(maybe_options: Union[pypesto.optimize.options.OptimizeOptions, Dict]) → pypesto.optimize.options.OptimizeOptions[source]¶ Returns a valid options object.
- Parameters
maybe_options (OptimizeOptions or dict) –
-
class
pypesto.optimize.Optimizer[source]¶ Bases:
abc.ABCThis is the optimizer base class, not functional on its own. An optimizer takes a problem, and possibly a start point, and then performs an optimization. It returns an OptimizerResult.
-
class
pypesto.optimize.OptimizerResult(id: Optional[str] = None, x: Optional[numpy.ndarray] = None, fval: Optional[float] = None, grad: Optional[numpy.ndarray] = None, hess: Optional[numpy.ndarray] = None, res: Optional[numpy.ndarray] = None, sres: Optional[numpy.ndarray] = None, n_fval: Optional[int] = None, n_grad: Optional[int] = None, n_hess: Optional[int] = None, n_res: Optional[int] = None, n_sres: Optional[int] = None, x0: Optional[numpy.ndarray] = None, fval0: Optional[float] = None, history: Optional[pypesto.objective.history.History] = None, exitflag: Optional[int] = None, time: Optional[float] = None, message: Optional[str] = None)[source]¶ Bases:
dictThe result of an optimizer run. Used as a standardized return value to map from the individual result objects returned by the employed optimizers to the format understood by pypesto.
Can be used like a dict.
-
id¶ Id of the optimizer run. Usually the start index.
-
x¶ The best found parameters.
-
fval¶ The best found function value, fun(x).
-
grad¶ The gradient at x.
-
hess¶ The Hessian at x.
-
res¶ The residuals at x.
-
sres¶ The residual sensitivities at x.
-
n_fval¶ Number of function evaluations.
-
n_grad¶ Number of gradient evaluations.
-
n_hess¶ Number of Hessian evaluations.
-
n_res¶ Number of residuals evaluations.
-
n_sres¶ Number of residual sensitivity evaluations.
-
x0¶ The starting parameters.
-
fval0¶ The starting function value, fun(x0).
-
history¶ Objective history.
-
exitflag¶ The exitflag of the optimizer.
-
time¶ Execution time.
Notes
Any field not supported by the optimizer is filled with None.
-
__init__(id: Optional[str] = None, x: Optional[numpy.ndarray] = None, fval: Optional[float] = None, grad: Optional[numpy.ndarray] = None, hess: Optional[numpy.ndarray] = None, res: Optional[numpy.ndarray] = None, sres: Optional[numpy.ndarray] = None, n_fval: Optional[int] = None, n_grad: Optional[int] = None, n_hess: Optional[int] = None, n_res: Optional[int] = None, n_sres: Optional[int] = None, x0: Optional[numpy.ndarray] = None, fval0: Optional[float] = None, history: Optional[pypesto.objective.history.History] = None, exitflag: Optional[int] = None, time: Optional[float] = None, message: Optional[str] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
update_to_full(problem: pypesto.problem.Problem) → None[source]¶ Updates values to full vectors/matrices
- Parameters
problem – problem which contains info about how to convert to full vectors or matrices
-
-
class
pypesto.optimize.PyswarmOptimizer(options: Optional[Dict] = None)[source]¶ Bases:
pypesto.optimize.optimizer.OptimizerGlobal optimization using pyswarm.
-
class
pypesto.optimize.PyswarmsOptimizer(par_popsize: float = 10, options: Optional[Dict] = None)[source]¶ Bases:
pypesto.optimize.optimizer.OptimizerGlobal optimization using pyswarms. Package homepage: https://pyswarms.readthedocs.io/en/latest/index.html
- Parameters
par_popsize – number of particles in the swarm, default value 10
options – Optimizer options that are directly passed on to pyswarms. c1: cognitive parameter c2: social parameter w: inertia parameter Default values are (c1,c2,w) = (0.5, 0.3, 0.9)
Examples
Arguments that can be passed to options:
- maxiter:
used to calculate the maximal number of funcion evaluations. Default: 1000
-
class
pypesto.optimize.ScipyDifferentialEvolutionOptimizer(options: Optional[Dict] = None)[source]¶ Bases:
pypesto.optimize.optimizer.OptimizerGlobal optimization using scipy’s differential evolution optimizer. Package homepage: https://docs.scipy.org/doc/scipy/reference/generated /scipy.optimize.differential_evolution.html
- Parameters
options – Optimizer options that are directly passed on to scipy’s optimizer.
Examples
Arguments that can be passed to options:
- maxiter:
used to calculate the maximal number of funcion evaluations by maxfevals = (maxiter + 1) * popsize * len(x) Default: 100
- popsize:
population size, default value 15
-
class
pypesto.optimize.ScipyOptimizer(method: str = 'L-BFGS-B', tol: float = 1e-09, options: Optional[Dict] = None)[source]¶ Bases:
pypesto.optimize.optimizer.OptimizerUse the SciPy optimizers. Find details on the optimizer and configuration options at: https://docs.scipy.org/doc/scipy/reference/generated/scipy. optimize.minimize.html#scipy.optimize.minimize
-
pypesto.optimize.minimize(problem: pypesto.problem.Problem, optimizer: Optional[pypesto.optimize.optimizer.Optimizer] = None, n_starts: int = 100, ids: Optional[Iterable[str]] = None, startpoint_method: Optional[Union[Callable, bool]] = None, result: Optional[pypesto.result.Result] = None, engine: Optional[pypesto.engine.base.Engine] = None, progress_bar: bool = True, options: Optional[pypesto.optimize.options.OptimizeOptions] = None, history_options: Optional[pypesto.objective.history.HistoryOptions] = None) → pypesto.result.Result[source]¶ This is the main function to call to do multistart optimization.
- Parameters
problem – The problem to be solved.
optimizer – The optimizer to be used n_starts times.
n_starts – Number of starts of the optimizer.
ids – Ids assigned to the startpoints.
startpoint_method – Method for how to choose start points. False means the optimizer does not require start points, e.g. for the ‘PyswarmOptimizer’.
result – A result object to append the optimization results to. For example, one might append more runs to a previous optimization. If None, a new object is created.
engine – Parallelization engine. Defaults to sequential execution on a SingleCoreEngine.
progress_bar – Whether to display a progress bar.
options – Various options applied to the multistart optimization.
history_options – Optimizer history options.
- Returns
Result object containing the results of all multistarts in result.optimize_result.
- Return type
result
-
pypesto.optimize.read_result_from_file(problem: pypesto.problem.Problem, history_options: pypesto.objective.history.HistoryOptions, identifier: str)[source]¶ Fill an OptimizerResult from history.
Profile¶
-
class
pypesto.profile.ProfileOptions(default_step_size: float = 0.01, min_step_size: float = 0.001, max_step_size: float = 1.0, step_size_factor: float = 1.25, delta_ratio_max: float = 0.1, ratio_min: float = 0.145, reg_points: int = 10, reg_order: int = 4, magic_factor_obj_value: float = 0.5)[source]¶ Bases:
dictOptions for optimization based profiling.
- Parameters
default_step_size – Default step size of the profiling routine along the profile path (adaptive step lengths algorithms will only use this as a first guess and then refine the update).
min_step_size – Lower bound for the step size in adaptive methods.
max_step_size – Upper bound for the step size in adaptive methods.
step_size_factor – Adaptive methods recompute the likelihood at the predicted point and try to find a good step length by a sort of line search algorithm. This factor controls step handling in this line search.
delta_ratio_max – Maximum allowed drop of the posterior ratio between two profile steps.
ratio_min – Lower bound for likelihood ratio of the profile, based on inverse chi2-distribution. The default 0.145 is slightly lower than the 95% quantile 0.1465 of a chi2 distribution with one degree of freedom.
reg_points – Number of profile points used for regression in regression based adaptive profile points proposal.
reg_order – Maximum degree of regression polynomial used in regression based adaptive profile points proposal.
magic_factor_obj_value – There is this magic factor in the old profiling code which slows down profiling at small ratios (must be >= 0 and < 1).
-
__init__(default_step_size: float = 0.01, min_step_size: float = 0.001, max_step_size: float = 1.0, step_size_factor: float = 1.25, delta_ratio_max: float = 0.1, ratio_min: float = 0.145, reg_points: int = 10, reg_order: int = 4, magic_factor_obj_value: float = 0.5)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
static
create_instance(maybe_options: Union[pypesto.profile.options.ProfileOptions, Dict]) → pypesto.profile.options.ProfileOptions[source]¶ Returns a valid options object.
- Parameters
maybe_options (ProfileOptions or dict) –
-
class
pypesto.profile.ProfilerResult(x_path: numpy.ndarray, fval_path: numpy.ndarray, ratio_path: numpy.ndarray, gradnorm_path: Optional[numpy.ndarray] = None, exitflag_path: Optional[numpy.ndarray] = None, time_path: Optional[numpy.ndarray] = None, time_total: float = 0.0, n_fval: int = 0, n_grad: int = 0, n_hess: int = 0, message: Optional[str] = None)[source]¶ Bases:
dictThe result of a profiler run. The standardized return return value from pypesto.profile, which can either be initialized from an OptimizerResult or from an existing ProfilerResult (in order to extend the computation).
Can be used like a dict.
-
x_path¶ The path of the best found parameters along the profile (Dimension: n_par x n_profile_points)
-
fval_path¶ The function values, fun(x), along the profile.
-
ratio_path¶ The ratio of the posterior function along the profile.
-
gradnorm_path¶ The gradient norm along the profile.
-
exitflag_path¶ The exitflags of the optimizer along the profile.
-
time_path¶ The computation time of the optimizer runs along the profile.
-
time_total¶ The total computation time for the profile.
-
n_fval¶ Number of function evaluations.
-
n_grad¶ Number of gradient evaluations.
-
n_hess¶ Number of Hessian evaluations.
-
message¶ Textual comment on the profile result.
Notes
Any field not supported by the profiler or the profiling optimizer is filled with None. Some fields are filled by pypesto itself.
-
__init__(x_path: numpy.ndarray, fval_path: numpy.ndarray, ratio_path: numpy.ndarray, gradnorm_path: Optional[numpy.ndarray] = None, exitflag_path: Optional[numpy.ndarray] = None, time_path: Optional[numpy.ndarray] = None, time_total: float = 0.0, n_fval: int = 0, n_grad: int = 0, n_hess: int = 0, message: Optional[str] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
append_profile_point(x: numpy.ndarray, fval: float, ratio: float, gradnorm: float = nan, time: float = nan, exitflag: float = nan, n_fval: int = 0, n_grad: int = 0, n_hess: int = 0) → None[source]¶ This function appends a new point to the profile path.
- Parameters
x – The parameter values.
fval – The function value at x.
ratio – The ratio of the function value at x by the optimal function value.
gradnorm – The gradient norm at x.
time – The computation time to find x.
exitflag – The exitflag of the optimizer (useful if an optimization was performed to find x).
n_fval – Number of function evaluations performed to find x.
n_grad – Number of gradient evaluations performed to find x.
n_hess – Number of Hessian evaluations performed to find x.
-
-
pypesto.profile.approximate_parameter_profile(problem: pypesto.problem.Problem, result: pypesto.result.Result, profile_index: Optional[Iterable[int]] = None, profile_list: Optional[int] = None, result_index: int = 0, n_steps: int = 100) → pypesto.result.Result[source]¶ Calculate profiles based on an approximation via a normal likelihood centered at the chosen optimal parameter value, with the covariance matrix being the Hessian or FIM.
- Parameters
problem – The problem to be solved.
result – A result object to initialize profiling and to append the profiling results to. For example, one might append more profiling runs to a previous profile, in order to merge these. The existence of an optimization result is obligatory.
profile_index – List with the profile indices to be computed (by default all of the free parameters).
profile_list – Integer which specifies whether a call to the profiler should create a new list of profiles (default) or should be added to a specific profile list.
result_index – Index from which optimization result profiling should be started (default: global optimum, i.e., index = 0).
n_steps – Number of profile steps in each dimension.
- Returns
The profile results are filled into result.profile_result.
- Return type
result
-
pypesto.profile.calculate_approximate_ci(xs: numpy.ndarray, ratios: numpy.ndarray, confidence_ratio: float) → Tuple[float, float][source]¶ Calculate approximate confidence interval based on profile. Interval bounds are linerly interpolated.
- Parameters
xs – The ordered parameter values along the profile for the coordinate of interest.
ratios – The likelihood ratios corresponding to the parameter values.
confidence_ratio – Minimum confidence ratio to base the confidence interval upon, as obtained via pypesto.profile.chi2_quantile_to_ratio.
- Returns
Bounds of the approximate confidence interval.
- Return type
lb, ub
-
pypesto.profile.chi2_quantile_to_ratio(alpha: float = 0.95, df: int = 1)[source]¶ Transform lower tail probability alpha for a chi2 distribution with df degrees of freedom to a profile likelihood ratio threshold.
- Parameters
alpha – Lower tail probability, defaults to 95% interval.
df – Degrees of freedom.
- Returns
Corresponds to a likelihood ratio.
- Return type
ratio
-
pypesto.profile.parameter_profile(problem: pypesto.problem.Problem, result: pypesto.result.Result, optimizer: pypesto.optimize.optimizer.Optimizer, engine: Optional[pypesto.engine.base.Engine] = None, profile_index: Optional[Iterable[int]] = None, profile_list: Optional[int] = None, result_index: int = 0, next_guess_method: Union[Callable, str] = 'adaptive_step_regression', profile_options: Optional[pypesto.profile.options.ProfileOptions] = None, progress_bar: bool = True) → pypesto.result.Result[source]¶ This is the main function to call to do parameter profiling.
- Parameters
problem – The problem to be solved.
result – A result object to initialize profiling and to append the profiling results to. For example, one might append more profiling runs to a previous profile, in order to merge these. The existence of an optimization result is obligatory.
optimizer – The optimizer to be used along each profile.
engine – The engine to be used.
profile_index – List with the parameter indices to be profiled (by default all free indices).
profile_list – Integer which specifies whether a call to the profiler should create a new list of profiles (default) or should be added to a specific profile list.
result_index – Index from which optimization result profiling should be started (default: global optimum, i.e., index = 0).
next_guess_method – Function handle to a method that creates the next starting point for optimization in profiling.
profile_options – Various options applied to the profile optimization.
progress_bar – Whether to display a progress bar.
- Returns
The profile results are filled into result.profile_result.
- Return type
result
-
pypesto.profile.validation_profile_significance(problem_full_data: pypesto.problem.Problem, result_training_data: pypesto.result.Result, result_full_data: Optional[pypesto.result.Result] = None, n_starts: Optional[int] = 1, optimizer: Optional[pypesto.optimize.optimizer.Optimizer] = None, engine: Optional[pypesto.engine.base.Engine] = None, lsq_objective: bool = False, return_significance: bool = True) → float[source]¶ A Validation Interval for significance alpha is a confidence region/ interval for a new validation experiment. 1 et al. (This method per default returns the significance = 1-alpha!)
The reasoning behind their approach is, that a validation data set is outside the validation interval, if fitting the full data set would lead to a fit $ heta_{new}$, that does not contain the old fit $ heta_{train}$ in their (Profile-Likelihood) based parameter-confidence intervals. (I.e. the old fit would be rejected by the fit of the full data.)
This method returns the significance of the validation data set (where result_full_data is the objective function for fitting both data sets). I.e. the largest alpha, such that there is a validation region/interval such that the validation data set lies outside this Validation Interval with probability alpha. (If one is interested in the opposite, set return_significance=False.)
- Parameters
problem_full_data – pypesto.problem, such that the objective is the negative-log-likelihood of the training and validation data set.
result_training_data – result object from the fitting of the training data set only.
result_full_data – pypesto.result object that contains the result of fitting training and validation data combined.
n_starts – number of starts for fitting the full data set (if result_full_data is not provided).
optimizer – optimizer used for refitting the data (if result_full_data is not provided).
engine – engine for refitting (if result_full_data is not provided).
lsq_objective – indicates if the objective of problem_full_data corresponds to a nllh (False), or a chi^2 value (True).
return_significance –
- indicates, if the function should return the significance (True) (i.e.
the probability, that the new data set lies outside the Confidence Interval for the validation experiment, as given by the method), or the largest alpha, such that the validation experiment still lies within the Confidence Interval (False). I.e. alpha = 1-significance.
- 1
Kreutz, Clemens, Raue, Andreas and Timmer, Jens. “Likelihood based observability analysis and confidence intervals for predictions of dynamic models”. BMC Systems Biology 2012/12. doi:10.1186/1752-0509-6-120
Sample¶
Draw samples from the distribution, with support for various samplers.
-
class
pypesto.sample.AdaptiveMetropolisSampler(options: Optional[Dict] = None)[source]¶ Bases:
pypesto.sample.metropolis.MetropolisSamplerMetropolis-Hastings sampler with adaptive proposal covariance.
-
__init__(options: Optional[Dict] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
classmethod
default_options()[source]¶ Convenience method to set/get default options.
- Returns
Default sampler options.
- Return type
default_options
-
initialize(problem: pypesto.problem.Problem, x0: numpy.ndarray)[source]¶ Initialize the sampler.
- Parameters
problem – The problem for which to sample.
x0 – Should, but is not required to, be used as initial parameter.
-
-
class
pypesto.sample.AdaptiveParallelTemperingSampler(internal_sampler: pypesto.sample.sampler.InternalSampler, betas: Optional[Sequence[float]] = None, n_chains: Optional[int] = None, options: Optional[Dict] = None)[source]¶ Bases:
pypesto.sample.parallel_tempering.ParallelTemperingSamplerParallel tempering sampler with adaptive temperature adaptation.
-
class
pypesto.sample.EmceeSampler(nwalkers: int = 1, sampler_args: Optional[dict] = None, run_args: Optional[dict] = None)[source]¶ Bases:
pypesto.sample.sampler.SamplerUse emcee for sampling.
Wrapper around https://emcee.readthedocs.io/en/stable/, see there for details.
-
__init__(nwalkers: int = 1, sampler_args: Optional[dict] = None, run_args: Optional[dict] = None)[source]¶ - Parameters
nwalkers (The number of walkers in the ensemble.) –
sampler_args – Further keyword arguments that are passed on to
emcee.EnsembleSampler.__init__.run_args – Further keyword arguments that are passed on to
emcee.EnsembleSampler.run_mcmc.
-
initialize(problem: pypesto.problem.Problem, x0: Union[numpy.ndarray, List[numpy.ndarray]]) → None[source]¶ Initialize the sampler.
- Parameters
problem – The problem for which to sample.
x0 – Should, but is not required to, be used as initial parameter.
-
-
class
pypesto.sample.InternalSampler(options: Optional[Dict] = None)[source]¶ Bases:
pypesto.sample.sampler.SamplerSampler to be used inside a parallel tempering sampler.
The last sample can be obtained via get_last_sample and set via set_last_sample.
-
abstract
get_last_sample() → pypesto.sample.sampler.InternalSample[source]¶ Get the last sample in the chain.
- Returns
The last sample in the chain in the exchange format.
- Return type
internal_sample
-
make_internal(temper_lpost: bool)[source]¶ This function can be called by parallel tempering samplers during initialization to allow the inner samplers to adjust to them being used as inner samplers. Default: Do nothing.
- Parameters
temper_lpost – Whether to temperate the posterior or only the likelihood.
-
abstract
-
class
pypesto.sample.McmcPtResult(trace_x: numpy.ndarray, trace_neglogpost: numpy.ndarray, trace_neglogprior: numpy.ndarray, betas: Iterable[float], burn_in: Optional[int] = None, time: float = 0.0, auto_correlation: Optional[float] = None, effective_sample_size: Optional[float] = None, message: Optional[str] = None)[source]¶ Bases:
dictThe result of a sampler run using Markov-chain Monte Carlo, and optionally parallel tempering.
Can be used like a dict.
- Parameters
trace_x ([n_chain, n_iter, n_par]) – Parameters.
trace_neglogpost ([n_chain, n_iter]) – Negative log posterior values.
trace_neglogprior ([n_chain, n_iter]) – Negative log prior values.
betas ([n_chain]) – The associated inverse temperatures.
burn_in ([n_chain]) – The burn in index.
time ([n_chain]) – The computation time.
auto_correlation ([n_chain]) – The estimated chain autcorrelation.
effective_sample_size ([n_chain]) – The estimated effective sample size.
message (str) – Textual comment on the profile result.
Here –
denotes the number of chains (n_chain) –
the number of (n_iter) –
(i.e. (iterations) –
chain length) (the) –
n_par the number of parameters. (and) –
-
__init__(trace_x: numpy.ndarray, trace_neglogpost: numpy.ndarray, trace_neglogprior: numpy.ndarray, betas: Iterable[float], burn_in: Optional[int] = None, time: float = 0.0, auto_correlation: Optional[float] = None, effective_sample_size: Optional[float] = None, message: Optional[str] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
class
pypesto.sample.MetropolisSampler(options: Optional[Dict] = None)[source]¶ Bases:
pypesto.sample.sampler.InternalSamplerSimple Metropolis-Hastings sampler with fixed proposal variance.
-
__init__(options: Optional[Dict] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
classmethod
default_options()[source]¶ Convenience method to set/get default options.
- Returns
Default sampler options.
- Return type
default_options
-
get_last_sample() → pypesto.sample.sampler.InternalSample[source]¶ Get the last sample in the chain.
- Returns
The last sample in the chain in the exchange format.
- Return type
internal_sample
-
initialize(problem: pypesto.problem.Problem, x0: numpy.ndarray)[source]¶ Initialize the sampler.
- Parameters
problem – The problem for which to sample.
x0 – Should, but is not required to, be used as initial parameter.
-
make_internal(temper_lpost: bool)[source]¶ This function can be called by parallel tempering samplers during initialization to allow the inner samplers to adjust to them being used as inner samplers. Default: Do nothing.
- Parameters
temper_lpost – Whether to temperate the posterior or only the likelihood.
-
-
class
pypesto.sample.ParallelTemperingSampler(internal_sampler: pypesto.sample.sampler.InternalSampler, betas: Optional[Sequence[float]] = None, n_chains: Optional[int] = None, options: Optional[Dict] = None)[source]¶ Bases:
pypesto.sample.sampler.SamplerSimple parallel tempering sampler.
-
__init__(internal_sampler: pypesto.sample.sampler.InternalSampler, betas: Optional[Sequence[float]] = None, n_chains: Optional[int] = None, options: Optional[Dict] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
adjust_betas(i_sample: int, swapped: Sequence[bool])[source]¶ Adjust temperature values. Default: Do nothing.
-
classmethod
default_options() → Dict[source]¶ Convenience method to set/get default options.
- Returns
Default sampler options.
- Return type
default_options
-
initialize(problem: pypesto.problem.Problem, x0: Union[numpy.ndarray, List[numpy.ndarray]])[source]¶ Initialize the sampler.
- Parameters
problem – The problem for which to sample.
x0 – Should, but is not required to, be used as initial parameter.
-
-
class
pypesto.sample.Pymc3Sampler(step_function=None, **kwargs)[source]¶ Bases:
pypesto.sample.sampler.SamplerWrapper around Pymc3 samplers.
- Parameters
step_function – A pymc3 step function, e.g. NUTS, Slice. If not specified, pymc3 determines one automatically (preferable).
**kwargs – Options are directly passed on to pymc3.sample.
-
__init__(step_function=None, **kwargs)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
initialize(problem: pypesto.problem.Problem, x0: numpy.ndarray)[source]¶ Initialize the sampler.
- Parameters
problem – The problem for which to sample.
x0 – Should, but is not required to, be used as initial parameter.
-
class
pypesto.sample.Sampler(options: Optional[Dict] = None)[source]¶ Bases:
abc.ABCSampler base class, not functional on its own.
The sampler maintains an internal chain, which is initialized in initialize, and updated in sample.
-
__init__(options: Optional[Dict] = None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
-
classmethod
default_options() → Dict[source]¶ Convenience method to set/get default options.
- Returns
Default sampler options.
- Return type
default_options
-
abstract
initialize(problem: pypesto.problem.Problem, x0: Union[numpy.ndarray, List[numpy.ndarray]])[source]¶ Initialize the sampler.
- Parameters
problem – The problem for which to sample.
x0 – Should, but is not required to, be used as initial parameter.
-
-
pypesto.sample.auto_correlation(result: pypesto.result.Result) → float[source]¶ Calculates the autocorrelation of the MCMC chains.
- Parameters
result – The pyPESTO result object with filled sample result.
- Returns
Estimate of the integrated autocorrelation time of the MCMC chains.
- Return type
auto_correlation
-
pypesto.sample.calculate_ci_mcmc_sample(result: pypesto.result.Result, ci_level: float = 0.95, exclude_burn_in: bool = True) → Tuple[numpy.ndarray, numpy.ndarray][source]¶ Calculate parameter credibility intervals based on MCMC samples.
- Parameters
result – The pyPESTO result object with filled sample result.
ci_level – Lower tail probability, defaults to 95% interval.
- Returns
Bounds of the MCMC percentile-based confidence interval.
- Return type
lb, ub
-
pypesto.sample.calculate_ci_mcmc_sample_prediction(simulated_values: numpy.ndarray, ci_level: float = 0.95) → Tuple[numpy.ndarray, numpy.ndarray][source]¶ Calculate prediction credibility intervals based on MCMC samples.
- Parameters
simulated_values – Simulated model states or model observables.
ci_level – Lower tail probability, defaults to 95% interval.
- Returns
Bounds of the MCMC-based prediction confidence interval.
- Return type
lb, ub
-
pypesto.sample.effective_sample_size(result: pypesto.result.Result) → float[source]¶ Calculate the effective sample size of the MCMC chains.
- Parameters
result – The pyPESTO result object with filled sample result.
- Returns
Estimate of the effective sample size of the MCMC chains.
- Return type
ess
-
pypesto.sample.geweke_test(result: pypesto.result.Result, zscore: float = 2.0) → int[source]¶ Calculates the burn-in of MCMC chains.
- Parameters
result – The pyPESTO result object with filled sample result.
zscore – The Geweke test threshold.
- Returns
Iteration where the first and the last fraction of the chain do not differ significantly regarding Geweke test -> Burn-In
- Return type
burn_in
-
pypesto.sample.sample(problem: pypesto.problem.Problem, n_samples: int, sampler: Optional[pypesto.sample.sampler.Sampler] = None, x0: Optional[Union[numpy.ndarray, List[numpy.ndarray]]] = None, result: Optional[pypesto.result.Result] = None) → pypesto.result.Result[source]¶ This is the main function to call to do parameter sampling.
- Parameters
problem – The problem to be solved. If None is provided, a
pypesto.AdaptiveMetropolisSampleris used.n_samples – Number of samples to generate.
sampler – The sampler to perform the actual sampling.
x0 – Initial parameter for the Markov chain. If None, the best parameter found in optimization is used. Note that some samplers require an initial parameter, some may ignore it. x0 can also be a list, to have separate starting points for parallel tempering chains.
result – A result to write to. If None provided, one is created from the problem.
- Returns
A result with filled in sample_options part.
- Return type
result
Result¶
The pypesto.Result object contains all results generated by the pypesto components. It contains sub-results for optimization, profiling, sampling.
-
class
pypesto.result.OptimizeResult[source]¶ Bases:
objectResult of the minimize() function.
-
append(optimizer_result: optimize.OptimizerResult)[source]¶ Append an optimizer result to the result object.
- Parameters
optimizer_result – The result of one (local) optimizer run.
-
as_dataframe(keys=None) → pandas.core.frame.DataFrame[source]¶ Get as pandas DataFrame. If keys is a list, return only the specified values.
-
-
class
pypesto.result.ProfileResult[source]¶ Bases:
objectResult of the profile() function.
It holds a list of profile lists. Each profile list consists of a list of ProfilerResult objects, one for each parameter.
-
append_empty_profile_list() → int[source]¶ Append an empty profile list to the list of profile lists.
- Returns
The index of the created profile list.
- Return type
index
-
append_profiler_result(profiler_result: profile.ProfilerResult = None, profile_list: int = None) → None[source]¶ Append the profiler result to the profile list.
- Parameters
profiler_result – The result of one profiler run for a parameter, or None if to be left empty.
profile_list – Index specifying the profile list to which we want to append. Defaults to the last list.
-
get_profiler_result(i_par: int, profile_list: Optional[int] = None)[source]¶ Get theprofiler result at parameter index i_par of profile list profile_list.
- Parameters
i_par – Integer specifying the profile index.
profile_list – Index specifying the profile list. Defaults to the last list.
-
set_profiler_result(profiler_result: profile.ProfilerResult, i_par: int, profile_list: int = None) → None[source]¶ Write a profiler result to the result object at i_par of profile list profile_list.
- Parameters
profiler_result – The result of one (local) profiler run.
i_par – Integer specifying the parameter index.
profile_list – Index specifying the profile list. Defaults to the last list.
-
-
class
pypesto.result.Result(problem=None)[source]¶ Bases:
objectUniversal result object for pypesto. The algorithms like optimize, profile, sample fill different parts of it.
-
problem¶ The problem underlying the results.
- Type
-
optimize_result¶ The results of the optimizer runs.
-
profile_result¶ The results of the profiler run.
-
sample_result¶ The results of the sampler run.
-
Visualize¶
pypesto comes with various visualization routines. To use these, import pypesto.visualize.
-
class
pypesto.visualize.ReferencePoint(reference=None, x=None, fval=None, color=None, legend=None)[source]¶ Bases:
dictReference point for plotting. Should contain a parameter value and an objective function value, may also contain a color and a legend.
Can be used like a dict.
-
x¶ Reference parameters.
- Type
ndarray
-
color¶ Color which should be used for reference point.
- Type
RGBA, optional
-
auto_color¶ flag indicating whether color for this reference point should be assigned automatically or whether it was assigned by user
- Type
boolean
-
-
pypesto.visualize.assign_clustered_colors(vals, balance_alpha=True, highlight_global=True)[source]¶ Cluster and assign colors.
- Parameters
vals (numeric list or array) – List to be clustered and assigned colors.
balance_alpha (bool (optional)) – Flag indicating whether alpha for large clusters should be reduced to avoid overplotting (default: True)
highlight_global (bool (optional)) – flag indicating whether global optimum should be highlighted
- Returns
colors – One for each element in ‘vals’.
- Return type
list of RGBA
-
pypesto.visualize.assign_clusters(vals)[source]¶ Find clustering.
- Parameters
vals (numeric list or array) – List to be clustered.
- Returns
clust (numeric list) – Indicating the corresponding cluster of each element from ‘vals’.
clustsize (numeric list) – Size of clusters, length equals number of clusters.
-
pypesto.visualize.assign_colors(vals, colors=None, balance_alpha=True, highlight_global=True)[source]¶ Assign colors or format user specified colors.
- Parameters
vals (numeric list or array) – List to be clustered and assigned colors.
colors (list, or RGBA, optional) – list of colors, or single color
balance_alpha (bool (optional)) – Flag indicating whether alpha for large clusters should be reduced to avoid overplotting (default: True)
highlight_global (bool (optional)) – flag indicating whether global optimum should be highlighted
- Returns
colors – One for each element in ‘vals’.
- Return type
list of RGBA
-
pypesto.visualize.create_references(references=None, x=None, fval=None, color=None, legend=None) → List[pypesto.visualize.reference_points.ReferencePoint][source]¶ This function creates a list of reference point objects from user inputs
- Parameters
references (ReferencePoint or dict or list, optional) – Will be converted into a list of RefPoints
x (ndarray, optional) – Parameter vector which should be used for reference point
fval (float, optional) – Objective function value which should be used for reference point
color (RGBA, optional) – Color which should be used for reference point.
legend (str) – legend text for reference point
- Returns
colors – One for each element in ‘vals’.
- Return type
list of RGBA
-
pypesto.visualize.delete_nan_inf(fvals: numpy.ndarray, x: Optional[numpy.ndarray] = None, xdim: Optional[int] = 1) → Tuple[numpy.ndarray, numpy.ndarray][source]¶ Delete nan and inf values in fvals. If parameters ‘x’ are passed, also the corresponding entries are deleted.
- Parameters
x – array of parameters
fvals – array of fval
xdim – dimension of x, in case x dimension cannot be inferred
- Returns
x – array of parameters without nan or inf
fvals – array of fval without nan or inf
-
pypesto.visualize.ensemble_crosstab_scatter_lowlevel(dataset: numpy.ndarray, component_labels: Optional[Sequence[str]] = None, **kwargs)[source]¶ Plot cross-classification table of scatter plots for different coordinates. Lowlevel routine for multiple UMAP and PCA plots, but can also be used to visualize, e.g., parameter traces across optimizer runs
- Parameters
dataset – array of data points to be shown as scatter plot
component_labels – labels for the x-axes and the y-axes
- Returns
A dictionary of plot axes.
- Return type
axs
-
pypesto.visualize.ensemble_identifiability(ensemble: pypesto.ensemble.ensemble.Ensemble, ax: Optional[matplotlib.axes._axes.Axes] = None, size: Optional[Tuple[float]] = (12, 6))[source]¶ Plots an overview about how many parameters hit the parameter bounds based on a ensemble of parameters. confidence intervals/credible ranges are computed via the ensemble mean plus/minus 1 standard deviation. This highlevel routine expects a ensemble object as input.
- Parameters
ensemble – ensemble of parameter vectors (from pypesto.ensemble)
ax – Axes object to use.
size – Figure size (width, height) in inches. Is only applied when no ax object is specified
- Returns
ax – The plot axes.
- Return type
matplotlib.Axes
-
pypesto.visualize.ensemble_scatter_lowlevel(dataset, ax: Optional[matplotlib.axes._axes.Axes] = None, size: Optional[Tuple[float]] = (12, 6), x_label: str = 'component 1', y_label: str = 'component 2', color_by: Optional[Sequence[float]] = None, color_map: str = 'viridis', background_color: Tuple[float, float, float, float] = (0.0, 0.0, 0.0, 1.0), marker_type: str = '.', scatter_size: float = 0.5, invert_scatter_order: bool = False)[source]¶ Create a scatter plot
- Parameters
dataset – array of data points in reduced dimension
ax – Axes object to use.
size – Figure size (width, height) in inches. Is only applied when no ax object is specified
x_label – The x-axis label
y_label – The y-axis label
color_by – A sequence/list of floats, which specify the color in the colormap
color_map – A colormap name known to pyplot
background_color – Background color of the axes object (defaults to black)
marker_type – Type of plotted markers
scatter_size – Size of plotted markers
invert_scatter_order – Specifies the order of plotting the scatter points, can be important in case of overplotting
- Returns
ax – The plot axes.
- Return type
matplotlib.Axes
-
pypesto.visualize.optimization_run_properties_one_plot(results: pypesto.result.Result, properties_to_plot: Optional[List[str]] = None, size: Tuple[float, float] = (18.5, 10.5), start_indices: Optional[Union[int, Iterable[int]]] = None, colors: Optional[Union[List[float], List[List[float]]]] = None, legends: Optional[Union[str, List[str]]] = None, plot_type: str = 'line') → matplotlib.axes._axes.Axes[source]¶ Plot stats for all optimization properties specified in properties_to_plot on one plot.
- Parameters
results – Optimization result obtained by ‘optimize.py’ or list of those
properties_to_plot – Optimization run properties that should be plotted
size – Figure size (width, height) in inches. Is only applied when no ax object is specified
start_indices – List of integers specifying the multistarts to be plotted or int specifying up to which start index should be plotted
colors – List of RGBA colors (one color per property in properties_to_plot), or single RGBA color. If not set and one result, clustering is done and colors are assigned automatically
legends – Labels, one label per optimization property
plot_type – Specifies plot type. Possible values: ‘line’ and ‘hist’
Examples
- optimization_properties_per_multistart(
result1, properties_to_plot=[‘time’], colors=[.5, .9, .9, .3])
- optimization_properties_per_multistart(
result1, properties_to_plot=[‘time’, ‘n_grad’], colors=[[.5, .9, .9, .3], [.2, .1, .9, .5]])
-
pypesto.visualize.optimization_run_properties_per_multistart(results: Union[pypesto.result.Result, Sequence[pypesto.result.Result]], properties_to_plot: Optional[List[str]] = None, size: Tuple[float, float] = (18.5, 10.5), start_indices: Optional[Union[int, Iterable[int]]] = None, colors: Optional[Union[List[float], List[List[float]]]] = None, legends: Optional[Union[str, List[str]]] = None, plot_type: str = 'line') → Dict[str, matplotlib.axes._subplots.AxesSubplot][source]¶ One plot per optimization property in properties_to_plot.
- Parameters
results – Optimization result obtained by ‘optimize.py’ or list of those
properties_to_plot – Optimization run properties that should be plotted
size – Figure size (width, height) in inches. Is only applied when no ax object is specified
start_indices – List of integers specifying the multistarts to be plotted or int specifying up to which start index should be plotted
colors – List of RGBA colors (one color per result in results), or single RGBA color. If not set and one result, clustering is done and colors are assigned automatically
legends – Labels for line plots, one label per result object
plot_type – Specifies plot type. Possible values: ‘line’ and ‘hist’
- Returns
ax
The plot axes.
Examples
- optimization_properties_per_multistart(
result1, properties_to_plot=[‘time’], colors=[.5, .9, .9, .3])
- optimization_properties_per_multistart(
[result1, result2], properties_to_plot=[‘time’], colors=[[.5, .9, .9, .3], [.2, .1, .9, .5]])
- optimization_properties_per_multistart(
result1, properties_to_plot=[‘time’, ‘n_grad’], colors=[.5, .9, .9, .3])
- optimization_properties_per_multistart(
[result1, result2], properties_to_plot=[‘time’, ‘n_fval’], colors=[[.5, .9, .9, .3], [.2, .1, .9, .5]])
-
pypesto.visualize.optimization_run_property_per_multistart(results: Union[pypesto.result.Result, Sequence[pypesto.result.Result]], opt_run_property: str, axes: Optional[matplotlib.axes._axes.Axes] = None, size: Tuple[float, float] = (18.5, 10.5), start_indices: Optional[Union[int, Iterable[int]]] = None, colors: Optional[Union[List[float], List[List[float]]]] = None, legends: Optional[Union[str, List[str]]] = None, plot_type: str = 'line') → matplotlib.axes._axes.Axes[source]¶ Plot stats for an optimization run property specified by opt_run_property. It is possible to plot a histogram or a line plot. In a line plot, on the x axis are the numbers of the multistarts, where the multistarts are ordered with respect to a function value. On the y axis of the line plot the value of the corresponding parameter for each multistart is displayed.
- Parameters
opt_run_property – optimization run property to plot. One of the ‘time’, ‘n_fval’, ‘n_grad’, ‘n_hess’, ‘n_res’, ‘n_sres’
results – Optimization result obtained by ‘optimize.py’ or list of those
axes – Axes object to use
size – Figure size (width, height) in inches. Is only applied when no ax object is specified
start_indices – List of integers specifying the multistarts to be plotted or int specifying up to which start index should be plotted
colors – List of RGBA colors (one color per result in results), or single RGBA color. If not set and one result, clustering is done and colors are assigned automatically
legends – Labels for line plots, one label per result object
plot_type – Specifies plot type. Possible values: ‘line’, ‘hist’, ‘both’
- Returns
The plot axes.
- Return type
ax
-
pypesto.visualize.optimizer_convergence(result: pypesto.result.Result, ax: Optional[matplotlib.axes._axes.Axes] = None, xscale: str = 'symlog', yscale: str = 'log', size: Tuple[float] = (18.5, 10.5)) → matplotlib.axes._axes.Axes[source]¶ Scatter plot of function values and gradient values at the end of optimization. Optimizer exit-message is encoded by color. Can help identifying convergence issues in optimization and guide tolerance refinement etc.
- Parameters
result – Optimization result obtained by ‘optimize.py’
ax – Axes object to use.
size – Figure size (width, height) in inches. Is only applied when no ax object is specified
xscale – Scale for x-axis
yscale – Scale for y-axis
- Returns
ax – The plot axes.
- Return type
matplotlib.Axes
-
pypesto.visualize.optimizer_history(results, ax=None, size=(18.5, 10.5), trace_x='steps', trace_y='fval', scale_y='log10', offset_y=None, colors=None, y_limits=None, start_indices=None, reference=None, legends=None)[source]¶ Plot history of optimizer. Can plot either the history of the cost function or of the gradient norm, over either the optimizer steps or the computation time.
- Parameters
results (pypesto.Result or list) – Optimization result obtained by ‘optimize.py’ or list of those
ax (matplotlib.Axes, optional) – Axes object to use.
size (tuple, optional) – Figure size (width, height) in inches. Is only applied when no ax object is specified
trace_x (str, optional) – What should be plotted on the x-axis? Possibilities: ‘time’, ‘steps’ Default: ‘steps’
trace_y (str, optional) – What should be plotted on the y-axis? Possibilities: ‘fval’, ‘gradnorm’, ‘stepsize’ Default: ‘fval’
scale_y (str, optional) – May be logarithmic or linear (‘log10’ or ‘lin’)
offset_y (float, optional) – Offset for the y-axis-values, as these are plotted on a log10-scale Will be computed automatically if necessary
colors (list, or RGBA, optional) – list of colors, or single color color or list of colors for plotting. If not set, clustering is done and colors are assigned automatically
y_limits (float or ndarray, optional) – maximum value to be plotted on the y-axis, or y-limits
start_indices (list or int) – list of integers specifying the multistart to be plotted or int specifying up to which start index should be plotted
reference (list, optional) – List of reference points for optimization results, containing et least a function value fval
legends (list or str) – Labels for line plots, one label per result object
- Returns
ax – The plot axes.
- Return type
matplotlib.Axes
-
pypesto.visualize.optimizer_history_lowlevel(vals, scale_y='log10', colors=None, ax=None, size=(18.5, 10.5), x_label='Optimizer steps', y_label='Objective value', legend_text=None)[source]¶ Plot optimizer history using list of numpy arrays.
- Parameters
vals (list of numpy arrays) – list of 2xn-arrays (x_values and y_values of the trace)
scale_y (str, optional) – May be logarithmic or linear (‘log10’ or ‘lin’)
colors (list, or RGBA, optional) – list of colors, or single color color or list of colors for plotting. If not set, clustering is done and colors are assigned automatically
ax (matplotlib.Axes, optional) – Axes object to use.
size (tuple, optional) – see waterfall
x_label (str) – label for x-axis
y_label (str) – label for y-axis
legend_text (str) – Label for line plots
- Returns
ax – The plot axes.
- Return type
matplotlib.Axes
-
pypesto.visualize.parameter_hist(result: pypesto.result.Result, parameter_name: str, bins: Union[int, str] = 'auto', ax: Optional[matplotlib.Axes] = None, size: Optional[Tuple[float]] = (18.5, 10.5), color: Optional[List[float]] = None, start_indices: Optional[Union[int, List[int]]] = None)[source]¶ Plot parameter values as a histogram.
- Parameters
result – Optimization result obtained by ‘optimize.py’
parameter_name – The name of the parameter that should be plotted
bins – Specifies bins of the histogram
ax – Axes object to use
size – Figure size (width, height) in inches. Is only applied when no ax object is specified
color – RGBA color.
start_indices – List of integers specifying the multistarts to be plotted or int specifying up to which start index should be plotted
- Returns
ax
The plot axes.
-
pypesto.visualize.parameters(results: Union[pypesto.result.Result, Sequence[pypesto.result.Result]], ax: Optional[matplotlib.axes._axes.Axes] = None, parameter_indices: Union[str, Sequence[int]] = 'free_only', lb: Optional[Union[numpy.ndarray, List[float]]] = None, ub: Optional[Union[numpy.ndarray, List[float]]] = None, size: Optional[Tuple[float, float]] = None, reference: Optional[List[pypesto.visualize.reference_points.ReferencePoint]] = None, colors: Optional[Union[List[float], List[List[float]]]] = None, legends: Optional[Union[str, List[str]]] = None, balance_alpha: bool = True, start_indices: Optional[Union[int, Iterable[int]]] = None, scale_to_interval: Optional[Tuple[float, float]] = None) → matplotlib.axes._axes.Axes[source]¶ Plot parameter values.
- Parameters
results – Optimization result obtained by ‘optimize.py’ or list of those
ax – Axes object to use.
parameter_indices – Specifies which parameters should be plotted. Allowed string values are ‘all’ (both fixed and free parameters will be plotted) and ‘free_only’ (only free parameters will be plotted)
lb – If not None, override result.problem.lb, problem.problem.ub. Dimension either result.problem.dim or result.problem.dim_full.
ub – If not None, override result.problem.lb, problem.problem.ub. Dimension either result.problem.dim or result.problem.dim_full.
size – Figure size (width, height) in inches. Is only applied when no ax object is specified
reference – List of reference points for optimization results, containing at least a function value fval
colors – list of RGBA colors, or single RGBA color If not set, clustering is done and colors are assigned automatically
legends – Labels for line plots, one label per result object
balance_alpha – Flag indicating whether alpha for large clusters should be reduced to avoid overplotting (default: True)
start_indices – list of integers specifying the multistarts to be plotted or int specifying up to which start index should be plotted
scale_to_interval – Tuple of bounds to which to scale all parameter values and bounds, or
Noneto use bounds as determined bylb, ub.
- Returns
The plot axes.
- Return type
ax
-
pypesto.visualize.parameters_lowlevel(xs: Sequence[Union[numpy.ndarray, List[float]]], fvals: Union[numpy.ndarray, List[float]], lb: Optional[Union[numpy.ndarray, List[float]]] = None, ub: Optional[Union[numpy.ndarray, List[float]]] = None, x_labels: Optional[Iterable[str]] = None, ax: Optional[matplotlib.axes._axes.Axes] = None, size: Optional[Tuple[float, float]] = None, colors: Optional[Sequence[Union[numpy.ndarray, List[float]]]] = None, linestyle: str = '-', legend_text: Optional[str] = None, balance_alpha: bool = True) → matplotlib.axes._axes.Axes[source]¶ Plot parameters plot using list of parameters.
- Parameters
xs – Including optimized parameters for each startpoint. Shape: (n_starts, dim).
fvals – Function values. Needed to assign cluster colors.
lb – The lower and upper bounds.
ub – The lower and upper bounds.
x_labels – Labels to be used for the parameters.
ax – Axes object to use.
size – see parameters
colors – One for each element in ‘fvals’.
linestyle – linestyle argument for parameter plot
legend_text – Label for line plots
balance_alpha – Flag indicating whether alpha for large clusters should be reduced to avoid overplotting (default: True)
- Returns
The plot axes.
- Return type
ax
-
pypesto.visualize.process_offset_y(offset_y: Optional[float], scale_y: str, min_val: float) → float[source]¶ compute offset for y-axis, depend on user settings
- Parameters
offset_y – value for offsetting the later plotted values, in order to ensure positivity if a semilog-plot is used
scale_y – Can be ‘lin’ or ‘log10’, specifying whether values should be plotted on linear or on log10-scale
min_val – Smallest value to be plotted
- Returns
offset_y – value for offsetting the later plotted values, in order to ensure positivity if a semilog-plot is used
- Return type
-
pypesto.visualize.process_result_list(results, colors=None, legends=None)[source]¶ assigns colors and legends to a list of results, check user provided lists
- Parameters
results (list or pypesto.Result) – list of pypesto.Result objects or a single pypesto.Result
colors (list, optional) – list of RGBA colors
- Returns
results (list of pypesto.Result) – list of pypesto.Result objects
colors (list of RGBA) – One for each element in ‘results’.
legends (list of str) – labels for line plots
-
pypesto.visualize.process_y_limits(ax, y_limits)[source]¶ apply user specified limits of y-axis
- Parameters
ax (matplotlib.Axes, optional) – Axes object to use.
y_limits (ndarray) – y_limits, minimum and maximum, for current axes object
- Returns
ax – Axes object to use.
- Return type
matplotlib.Axes, optional
-
pypesto.visualize.profile_cis(result: pypesto.result.Result, confidence_level: float = 0.95, profile_indices: Optional[Sequence[int]] = None, profile_list: int = 0, color: Union[str, tuple] = 'C0', show_bounds: bool = False, ax: Optional[matplotlib.axes._axes.Axes] = None) → matplotlib.axes._axes.Axes[source]¶ Plot approximate confidence intervals based on profiles.
- Parameters
result – The result object after profiling.
confidence_level – The confidence level in (0,1), which is translated to an approximate threshold assuming a chi2 distribution, using pypesto.profile.chi2_quantile_to_ratio.
profile_indices – List of integer values specifying which profiles should be plotted. Defaults to the indices for which profiles were generated in profile list profile_list.
profile_list – Index of the profile list to be used.
color – Main plot color.
show_bounds – Whether to show, and extend the plot to, the lower and upper bounds.
ax – Axes object to use. Default: Create a new one.
-
pypesto.visualize.profile_lowlevel(fvals, ax=None, size: Tuple[float, float] = (18.5, 6.5), color=None, legend_text: Optional[str] = None, show_bounds: bool = False, lb: Optional[float] = None, ub: Optional[float] = None)[source]¶ Lowlevel routine for plotting one profile, working with a numpy array only
- Parameters
fvals (numeric list or array) – Values to plot.
ax (matplotlib.Axes, optional) – Axes object to use.
size (tuple, optional) – Figure size (width, height) in inches. Is only applied when no ax object is specified.
color (RGBA, optional) – Color for profiles in plot.
legend_text (str) – Label for line plots.
show_bounds – Whether to show, and extend the plot to, the lower and upper bounds.
lb – Lower bound.
ub – Upper bound.
- Returns
ax – The plot axes.
- Return type
matplotlib.Axes
-
pypesto.visualize.profiles(results: Union[pypesto.result.Result, Sequence[pypesto.result.Result]], ax=None, profile_indices: Optional[Sequence[int]] = None, size: Sequence[float] = (18.5, 6.5), reference: Optional[Union[pypesto.visualize.reference_points.ReferencePoint, Sequence[pypesto.visualize.reference_points.ReferencePoint]]] = None, colors=None, legends: Optional[Sequence[str]] = None, x_labels: Optional[Sequence[str]] = None, profile_list_ids: Union[int, Sequence[int]] = 0, ratio_min: float = 0.0, show_bounds: bool = False)[source]¶ Plot classical 1D profile plot (using the posterior, e.g. Gaussian like profile)
- Parameters
results (list or pypesto.Result) – List of or single pypesto.Result after profiling.
ax (list of matplotlib.Axes, optional) – List of axes objects to use.
profile_indices (list of integer values) – List of integer values specifying which profiles should be plotted.
size (tuple, optional) – Figure size (width, height) in inches. Is only applied when no ax object is specified.
reference (list, optional) – List of reference points for optimization results, containing at least a function value fval.
colors (list, or RGBA, optional) – List of colors, or single color.
legends (list or str, optional) – Labels for line plots, one label per result object.
x_labels (list of str) – Labels for parameter value axes (e.g. parameter names).
profile_list_ids (int or list of ints, optional) – Index or list of indices of the profile lists to be used for profiling.
ratio_min – Minimum ratio below which to cut off.
show_bounds – Whether to show, and extend the plot to, the lower and upper bounds.
- Returns
ax – The plot axes.
- Return type
matplotlib.Axes
-
pypesto.visualize.profiles_lowlevel(fvals, ax=None, size: Tuple[float, float] = (18.5, 6.5), color=None, legend_text: Optional[str] = None, x_labels=None, show_bounds: bool = False, lb_full=None, ub_full=None)[source]¶ Lowlevel routine for profile plotting, working with a list of arrays only, opening different axes objects in case
- Parameters
fvals (numeric list or array) – Values to plot.
ax (list of matplotlib.Axes, optional) – List of axes object to use.
size (tuple, optional) – Figure size (width, height) in inches. Is only applied when no ax object is specified.
size – Figure size (width, height) in inches. Is only applied when no ax object is specified.
color (RGBA, optional) – Color for profiles in plot.
legend_text (List[str]) – Label for line plots.
legend_text – Label for line plots.
show_bounds – Whether to show, and extend the plot to, the lower and upper bounds.
lb_full – Lower bound.
ub_full – Upper bound.
- Returns
ax – The plot axes.
- Return type
matplotlib.Axes
-
pypesto.visualize.projection_scatter_pca(pca_coordinates: numpy.ndarray, components: Sequence[int] = (0, 1), **kwargs)[source]¶ Plot a scatter plots for PCA coordinates. Creates either one or multiple scatter plots, depending on the number of coordinates passed to it.
- Parameters
pca_coordinates – array of pca coordinates (returned as first output by the routine get_pca_representation) to be shown as scatter plot
components – Components to be plotted (corresponds to columns of pca_coordinates)
- Returns
Either one axes object, or a dictionary of plot axes (depending on the number of coordinates passed)
- Return type
axs
-
pypesto.visualize.projection_scatter_umap(umap_coordinates: numpy.ndarray, components: Sequence[int] = (0, 1), **kwargs)[source]¶ Plot a scatter plots for UMAP coordinates. Creates either one or multiple scatter plots, depending on the number of coordinates passed to it.
- Parameters
umap_coordinates – array of umap coordinates (returned as first output by the routine get_umap_representation) to be shown as scatter plot
components – Components to be plotted (corresponds to columns of umap_coordinates)
- Returns
Either one axes object, or a dictionary of plot axes (depending on the number of coordinates passed)
- Return type
axs
-
pypesto.visualize.projection_scatter_umap_original(umap_object: None, color_by: Optional[Sequence[float]] = None, components: Sequence[int] = (0, 1), **kwargs)[source]¶ Wrapper around umap.plot.points. Similar to projection_scatter_umap, but uses the original plotting routine from umap.plot.
- Parameters
umap_object – umap object (returned as second output by get_umap_representation) to be shown as scatter plot
color_by – A sequence/list of floats, which specify the color in the colormap
components – Components to be plotted (corresponds to columns of umap_coordinates)
- Returns
ax – The plot axes.
- Return type
matplotlib.Axes
-
pypesto.visualize.sampling_1d_marginals(result: pypesto.result.Result, i_chain: int = 0, par_indices: Optional[Sequence[int]] = None, stepsize: int = 1, plot_type: str = 'both', bw: str = 'scott', suptitle: Optional[str] = None, size: Optional[Tuple[float, float]] = None)[source]¶ Plot marginals.
- Parameters
result – The pyPESTO result object with filled sample result.
i_chain – Which chain to plot. Default: First chain.
par_indices (list of integer values) – List of integer values specifying which parameters to plot. Default: All parameters are shown.
stepsize – Only one in stepsize values is plotted.
plot_type ({'hist'|'kde'|'both'}) – Specify whether to plot a histogram (‘hist’), a kernel density estimate (‘kde’), or both (‘both’).
bw ({'scott', 'silverman' | scalar | pair of scalars}) – Kernel bandwidth method.
suptitle – Figure super title.
size – Figure size in inches.
- Returns
ax
- Return type
matplotlib-axes
-
pypesto.visualize.sampling_fval_traces(result: pypesto.result.Result, i_chain: int = 0, full_trace: bool = False, stepsize: int = 1, title: Optional[str] = None, size: Optional[Tuple[float, float]] = None, ax: Optional[matplotlib.axes._axes.Axes] = None)[source]¶ Plot log-posterior (=function value) over iterations.
- Parameters
result – The pyPESTO result object with filled sample result.
i_chain – Which chain to plot. Default: First chain.
full_trace – Plot the full trace including warm up. Default: False.
stepsize – Only one in stepsize values is plotted.
title – Axes title.
size (ndarray) – Figure size in inches.
ax – Axes object to use.
- Returns
The plot axes.
- Return type
ax
-
pypesto.visualize.sampling_parameter_cis(result: pypesto.result.Result, alpha: Optional[Sequence[int]] = None, step: float = 0.05, show_median: bool = True, title: Optional[str] = None, size: Optional[Tuple[float, float]] = None, ax: Optional[matplotlib.axes._axes.Axes] = None) → matplotlib.axes._axes.Axes[source]¶ Plot MCMC-based parameter credibility intervals for one or more credibility levels.
- Parameters
result – The pyPESTO result object with filled sample result.
alpha – List of lower tail probabilities, defaults to 95% interval.
step – Height of boxes for projectile plot, defaults to 0.05.
show_median – Plot the median of the MCMC chain. Default: True.
title – Axes title.
size (ndarray) – Figure size in inches.
ax – Axes object to use.
- Returns
The plot axes.
- Return type
ax
-
pypesto.visualize.sampling_parameter_traces(result: pypesto.result.Result, i_chain: int = 0, par_indices: Optional[Sequence[int]] = None, full_trace: bool = False, stepsize: int = 1, use_problem_bounds: bool = True, suptitle: Optional[str] = None, size: Optional[Tuple[float, float]] = None, ax: Optional[matplotlib.axes._axes.Axes] = None)[source]¶ Plot parameter values over iterations.
- Parameters
result – The pyPESTO result object with filled sample result.
i_chain – Which chain to plot. Default: First chain.
par_indices (list of integer values) – List of integer values specifying which parameters to plot. Default: All parameters are shown.
full_trace – Plot the full trace including warm up. Default: False.
stepsize – Only one in stepsize values is plotted.
use_problem_bounds – Defines if the y-limits shall be the lower and upper bounds of parameter estimation problem.
suptitle – Figure suptitle.
size – Figure size in inches.
ax – Axes object to use.
- Returns
The plot axes.
- Return type
ax
-
pypesto.visualize.sampling_prediction_trajectories(ensemble_prediction: pypesto.ensemble.ensemble.EnsemblePrediction, levels: Union[float, Sequence[float]], title: Optional[str] = None, size: Optional[Tuple[float, float]] = None, axes: Optional[matplotlib.axes._axes.Axes] = None, labels: Optional[Dict[str, str]] = None, axis_label_padding: int = 50, groupby: str = 'condition', condition_gap: float = 0.01, condition_ids: Optional[Sequence[str]] = None, output_ids: Optional[Sequence[str]] = None) → matplotlib.axes._axes.Axes[source]¶ Plot MCMC-based prediction credibility intervals for the model states or outputs. One or various credibility levels can be depicted. Plots are grouped by condition.
- Parameters
result – The pyPESTO result object with filled sample result.
levels – Credibility levels, e.g. [95] for a 95% credibility interval. See the
_get_level_percentiles()method for a description of how these levels are handled, and current limitations.title – Axes title.
size (ndarray) – Figure size in inches.
axes – Axes object to use.
labels – Keys should be ensemble output IDs, values should be the desired label for that output. Defaults to output IDs.
axis_label_padding – Pixels between axis labels and plots.
groupby – Group plots by pypesto.predict.constants.OUTPUT or pypesto.predict.constants.CONDITION.
condition_gap – Gap between conditions when groupby == pypesto.predict.constants.CONDITION.
condition_ids – If provided, only data for the provided condition IDs will be plotted.
output_ids – If provided, only data for the provided output IDs will be plotted.
- Returns
The plot axes.
- Return type
axes
-
pypesto.visualize.sampling_scatter(result: pypesto.result.Result, i_chain: int = 0, stepsize: int = 1, suptitle: Optional[str] = None, diag_kind: str = 'kde', size: Optional[Tuple[float, float]] = None)[source]¶ Parameter scatter plot.
- Parameters
result – The pyPESTO result object with filled sample result.
i_chain – Which chain to plot. Default: First chain.
stepsize – Only one in stepsize values is plotted.
suptitle – Figure super title.
diag_kind – Visualization mode for marginal densities {‘auto’, ‘hist’, ‘kde’, None}
size – Figure size in inches.
- Returns
The plot axes.
- Return type
ax
-
pypesto.visualize.waterfall(results: Union[pypesto.result.Result, Sequence[pypesto.result.Result]], ax: Optional[matplotlib.axes._axes.Axes] = None, size: Optional[Tuple[float]] = (18.5, 10.5), y_limits: Optional[Tuple[float]] = None, scale_y: Optional[str] = 'log10', offset_y: Optional[float] = None, start_indices: Optional[Union[Sequence[int], int]] = None, reference: Optional[Sequence[pypesto.visualize.reference_points.ReferencePoint]] = None, colors: Optional[Union[Tuple[float, float, float, float], Sequence[Tuple[float, float, float, float]]]] = None, legends: Optional[Union[Sequence[str], str]] = None)[source]¶ Plot waterfall plot.
- Parameters
results – Optimization result obtained by ‘optimize.py’ or list of those
ax (matplotlib.Axes, optional) – Axes object to use.
size – Figure size (width, height) in inches. Is only applied when no ax object is specified
y_limits (float or ndarray, optional) – maximum value to be plotted on the y-axis, or y-limits
scale_y – May be logarithmic or linear (‘log10’ or ‘lin’)
offset_y – offset for the y-axis, if it is supposed to be in log10-scale
start_indices – Integers specifying the multistart to be plotted or int specifying up to which start index should be plotted
reference – Reference points for optimization results, containing at least a function value fval
colors – Colors or single color for plotting. If not set, clustering is done and colors are assigned automatically
legends – Labels for line plots, one label per result object
- Returns
ax – The plot axes.
- Return type
matplotlib.Axes
-
pypesto.visualize.waterfall_lowlevel(fvals, scale_y='log10', offset_y=0.0, ax=None, size=(18.5, 10.5), colors=None, legend_text=None)[source]¶ Plot waterfall plot using list of function values.
- Parameters
fvals (numeric list or array) – Including values need to be plotted.
scale_y (str, optional) – May be logarithmic or linear (‘log10’ or ‘lin’)
offset_y – offset for the y-axis, if it is supposed to be in log10-scale
ax (matplotlib.Axes, optional) – Axes object to use.
size (tuple, optional) – see waterfall
colors (list, or RGBA, optional) – list of colors, or single color color or list of colors for plotting. If not set, clustering is done and colors are assigned automatically
legend_text (str) – Label for line plots
- Returns
ax – The plot axes.
- Return type
matplotlib.Axes
Engines¶
The execution of the multistarts can be parallelized in different ways, e.g. multi-threaded or cluster-based. Note that it is not checked whether a single task itself is internally parallelized.
-
class
pypesto.engine.MultiProcessEngine(n_procs: Optional[int] = None)[source]¶ Bases:
pypesto.engine.base.EngineParallelize the task execution using multiprocessing.
- Parameters
n_procs – The maximum number of processes to use in parallel. Defaults to the number of CPUs available on the system according to os.cpu_count(). The effectively used number of processes will be the minimum of n_procs and the number of tasks submitted.
-
class
pypesto.engine.MultiThreadEngine(n_threads: Optional[int] = None)[source]¶ Bases:
pypesto.engine.base.EngineParallelize the task execution using multithreading.
- Parameters
n_threads – The maximum number of threads to use in parallel. Defaults to the number of CPUs available on the system according to os.cpu_count(). The effectively used number of threads will be the minimum of n_threads and the number of tasks submitted.
-
class
pypesto.engine.SingleCoreEngine[source]¶ Bases:
pypesto.engine.base.EngineDummy engine for sequential execution on one core. Note that the objective itself may be multithreaded.
Startpoint¶
Methods for selecting points that can be used as start points for multistart optimization. All methods have the form
method(**kwargs) -> startpoints
where the kwargs can/should include the following parameters, which are passed by pypesto:
- n_starts: int
Number of points to generate.
- lb, ub: ndarray
Lower and upper bound, may for most methods not contain nan or inf values.
- x_guesses: ndarray, shape=(g, dim), optional
Parameter guesses by the user, where g denotes the number of guesses. Note that these are only possibly taken as reference points to generate new start points (e.g. to maximize some distance) depending on the method, but regardless of g, there are always n_starts points generated and returned.
- objective: pypesto.Objective, optional
The objective can be used to evaluate the goodness of start points.
- max_n_fval: int, optional
The maximum number of evaluations of the objective function allowed.
-
pypesto.startpoint.assign_startpoints(n_starts: int, startpoint_method: Callable, problem: pypesto.problem.Problem, startpoint_resample: bool) → numpy.ndarray[source]¶ Assign start points.
-
pypesto.startpoint.latin_hypercube(**kwargs) → numpy.ndarray[source]¶ Generate latin hypercube points.
- Parameters
n_starts – number of starting points to be sampled.
lb – lower bound.
ub – upper bound.
smooth – indicates if a (uniformly chosen) random starting point within the hypercube [i/n_starts, (i+1)/n_starts] should be chosen (True) or the midpoint of the interval (False). Default is True.
-
pypesto.startpoint.uniform(**kwargs) → numpy.ndarray[source]¶ Generate uniform points.
Storage¶
Saving and loading traces and results objects.
-
class
pypesto.store.OptimizationResultHDF5Reader(storage_filename: str)[source]¶ Bases:
objectReader of the HDF5 result files written by class OptimizationResultHDF5Writer.
-
storage_filename¶ HDF5 result file name
-
read() → pypesto.result.Result[source]¶ Read HDF5 result file and return pyPESTO result object.
-
-
class
pypesto.store.OptimizationResultHDF5Writer(storage_filename: str)[source]¶ Bases:
objectWriter of the HDF5 result files.
-
storage_filename¶ HDF5 result file name
-
write(result: pypesto.result.Result, overwrite=False)[source]¶ Write HDF5 result file from pyPESTO result object.
-
-
class
pypesto.store.ProblemHDF5Reader(storage_filename: str)[source]¶ Bases:
objectReader of the HDF5 problem files written by class ProblemHDF5Writer.
-
storage_filename¶ HDF5 problem file name
-
read(objective: Optional[pypesto.objective.base.ObjectiveBase] = None) → pypesto.problem.Problem[source]¶ Read HDF5 problem file and return pyPESTO problem object.
- Parameters
objective – Objective function which is currently not saved to storage.
- Returns
A problem instance with all attributes read in.
- Return type
problem
-
-
class
pypesto.store.ProblemHDF5Writer(storage_filename: str)[source]¶ Bases:
objectWriter of the HDF5 problem files.
-
storage_filename¶ HDF5 result file name
-
-
class
pypesto.store.ProfileResultHDF5Reader(storage_filename: str)[source]¶ Bases:
objectReader of the HDF5 result files written by class OptimizationResultHDF5Writer.
-
storage_filename¶ HDF5 result file name
-
read() → pypesto.result.Result[source]¶ Read HDF5 result file and return pyPESTO result object.
-
-
class
pypesto.store.ProfileResultHDF5Writer(storage_filename: str)[source]¶ Bases:
objectWriter of the HDF5 result files.
-
storage_filename¶ HDF5 result file name
-
write(result: pypesto.result.Result, overwrite: bool = False)[source]¶ Write HDF5 result file from pyPESTO result object.
-
-
class
pypesto.store.SamplingResultHDF5Reader(storage_filename: str)[source]¶ Bases:
objectReader of the HDF5 result files written by class SamplingResultHDF5Writer.
-
storage_filename¶ HDF5 result file name
-
read() → pypesto.result.Result[source]¶ Read HDF5 result file and return pyPESTO result object.
-
-
class
pypesto.store.SamplingResultHDF5Writer(storage_filename: str)[source]¶ Bases:
objectWriter of the HDF5 sampling files.
-
storage_filename¶ HDF5 result file name
-
write(result: pypesto.result.Result, overwrite: bool = False)[source]¶ Write HDF5 sampling file from pyPESTO result object.
-
-
pypesto.store.get_or_create_group(f: Union[h5py._hl.files.File, h5py._hl.group.Group], group_path: str) → h5py._hl.group.Group[source]¶ Helper function that returns a group object for the group with group_path relative to f. Creates it if it doesn’t exist.
-
pypesto.store.f¶ should be checked
- Type
file or group where existence of a group with the path group_path
-
pypesto.store.group_path¶ - Type
the path or simply the name of the group that should exist in f
- Returns
hdf5 group object with specified path.
- Return type
grp
-
-
pypesto.store.load_objective_config(filename: str)[source]¶ Load the objective information stored in f
- Parameters
f – The name of the file in which the information are stored.
Returns – A dictionary of the information, stored instead of the actual objective in problem.objective.
-
pypesto.store.read_result(filename: str, problem: bool = True, optimize: bool = False, profile: bool = False, sample: bool = False) → pypesto.result.Result[source]¶ This is a function that saves the whole pypesto.Result object in an HDF5 file. With booleans one can choose more detailed what to save.
- Parameters
filename – The HDF5 filename.
problem – Read the problem.
optimize – Read the optimize result.
profile – Read the profile result.
sample – Read the sample result.
- Returns
Result object containing the results stored in HDF5 file.
- Return type
result
-
pypesto.store.write_array(f: h5py._hl.group.Group, path: str, values: Collection) → None[source]¶ Write array to hdf5
- Parameters
f – h5py.Group where dataset should be created
path – path of the dataset to create
values – array to write
-
pypesto.store.write_result(result: pypesto.result.Result, filename: str, overwrite: bool = False, problem: bool = True, optimize: bool = True, profile: bool = True, sample: bool = True)[source]¶ Save whole pypesto.Result to hdf5 file.
Boolean indicators allow specifying what to save.
- Parameters
result – The
pypesto.Resultobject to be saved.filename – The HDF5 filename.
overwrite – Boolean, whether already existing results should be overwritten.
problem – Read the problem.
optimize – Read the optimize result.
profile – Read the profile result.
sample – Read the sample result.
Logging¶
Logging convenience functions.
-
pypesto.logging.log(name: str = 'pypesto', level: int = 20, console: bool = True, filename: str = '')[source]¶ Log messages from a specified name with a specified level to any combination of console and file.
- Parameters
name – The name of the logger.
level – The output level to use.
console – If True, messages are logged to console.
filename – If specified, messages are logged to a file with this name.
Ensemble¶
-
class
pypesto.ensemble.Ensemble(x_vectors: numpy.ndarray, x_names: Optional[Sequence[str]] = None, vector_tags: Optional[Sequence[Tuple[int, int]]] = None, ensemble_type: Optional[pypesto.ensemble.constants.EnsembleType] = None, predictions: Optional[Sequence[pypesto.ensemble.ensemble.EnsemblePrediction]] = None, lower_bound: Optional[numpy.ndarray] = None, upper_bound: Optional[numpy.ndarray] = None)[source]¶ Bases:
objectA ensemble is a wrapper around an numpy array. It comes with some convenience functionality: It allows to map parameter values via identifiers to the correct parameters, it allows to compute summaries of the parameter vectors (mean, standard deviation, median, percentiles) more easily, and it can store predictions made by pyPESTO, such that the parameter ensemble and the predictions are linked to each other.
-
__init__(x_vectors: numpy.ndarray, x_names: Optional[Sequence[str]] = None, vector_tags: Optional[Sequence[Tuple[int, int]]] = None, ensemble_type: Optional[pypesto.ensemble.constants.EnsembleType] = None, predictions: Optional[Sequence[pypesto.ensemble.ensemble.EnsemblePrediction]] = None, lower_bound: Optional[numpy.ndarray] = None, upper_bound: Optional[numpy.ndarray] = None)[source]¶ Constructor.
- Parameters
x_vectors – parameter vectors of the ensemble, in the format n_parameter x n_vectors
x_names – Names or identifiers of the parameters
vector_tags – Additional tag, which adds information about the the parameter vectors of the form (optimization_run, optimization_step) if the ensemble is created from an optimization result or (sampling_chain, sampling_step) if the ensemble is created from a sampling result.
ensemble_type – Type of ensemble: Ensemble (default), sample, or unprocessed_chain Samples are meant to be representative, ensembles can be any ensemble of parameters, and unprocessed chains still have burn-ins
predictions – List of EnsemblePrediction objects
lower_bound – array of potential lower bounds for the parameters
upper_bound – array of potential upper bounds for the parameters
-
check_identifiability() → pandas.core.frame.DataFrame[source]¶ Use ensemble mean and standard deviation to assess (in a rudimentary way) whether or not parameters are identifiable. Returns a dataframe with tuples, which specify whether or not the lower and the upper bounds are violated.
- Returns
DataFrame indicating parameter identifiability based on mean plus/minus standard deviations and parameter bounds
- Return type
parameter_identifiability
-
compute_summary(percentiles_list: Sequence[int] = (5, 20, 80, 95))[source]¶ This function computes the mean, the median, the standard deviation and possibly percentiles for the parameters of the ensemble. Those summary results are added as a data member to the EnsemblePrediction object.
- Parameters
percentiles_list – List or tuple of percent numbers for the percentiles
- Returns
Dict with mean, std, median, and percentiles of parameter vectors
- Return type
summary
-
static
from_optimization_endpoints(result: pypesto.result.Result, cutoff: float = inf, max_size: int = inf, **kwargs)[source]¶ Construct an ensemble from an optimization result.
- Parameters
result – A pyPESTO result that contains an optimization result.
cutoff – Exclude parameters from the optimization if the nllh is higher than the cutoff.
max_size – The maximum size the ensemble should be.
- Returns
- Return type
The ensemble.
-
static
from_optimization_history(result: pypesto.result.Result, cutoff: float = inf, max_size: int = inf, max_per_start: int = inf, distribute: bool = True, **kwargs)[source]¶ Construct an ensemble from the history of an optimization.
- Parameters
result – A pyPESTO result that contains an optimization result with history recorded.
cutoff – Exclude parameters from the optimization if the nllh is higher than the cutoff.
max_size – The maximum size the ensemble should be.
max_per_start – The maximum number of vectors to be included from a single optimization start.
distribute – Boolean flag, whether the best (False) values from the start should be taken or whether the indices should be more evenly distributed.
- Returns
- Return type
The ensemble.
-
static
from_sample(result: pypesto.result.Result, remove_burn_in: bool = True, chain_slice: Optional[slice] = None, **kwargs)[source]¶ Construct an ensemble from a sample.
- Parameters
result – A pyPESTO result that contains a sample result.
remove_burn_in – Exclude parameter vectors from the ensemble if they are in the “burn-in”.
chain_slice – Subset the chain with a slice. Any “burn-in” removal occurs first.
- Returns
- Return type
The ensemble.
-
predict(predictor: Callable, prediction_id: Optional[str] = None, sensi_orders: Tuple = (0), default_value: Optional[float] = None, mode: str = 'mode_fun', engine: Optional[pypesto.engine.base.Engine] = None, progress_bar: bool = True) → pypesto.ensemble.ensemble.EnsemblePrediction[source]¶ Convenience function to run predictions for a full ensemble: User needs to hand over a predictor function and settings, then all results are grouped as EnsemblePrediction for the whole ensemble
- Parameters
predictor – Prediction function, e.g., an AmiciPredictor
prediction_id – Identifier for the predictions
sensi_orders – Specifies which sensitivities to compute, e.g. (0,1) -> fval, grad
default_value – If parameters are needed in the mapping, which are not found in the parameter source, it can make sense to fill them up with this default value (e.g. np.nan) in some cases (to be used with caution though).
mode – Whether to compute function values or residuals.
engine – Parallelization engine. Defaults to sequential execution on a SingleCoreEngine.
progress_bar – Whether to display a progress bar.
- Returns
- Return type
The prediction of the ensemble.
-
-
class
pypesto.ensemble.EnsemblePrediction(predictor: Optional[Callable[[Sequence], pypesto.predict.result.PredictionResult]] = None, prediction_id: Optional[str] = None, prediction_results: Optional[Sequence[pypesto.predict.result.PredictionResult]] = None, lower_bound: Optional[Sequence[numpy.ndarray]] = None, upper_bound: Optional[Sequence[numpy.ndarray]] = None)[source]¶ Bases:
objectA ensemble prediction consists of an ensemble, i.e., a set of parameter vectors and their identifiers such as a sample, and a prediction function. It can be attached to a ensemble-type object
-
__init__(predictor: Optional[Callable[[Sequence], pypesto.predict.result.PredictionResult]] = None, prediction_id: Optional[str] = None, prediction_results: Optional[Sequence[pypesto.predict.result.PredictionResult]] = None, lower_bound: Optional[Sequence[numpy.ndarray]] = None, upper_bound: Optional[Sequence[numpy.ndarray]] = None)[source]¶ Constructor.
- Parameters
predictor – Prediction function, e.g., an AmiciPredictor, which takes a parameter vector as input and outputs a PredictionResult object
prediction_id – Identifier for the predictions
prediction_results – List of Prediction results
lower_bound – Array of potential lower bounds for the predictions, should have the same shape as the output of the predictions, i.e., a list of numpy array (one list entry per condition), with the arrays having the shape of n_timepoints x n_outputs for each condition.
upper_bound – array of potential upper bounds for the parameters
-
compute_summary(percentiles_list: Sequence[int] = (5, 20, 80, 95)) → Dict[source]¶ Compute the mean, the median, the standard deviation and possibly percentiles from the ensemble prediction results. Those summary results are added as a data member to the EnsemblePrediction object.
- Parameters
percentiles_list – List or tuple of percent numbers for the percentiles
- Returns
dictionary of predictions results with the keys mean, std, median, percentiles, …
- Return type
summary
-
condense_to_arrays()[source]¶ This functions reshapes the predictions results to an array and adds them as a member to the EnsemblePrediction objects. It’s meant to be used only if all conditions of a prediction have the same observables, as this is often the case for large-scale data sets taken from online databases or similar.
-
-
class
pypesto.ensemble.EnsembleType(value)[source]¶ Bases:
enum.EnumAn enumeration.
-
ensemble= 1¶
-
sample= 2¶
-
unprocessed_chain= 3¶
-
-
class
pypesto.ensemble.Enum(value)[source]¶ Bases:
objectGeneric enumeration.
Derive from this class to define new enumerations.
-
name¶ The name of the Enum member.
-
value¶ The value of the Enum member.
-
-
pypesto.ensemble.get_covariance_matrix_parameters(ens: pypesto.ensemble.ensemble.Ensemble) → numpy.ndarray[source]¶ Compute the covariance of ensemble parameters.
- Parameters
ens – Ensemble object containing a set of parameter vectors
- Returns
covariance matrix of ensemble parameters
- Return type
covariance_matrix
-
pypesto.ensemble.get_covariance_matrix_predictions(ens: Union[pypesto.ensemble.ensemble.Ensemble, pypesto.ensemble.ensemble.EnsemblePrediction], prediction_index: int = 0) → numpy.ndarray[source]¶ Compute the covariance of ensemble predictions.
- Parameters
ens – Ensemble object containing a set of parameter vectors and a set of predictions or EnsemblePrediction object containing only predictions
prediction_index – index telling which prediction from the list should be analyzed
- Returns
covariance matrix of ensemble predictions
- Return type
covariance_matrix
-
pypesto.ensemble.get_pca_representation_parameters(ens: pypesto.ensemble.ensemble.Ensemble, n_components: int = 2, rescale_data: bool = True, rescaler: Optional[Callable] = None) → Tuple[source]¶ Compute the representation with reduced dimensionality via principal component analysis (with a given number of principal components) of the parameter ensemble.
- Parameters
ens – Ensemble objects containing a set of parameter vectors
n_components – number of components for the dimension reduction
rescale_data – flag indicating whether the principal components should be rescaled using a rescaler function (e.g., an arcsinh function)
rescaler – callable function to rescale the output of the PCA (defaults to numpy.arcsinh)
- Returns
principal_components – principal components of the parameter vector ensemble
pca_object – returned fitted pca object from sklearn.decomposition.PCA()
-
pypesto.ensemble.get_pca_representation_predictions(ens: Union[pypesto.ensemble.ensemble.Ensemble, pypesto.ensemble.ensemble.EnsemblePrediction], prediction_index: int = 0, n_components: int = 2, rescale_data: bool = True, rescaler: Optional[Callable] = None) → Tuple[source]¶ Compute the representation with reduced dimensionality via principal component analysis (with a given number of principal components) of the ensemble prediction.
- Parameters
ens – Ensemble objects containing a set of parameter vectors and a set of predictions or EnsemblePrediction object containing only predictions
prediction_index – index telling which prediction from the list should be analyzed
n_components – number of components for the dimension reduction
rescale_data – flag indicating whether the principal components should be rescaled using a rescaler function (e.g., an arcsinh function)
rescaler – callable function to rescale the output of the PCA (defaults to numpy.arcsinh)
- Returns
principal_components – principal components of the parameter vector ensemble
pca_object – returned fitted pca object from sklearn.decomposition.PCA()
-
pypesto.ensemble.get_percentile_label(percentile: Union[float, int, str]) → str[source]¶ Convert a percentile to a label.
Labels for percentiles are used at different locations (e.g. ensemble prediction code, and visualization code). This method ensures that the same percentile is labeled identically everywhere.
The percentile is rounded to two decimal places in the label representation if it is specified to more decimal places. This is for readability in plotting routines, and to avoid float to string conversion issues related to float precision.
- Parameters
percentile – The percentile value that will be used to generate a label.
- Returns
- Return type
The label of the (possibly rounded) percentile.
-
pypesto.ensemble.get_spectral_decomposition_lowlevel(matrix: numpy.ndarray, normalize: bool = False, only_separable_directions: bool = False, cutoff_absolute_separable: float = 1e-16, cutoff_relative_separable: float = 1e-16, only_identifiable_directions: bool = False, cutoff_absolute_identifiable: float = 1e-16, cutoff_relative_identifiable: float = 1e-16) → Tuple[numpy.ndarray, numpy.ndarray][source]¶ Compute the spectral decomposition of ensemble parameters or predictions.
- Parameters
matrix – symmetric matrix (typically a covariance matrix) of parameters or predictions
normalize – flag indicating whether the returned Eigenvalues should be normalized with respect to the largest Eigenvalue
only_separable_directions – return only separable directions according to cutoff_[absolute/relative]_separable
cutoff_absolute_separable – Consider only eigenvalues of the covariance matrix above this cutoff (only applied when only_separable_directions is True)
cutoff_relative_separable – Consider only eigenvalues of the covariance matrix above this cutoff, when rescaled with the largest eigenvalue (only applied when only_separable_directions is True)
only_identifiable_directions – return only identifiable directions according to cutoff_[absolute/relative]_identifiable
cutoff_absolute_identifiable – Consider only low eigenvalues of the covariance matrix with inverses above of this cutoff (only applied when only_identifiable_directions is True)
cutoff_relative_identifiable – Consider only low eigenvalues of the covariance matrix when rescaled with the largest eigenvalue with inverses above of this cutoff (only applied when only_identifiable_directions is True)
- Returns
eigenvalues – Eigenvalues of the covariance matrix
eigenvectors – Eigenvectors of the covariance matrix
-
pypesto.ensemble.get_spectral_decomposition_parameters(ens: pypesto.ensemble.ensemble.Ensemble, normalize: bool = False, only_separable_directions: bool = False, cutoff_absolute_separable: float = 1e-16, cutoff_relative_separable: float = 1e-16, only_identifiable_directions: bool = False, cutoff_absolute_identifiable: float = 1e-16, cutoff_relative_identifiable: float = 1e-16) → Tuple[numpy.ndarray, numpy.ndarray][source]¶ Compute the spectral decomposition of ensemble parameters.
- Parameters
ens – Ensemble object containing a set of parameter vectors
normalize – flag indicating whether the returned Eigenvalues should be normalized with respect to the largest Eigenvalue
only_separable_directions – return only separable directions according to cutoff_[absolute/relative]_separable
cutoff_absolute_separable – Consider only eigenvalues of the covariance matrix above this cutoff (only applied when only_separable_directions is True)
cutoff_relative_separable – Consider only eigenvalues of the covariance matrix above this cutoff, when rescaled with the largest eigenvalue (only applied when only_separable_directions is True)
only_identifiable_directions – return only identifiable directions according to cutoff_[absolute/relative]_identifiable
cutoff_absolute_identifiable – Consider only low eigenvalues of the covariance matrix with inverses above of this cutoff (only applied when only_identifiable_directions is True)
cutoff_relative_identifiable – Consider only low eigenvalues of the covariance matrix when rescaled with the largest eigenvalue with inverses above of this cutoff (only applied when only_identifiable_directions is True)
- Returns
eigenvalues – Eigenvalues of the covariance matrix
eigenvectors – Eigenvectors of the covariance matrix
-
pypesto.ensemble.get_spectral_decomposition_predictions(ens: pypesto.ensemble.ensemble.Ensemble, normalize: bool = False, only_separable_directions: bool = False, cutoff_absolute_separable: float = 1e-16, cutoff_relative_separable: float = 1e-16, only_identifiable_directions: bool = False, cutoff_absolute_identifiable: float = 1e-16, cutoff_relative_identifiable: float = 1e-16) → Tuple[numpy.ndarray, numpy.ndarray][source]¶ Compute the spectral decomposition of ensemble predictions.
- Parameters
ens – Ensemble object containing a set of parameter vectors and a set of predictions or EnsemblePrediction object containing only predictions
normalize – flag indicating whether the returned Eigenvalues should be normalized with respect to the largest Eigenvalue
only_separable_directions – return only separable directions according to cutoff_[absolute/relative]_separable
cutoff_absolute_separable – Consider only eigenvalues of the covariance matrix above this cutoff (only applied when only_separable_directions is True)
cutoff_relative_separable – Consider only eigenvalues of the covariance matrix above this cutoff, when rescaled with the largest eigenvalue (only applied when only_separable_directions is True)
only_identifiable_directions – return only identifiable directions according to cutoff_[absolute/relative]_identifiable
cutoff_absolute_identifiable – Consider only low eigenvalues of the covariance matrix with inverses above of this cutoff (only applied when only_identifiable_directions is True)
cutoff_relative_identifiable – Consider only low eigenvalues of the covariance matrix when rescaled with the largest eigenvalue with inverses above of this cutoff (only applied when only_identifiable_directions is True)
- Returns
eigenvalues – Eigenvalues of the covariance matrix
eigenvectors – Eigenvectors of the covariance matrix
-
pypesto.ensemble.get_umap_representation_parameters(ens: pypesto.ensemble.ensemble.Ensemble, n_components: int = 2, normalize_data: bool = False, **kwargs) → Tuple[source]¶ Compute the representation with reduced dimensionality via umap (with a given number of umap components) of the parameter ensemble. Allows to pass on additional keyword arguments to the umap routine.
- Parameters
ens – Ensemble objects containing a set of parameter vectors
n_components – number of components for the dimension reduction
normalize_data – flag indicating whether the parameter ensemble should be rescaled with mean and standard deviation
- Returns
umap_components – first components of the umap embedding
umap_object – returned fitted umap object from umap.UMAP()
-
pypesto.ensemble.get_umap_representation_predictions(ens: Union[pypesto.ensemble.ensemble.Ensemble, pypesto.ensemble.ensemble.EnsemblePrediction], prediction_index: int = 0, n_components: int = 2, normalize_data: bool = False, **kwargs) → Tuple[source]¶ Compute the representation with reduced dimensionality via umap (with a given number of umap components) of the ensemble predictions. Allows to pass on additional keyword arguments to the umap routine.
- Parameters
ens – Ensemble objects containing a set of parameter vectors and a set of predictions or EnsemblePrediction object containing only predictions
prediction_index – index telling which prediction from the list should be analyzed
n_components – number of components for the dimension reduction
normalize_data – flag indicating whether the parameter ensemble should be rescaled with mean and standard deviation
- Returns
umap_components – first components of the umap embedding
umap_object – returned fitted umap object from umap.UMAP()
-
pypesto.ensemble.read_ensemble_prediction_from_h5(predictor: Optional[Callable[[Sequence], pypesto.predict.result.PredictionResult]], input_file: str)[source]¶
-
pypesto.ensemble.read_from_csv(path: str, sep: str = '\t', index_col: int = 0, headline_parser: Optional[Callable] = None, ensemble_type: Optional[pypesto.ensemble.constants.EnsembleType] = None, lower_bound: Optional[numpy.ndarray] = None, upper_bound: Optional[numpy.ndarray] = None)[source]¶ function for creating an ensemble from a csv file
- Parameters
path – path to csv file to read in parameter ensemble
sep – separator in csv file
index_col – index column in csv file
headline_parser – A function which reads in the headline of the csv file and converts it into vector_tags (see constructor of Ensemble for more details)
ensemble_type – Ensemble type: representative sample or random ensemble
lower_bound – array of potential lower bounds for the parameters
upper_bound – array of potential upper bounds for the parameters
- Returns
Ensemble object of parameter vectors
- Return type
result
-
pypesto.ensemble.read_from_df(dataframe: pandas.core.frame.DataFrame, headline_parser: Optional[Callable] = None, ensemble_type: Optional[pypesto.ensemble.constants.EnsembleType] = None, lower_bound: Optional[numpy.ndarray] = None, upper_bound: Optional[numpy.ndarray] = None)[source]¶ function for creating an ensemble from a csv file
- Parameters
dataframe – pandas.DataFrame to read in parameter ensemble
headline_parser – A function which reads in the headline of the csv file and converts it into vector_tags (see constructor of Ensemble for more details)
ensemble_type – Ensemble type: representative sample or random ensemble
lower_bound – array of potential lower bounds for the parameters
upper_bound – array of potential upper bounds for the parameters
- Returns
Ensemble object of parameter vectors
- Return type
result
Contribute¶
Workflow¶
If you start working on a new feature or a fix, please create an issue on
GitHub shortly describing the issue and assign yourself.
Your startpoint should always be the develop branch, which contains the
lastest updates.
Create an own branch or fork, on which you can implement your changes. To get your work merged, please:
create a pull request to the
developbranch with a meaningful summary,check that code changes are covered by tests, and all tests pass,
check that the documentation is up-to-date,
request a code review from the main developers.
Environment¶
If you contribute to the development of pyPESTO, install developer requirements via:
pip install -r requirements-dev.txt
This installs the tools described below.
Pre-commit hooks¶
Firstly, this installs a pre-commit tool. To add those hooks to the .git folder of your local clone such that they are run on every commit, run:
pre-commit install
When adding new hooks, consider manually running pre-commit run --all-files
once as usually only the diff is checked. The configuration is specified in
.pre-commit-config.yaml.
Should it be necessary to perform commits without pre-commit verification,
use git commit --no-verify or the shortform -n.
GitHub Actions¶
For automatic continuous integration testing, we use GitHub Actions. All tests
are run there on pull requests and required to pass. The configuration is
specified in .github/workflows/ci.yml.
Documentation¶
To make pyPESTO easily usable, we try to provide good documentation, including code annotation and usage examples. The documentation is hosted at pypesto.readthedocs.io and updated automatically on merges to the main branches. To create the documentation locally, first install the requirements via:
pip install .[doc]
and then compile the documentation via:
cd doc
make html
The documentation is then under doc/_build.
Alternatively, the documentation can be compiled and tested via a single line:
tox -e doc
When adding code, all modules, classes, functions, parameters, code blocks should be properly documented.
For docstrings, we follow the numpy docstring standard. Check here for a detailed explanation.
Unit tests¶
Unit tests are located in the test folder. All files starting with
test_ contain tests and are automatically run on GitHub Actions.
Run them locally via e.g.:
tox -e base
with base covering basic tests, but some parts (optimize,petab,...)
being in separate subfolders. This boils mostly down to e.g.:
pytest test/base
You can also run only specific tests.
Unit tests can be written with pytest or unittest.
Code changes should always be covered by unit tests. It might not always be easy to test code which is based on random sampling, but we still encourage general sanity and integration tests. We highly encourage a test-driven development style.
Deploy¶
New production releases should be created every time the main branch is
updated.
Versions¶
For version numbers, we use A.B.C, where
Cis increased for bug fixes,Bis increased for new features and minor API breaking changes,Ais increased for major API breaking changes,
as suggested by the Python packaging guide.
Create a new release¶
After new commits have been added via pull requests to the develop branch,
changes can be merged to main and a new version of pyPESTO can be released.
Merge into main¶
create a pull request from
developtomain,check that all code changes are covered by tests and all tests pass,
check that the documentation is up-to-date,
adapt the version number in
pypesto/version.py(see above),update the release notes in
CHANGELOG.rst,request a code review,
merge into the origin
mainbranch.
To be able to actually perform the merge, sufficient rights may be required. Also, at least one review is required.
Create a release on GitHub¶
After merging into main, create a new release on GitHub. This can be done
either directly on the project GitHub website, or via the CLI as described
in
Git Basics - Tagging.
In the release form,
specify a tag with the new version as specified in
pypesto/version.py,include the latest additions to
CHANGELOG.rstin the release description.
Upload to PyPI¶
The upload to the python package index PyPI has been automatized via GitHub Actions and is triggered whenever a new release tag is published.
Should it be necessary to manually upload a new version to PyPI, proceed as follows: First, a so called “wheel” is created via:
python setup.py bdist_wheel
A wheel is essentially a zip archive which contains the source code and the binaries (if any).
This archive is uploaded using twine:
twine upload dist/pypesto-x.y.z-py3-non-any.wheel
replacing x.y.z by the respective version number.
For a more in-depth discussion see also the section on distributing packages of the Python packaging guide.
Release notes¶
0.2 series¶
0.2.7 (2021-07-30)¶
- Finite Differences:
Adaptive finite differences (#671)
Add helper function for checking gradients of objectives (#690)
Small bug fixes (#711, #714)
- Storage:
Store representation of the objective (#669)
Minor fixes in HDF5 history (#679)
HDF5 reader for ensemble predictions (#681)
Update storage demo jupyter notebook (#699)
Option to trim trace to be monotonically decreasing (#705)
- General:
Improved tests and bug fixes of validation intervals (#676, #685)
Add input file validation via PEtab linter for PEtab import (#678)
Remove default values from docstring (#680)
Minor fixes/improvements of ensembles (#687, #688)
Fix sorting of optimization values including NaN values (#691)
Specify axis limits for plotting (#693)
Minor fixes in visualization (#696)
Add installation option all_optimizers (#695)
Improve installation documentation (#689)
Update pysb and BNG version on GitHub Actions (#697)
Bug fix in steady state guesses (#715)
0.2.6 (2021-05-17)¶
- Objective:
Basic finite differences (#666)
Fix factor 2 in res/fval values (#619)
- Optimization:
Sort optimization results when appending (#668)
Read optimizer result from HDF5 (previously only CSV) (#663)
- Storage:
Load ensemble from HDF5 (#640)
- CI:
Add flake8 checks as pre-commit hook (#662)
Add efficient biological conversion reaction test model (#619)
- General:
No automatic import of the predict module (#657)
Assert unique problem parameter names (#665)
Load ensemble from optimization result with and without history usage (#640)
Calculate validation profile significance (#658)
Set pypesto screen logger to “INFO” by default (#667)
- Minor fixes:
Fix axis variable overwriting in visualize.sampling_parameter_traces (#665)
0.2.5 (2021-05-04)¶
- Objectives:
New Aesara objectve (#623, #629, #635)
- Sampling:
New Emcee sampler (#606)
Fix compatibility to new Theano version (#650)
- Storage:
Improve hdf5 storage documentation (#612)
Hdf5 history for MultiProcessEngine (#650)
Minor fixes (#637, #638, #645, #649)
- Visualization:
Fix bounds of parameter plots (#601)
Fix waterfall plots with multiple results (#611)
- CI:
Move CI tests on GitHub Actions to python 3.9 (#598)
Add issue template (#604)
Update BionetGen Link (#630)
Introduce project.toml (#634)
- General:
Introduce progress bar for optimization, profiles and ensembles (#641)
Extend gradient checking functionality (#644)
- Minor fixes:
Fix installation of ipopt (#599)
Fix Zenodo link (#601)
Fix duplicates in documentation (#603)
Fix least squares optimizers (#617 #631 #632)
Fix trust region options (#616)
Fix slicing for new AMICI release (#621)
Refactor and document latin hypercube sampling (#647)
Fix missing SBML name in PEtab import (#648)
0.2.4 (2021-03-12)¶
- Ensembles/Sampling:
General ensemble analysis, visualization, storage (#557, #565, #568)
Calculate and plot MCMC parameter and prediction CIs via ensemble definition, parallelize ensemble predictions (#490)
- Optimization:
New optimizer: SciPy Differential Evolution (#543)
Set fides default to hybrid (#578)
- AMICI:
Make guess_steadystate less restrictive (#561) and have a more intuitive default behavior (#562, #582)
Customize time points (#490)
- Storage:
Save HDF5 history with SingleCoreEngine (#564)
Add read/write function for whole results (#589)
- Engines:
MPI based distributed parallelization (#542)
- Visualization:
Speed up waterfall plots by resizing scales only once (#577)
Change waterfall default offset to 1 - minimum (#593)
- CI:
Move GHA CI tests to pull request level for better cooperability (#574)
Streamline test environments using tox and pre-commit hooks (#579)
Test profile and sampling storage (#585)
Update for Ubuntu 20.04, add rerun on failure (#587)
Minor fixes (release notes #558, nlop tests #559, close files #495, visualization #554, deployment #560, flakiness #570, aggregated deepcopy #572, respect user-provided offsets #576, update to SWIG 4 #591, check overwrite in profile writing #566)
0.2.3 (2021-01-18)¶
- New optimizers:
FIDES (#506, #503 # 500)
NLopt (#493)
- Extended PEtab support:
PySB import (#437)
Support of PEtab’s initializationPriors (#535)
Support of prior parameterScale{Normal,Laplace} (#520)
Example notebook for synthetic data generation (#482)
- General new and improved functionality:
Predictions (#544)
Move tests to GitHub Actions (#524)
Parallelize profile calculation (#532)
Save x_guesses in pypesto.problem (#494)
Improved finite difference gradients (#464)
Support of unconstrained optimization (#519)
Additional NaN check for fval, grad and hessian (#521)
Add sanity checks for optimizer bounds (#516)
- Improvements in storage:
Fix hdf5 export of optimizer history (#536)
Fix reading x_names from hdf5 history (#528)
Storage does not save empty arrays (#489)
hdf5 storage sampling (#546)
hdf5 storage parameter profiles (#546)
- Improvements in the visualization routines:
Plot parameter values as histogram (#485)
Fix y axis limits in waterfall plots (#503)
Fix color scheme in visualization (#498)
Improved visualization of optimization results (#486)
Several small bug fixes (#547, #541, #538, #533, #512, #508)
0.2.2 (2020-10-05)¶
New optimizer: CMA-ES (#457)
New plot: Optimizer convergence summary (#446)
- Fixes in visualization:
Type checks for reference points (#460)
y_limits in waterfall plots with multiple results (#475)
Support of new amici release (#469)
- Multiple fixes in optimization code:
Remove unused argument for dlib optimizer (#466)
Add check for installation of ipopt (#470)
Add maxiter as default option of dlib (#474)
Numpy based subindexing in amici_util (#462)
Check amici/PEtab installation (#477)
0.2.1 (2020-09-07)¶
Example Notebook for prior functionality (#438)
Changed parameter indexing in profiling routines (#419)
Basic sanity checking for parameter fixing (#420)
- Bug fixes in:
Displaying of multi start optimization (#430)
AMICI error output (#428)
Axes scaling/limits in waterfall plots (#441)
Priors (PEtab import, error handling) (#448, #452, #454)
Improved sampling diagnostics (e.g. effective samples size) (#426)
Improvements and bug fixes in parameter plots (#425)
0.2.0 (2020-06-17)¶
Major:
Modularize import, to import optimization, sampling and profiling separately (#413)
Minor:
- Bug fixes in
sampling (#412)
visualization (#405)
PEtab import (#403)
Hessian computation (#390)
Improve hdf5 error output (#409)
Outlaw large new files in GitHub commits (#388)
0.1 series¶
0.1.0 (2020-06-17)¶
Objective
Write solver settings to stream to enable serialization for distributed systems (#308)
- Refactor objective function (#347)
Removes necessity for all of the nasty binding/undbinding in AmiciObjective
Substantially reduces the complexity of the AggregatedObjective class
Aggregation of functions with inconsistent sensi_order/mode support
Introduce ObjectiveBase as an abstract Objective class
Introduce FunctionObjective for objectives from functions
Implement priors with gradients, integrate with PEtab (#357)
Fix minus sign in AmiciObjective.get_error_output (#361)
Implement a prior class, derivatives for standard models, interface with PEtab (#357)
Use amici.import_model_module to resolve module loading failure (#384)
Problem
Tidy up problem vectors using properties (#393)
Optimization
Interface IpOpt optimizer (#373)
Profiles
Tidy up profiles (#356)
Refactor profiles; add locally approximated profiles (#369)
Fix profiling and visualization with fixed parameters (#393)
Sampling
Geweke test for sampling convergence (#339)
Implement basic Pymc3 sampler (#351)
Make theano for pymc3 an optional dependency (allows using pypesto without pymc3) (#356)
Progress bar for MCMC sampling (#366)
Fix Geweke test crash for small sample sizes (#376)
In parallel tempering, allow to only temperate the likelihood, not the prior (#396)
History and storage
Allow storing results in a pre-filled hdf5 file (#290)
Various fixes of the history (reduced vs. full parameters, read-in from file, chi2 values) (#315)
Fix proper dimensions in result for failed start (#317)
Create required directories before creating hdf5 file (#326)
Improve storage and docs documentation (#328)
Fix storing x_free_indices in hdf5 result (#334)
Fix problem hdf5 return format (#336)
Implement partial trace extraction, simplify History API (#337)
Save really all attributes of a Problem to hdf5 (#342)
Visualization
Customizable xLabels and tight layout for profile plots (#331)
Fix non-positive bottom ylim on a log-scale axis in waterfall plots (#348)
Fix “palette list has the wrong number of colors” in sampling plots (#372)
Allow to plot multiple profiles from one result (#399)
Logging
Allow easier specification of only logging for submodules (#398)
Tests
Speed up travis build (#329)
Update travis test system to latest ubuntu and python 3.8 (#330)
Additional code quality checks, minor simplifications (#395)
0.0 series¶
0.0.13 (2020-05-03)¶
Tidy up and speed up tests (#265 and others).
Basic self-implemented Adaptive Metropolis and Adaptive Parallel Tempering sampling routines (#268).
Fix namespace sample -> sampling (#275).
Fix covariance matrix regularization (#275).
Fix circular dependency PetabImporter - PetabAmiciObjective via AmiciObjectBuilder, PetabAmiciObjective becomes obsolete (#274).
Define AmiciCalculator to separate the AMICI call logic (required for hierarchical optimization) (#277).
Define initialize function for resetting steady states in AmiciObjective (#281).
Fix scipy least squares options (#283).
Allow failed starts by default (#280).
Always copy parameter vector in objective to avoid side effects (#291).
Add Dockerfile (#288).
Fix header names in CSV history (#299).
Documentation:
Use imported members in autodoc (#270).
Enable python syntax highlighting in notebooks (#271).
0.0.12 (2020-04-06)¶
Add typehints to global functions and classes.
Add PetabImporter.rdatas_to_simulation_df function (all #235).
Adapt y scale in waterfall plot if convergence was too good (#236).
Clarify that Objective is of type negative log-posterior, for minimization (#243).
Tidy up AmiciObjective.parameter_mapping as implemented in AMICI now (#247).
Add MultiThreadEngine implementing multi-threading aside the MultiProcessEngine implementing multi-processing (#254).
Fix copying and pickling of AmiciObjective (#252, #257).
Remove circular dependence history-objective (#254).
Fix problem of visualizing results with failed starts (#249).
Rework history: make thread-safe, use factory methods, make context-specific (#256).
Improve PEtab usage example (#258).
Define history base contract, enabling different backends (#260).
Store optimization results to HDF5 (#261).
Simplify tests (#263).
Breaking changes:
HistoryOptions passed to pypesto.minimize instead of Objective (#256).
GlobalOptimizer renamed to PyswarmOptimizer (#235).
0.0.11 (2020-03-17)¶
Rewrite AmiciObjective and PetabAmiciObjective simulation routine to directly use amici.petab_objective routines (#209, #219, #225).
Implement petab test suite checks (#228).
Various error fixes, in particular regarding PEtab and visualization.
Improve trace structure.
Fix conversion between fval and chi2, fix FIM (all #223).
0.0.10 (2019-12-04)¶
Only compute FIM when sensitivities are available (#194).
Fix documentation build (#197).
Add support for pyswarm optimizer (#198).
Run travis tests for documentation and notebooks only on pull requests (#199).
0.0.9 (2019-10-11)¶
Update to AMICI 0.10.13, fix API changes (#185).
Start using PEtab import from AMICI to be able to import constant species (#184, #185)
Require PEtab>=0.0.0a16 (#183)
0.0.8 (2019-09-01)¶
Add logo (#178).
Fix petab API changes (#179).
Some minor bugfixes (#168).
0.0.7 (2019-03-21)¶
Support noise models in Petab and Amici.
Minor Petab update bug fixes.
0.0.6 (2019-03-13)¶
Several minor error fixes, in particular on tests and steady state.
0.0.5 (2019-03-11)¶
Introduce AggregatedObjective to use multiple objectives at once.
Estimate steady state in AmiciObjective.
Check amici model build version in PetabImporter.
Use Amici multithreading in AmiciObjective.
Allow to sort multistarts by initial value.
Show usage of visualization routines in notebooks.
Various fixes, in particular to visualization.
0.0.4 (2019-02-25)¶
Implement multi process parallelization engine for optimization.
Introduce PrePostProcessor to more reliably handle pre- and post-processing.
Fix problems with simulating for multiple conditions.
Add more visualization routines and options for those (colors, reference points, plotting of lists of result obejcts)
0.0.3 (2019-01-30)¶
Import amici models and the petab data format automatically using pypesto.PetabImporter.
Basic profiling routines.
0.0.2 (2018-10-18)¶
Fix parameter values
Record trace of function values
Amici objective to directly handle amici models
0.0.1 (2018-07-25)¶
Basic framework and implementation of the optimization
Authors¶
This package is mainly developed by:
Yannik Schälte
Jakob Vanhoefer
Fabian Fröhlich
Paul Stapor
with major contributions by:
Dantong Wang
Daniel Weindl
Polina Lakrisenko
Elba Raimúndez
Leonard Schmiester
Dilan Pathirana
Paul Jonas Jost
Lorenzo Contento
Erika Dudkin
Simon Merkt
Carolin Loos
Philipp Städter
Contact¶
Discovered an error? Need help? Not sure if something works as intended? Please contact us!
Yannik Schälte: yannik.schaelte@gmail.com
License¶
Copyright (c) 2018, Jan Hasenauer
All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Logo¶
pyPESTO’s logo can be found in multiple variants in the doc/logo directory on github, in svg and png format. It is made available under a creative commons CC0 license. You are encouraged to use it e.g. in presentations and posters.
We thank Patrick Beart for his contribution to the logo.