def plotQuantity(self, quantity_id, param_values):
''' Plot a simulated quantity vs its data points using Tellurium.'''
from data import measured_quantity_ids, measured_quantity_id_to_name_map
from data import t1, t2, time_end, n1, n2, n3
quantity_name = measured_quantity_id_to_name_map.get(quantity_id,quantity_id)
iq = measured_quantity_ids.index(quantity_id)
reference_data = array(self.reference_values[:,iq])
r = RoadRunner(self.sbml)
r.reset()
r.resetAll()
r.resetToOrigin()
self._setParameterVector(param_values, self.param_list, r)
# r.oneStep(0., 10)
# print('plotQuantity OAA\' = {}'.format(r["OAA'"]))
s1 = r.simulate(0., t1, n1, ['time', quantity_id])
s2 = r.simulate(t1, t2, n2, ['time', quantity_id])
# print(quantity_id)
# if quantity_id == 'GLC':
# print('BM before {}'.format(r['[BM]']))
# print(iq)
# print(reference_data)
s3 = r.simulate(t2, time_end, n3, ['time', quantity_id])
sim = vstack((
s1,
s2,
s3,
))
assert sim.shape[0] == reference_data.shape[0]
residuals = sim[:,1] - reference_data
r.reset()
r.resetAll()
r.resetToOrigin()
self._setParameterVector(param_values, self.param_list, r)
# self._setParameterVector(param_values, self.param_list, r)
s = r.simulate(0,time_end,1000,['time',quantity_id])
import tellurium as te
te.plot(sim[:,0], reference_data, scatter=True,
name=quantity_name+' data', show=False,
title=quantity_name,
error_y_pos=maximum(residuals,0),
error_y_neg=-minimum(residuals,0))
te.plot(s[:,0], s[:,1], name=quantity_name+' sim')
class B3Problem(TimecourseSimBiopredyn):
''' Class that performs a timecourse simulation
and evaluates the objective function for b1.'''
def __init__(self, sbml):
self.sbml = sbml
self.r = RoadRunner(sbml)
from data import measured_quantity_ids, exp_data
self.measured_quantity_ids = measured_quantity_ids
self.reference_values = exp_data
self.reference_value_means_squared = mean(self.reference_values, axis=0)**2
from params import new_param_ids as param_ids
self.param_list = param_ids
self.penalty_scale = 1.
def evaluate(self, x):
# type: (array) -> SupportsFloat
"""
Evaluate and return the objective function.
"""
from interruptingcow import timeout
# from data import time_end, n_points
from data import t1, t2, time_end, n1, n2, n3
self.reset()
self.r.resetAll()
self.r.resetToOrigin()
self.setParameterVector(x)
self.r.reset()
def worker():
# sim = array(self.r.simulate(0., time_end, n_points, self.measured_quantity_ids))
s1 = self.r.simulate(0., t1, n1, self.measured_quantity_ids)
s2 = self.r.simulate(t1, t2, n2, self.measured_quantity_ids)
s3 = self.r.simulate(t2, time_end, n3, self.measured_quantity_ids)
sim = vstack((
s1,
s2,
s3,
))
residuals = sim-self.reference_values
normalized_mse_per_quantity = mean(residuals**2,axis=0)/self.reference_value_means_squared
# from pprint import pprint
# print('residuals:')
# pprint({id: value for id,value in zip(self.measured_quantity_ids, sqrt(normalized_mse_per_quantity))})
return sqrt(mean(normalized_mse_per_quantity))
try:
with timeout(10, StalledSimulation):
return worker()
except (RuntimeError, StalledSimulation):
# if convergence fails, use a penalty score
return 1e9*self.penalty_scale
def plotQuantity(self, quantity_id, param_values):
''' Plot a simulated quantity vs its data points using Tellurium.'''
from data import measured_quantity_ids, measured_quantity_id_to_name_map
from data import t1, t2, time_end, n1, n2, n3
quantity_name = measured_quantity_id_to_name_map.get(quantity_id,quantity_id)
iq = measured_quantity_ids.index(quantity_id)
reference_data = array(self.reference_values[:,iq])
r = RoadRunner(self.sbml)
r.reset()
r.resetAll()
r.resetToOrigin()
self._setParameterVector(param_values, self.param_list, r)
# r.oneStep(0., 10)
# print('plotQuantity OAA\' = {}'.format(r["OAA'"]))
s1 = r.simulate(0., t1, n1, ['time', quantity_id])
s2 = r.simulate(t1, t2, n2, ['time', quantity_id])
# print(quantity_id)
# if quantity_id == 'GLC':
# print('BM before {}'.format(r['[BM]']))
# print(iq)
# print(reference_data)
s3 = r.simulate(t2, time_end, n3, ['time', quantity_id])
sim = vstack((
s1,
s2,
s3,
))
assert sim.shape[0] == reference_data.shape[0]
residuals = sim[:,1] - reference_data
r.reset()
r.resetAll()
r.resetToOrigin()
self._setParameterVector(param_values, self.param_list, r)
# self._setParameterVector(param_values, self.param_list, r)
s = r.simulate(0,time_end,1000,['time',quantity_id])
import tellurium as te
te.plot(sim[:,0], reference_data, scatter=True,
name=quantity_name+' data', show=False,
title=quantity_name,
error_y_pos=maximum(residuals,0),
error_y_neg=-minimum(residuals,0))
te.plot(s[:,0], s[:,1], name=quantity_name+' sim')
# print('deviation for {}: {}/{} = {}'.format(quantity_id, sqrt(mean(residuals**2)), sqrt(self.reference_value_means_squared[iq]), sqrt(mean(residuals**2)/self.reference_value_means_squared[iq])))
def getParameterValue(self,param_index):
from params import param_index_to_name_map
try:
return self.r[param_index_to_name_map[param_index]]
except KeyError:
raise KeyError('No such parameter for index {}, must be 0-1758 inclusive'.format(param_index))
class B5Problem(TimecourseSimBiopredyn):
''' Class that performs a timecourse simulation
and evaluates the objective function for b1.'''
def __init__(self, sbml):
self.sbml = sbml
self.r = RoadRunner(sbml)
self.r.integrator.absolute_tolerance = 1e-15
self.r.integrator.relative_tolerance = 1e-9
self.r.integrator.stiff = True
from observables import observables
self.measured_quantity_ids = observables
from json import load
with open(join(dirname(realpath(__file__)), 'exp_data.json')) as f:
self.reference_value_collection = [array(a) for a in load(f)]
self.reference_value_means_squared_collection = []
for a in self.reference_value_collection:
self.reference_value_means_squared_collection.append(
mean(a, axis=0)**2)
with open(join(dirname(realpath(__file__)), 'exp_y0.json')) as f:
self.exp_y0_collection = [array(a) for a in load(f)]
with open(join(dirname(realpath(__file__)), 'stimuli.json')) as f:
self.stimuli_collection = [d for d in load(f)]
from parameters import param_ids
self.param_list = param_ids
self.penalty_scale = 1.
def setExperimentNumber(self, n):
'''
Villaverde et al. use a set of 10 different experiments with respective
different stimuli combinations and expected results.
This method initialized appropriate variables for the given experiment.
'''
self.reference_values = self.reference_value_collection[n]
self.reference_value_means_squared = self.reference_value_means_squared_collection[
n]
self.exp_y0 = self.exp_y0_collection[n]
from species import species
for k, s in enumerate(species):
self.r.setValue('init({})'.format(s), float(self.exp_y0[k]))
self.stimuli = self.stimuli_collection[n]
for s, b in self.stimuli.items():
print('{} = {}'.format(s, b * 1.))
self.r[s] = b * 1.
def evaluate(self, x):
# type: (array) -> SupportsFloat
"""
Evaluate and return the objective function.
"""
from interruptingcow import timeout
for n in range(10):
self.setExperimentNumber(n)
self.reset()
def worker():
self.r.reset()
self.r.resetAll()
self.setParameterVector(x, exponential=False)
sim = self.r.simulate(0., 30., 16, self.measured_quantity_ids)
residuals = sim - self.reference_values
normalized_mse_per_quantity = mean(
residuals**2, axis=0) / self.reference_value_means_squared
return sqrt(mean(normalized_mse_per_quantity))
try:
with timeout(10, StalledSimulation):
return worker()
except (RuntimeError, StalledSimulation):
# if convergence fails, use a penalty score
return 1e9 * self.penalty_scale
def plotQuantity(self, quantity_id, param_values, exp_number):
''' Plot a simulated quantity vs its data points using Tellurium.'''
self.setExperimentNumber(exp_number)
iq = self.measured_quantity_ids.index(quantity_id)
reference_data = array(self.reference_values[:, iq])
# self.r.reset()
# self.r.resetAll()
# # r.resetToOrigin()
# self.setParameterVector(param_values, exponential=False)
# sim = self.r.simulate(0., 30., 16, ['time', quantity_id])
# # print(self.r.getReactionRates())
# assert sim.shape[0] == reference_data.shape[0]
# residuals = sim[:,1] - reference_data
self.r.reset()
self.r.resetAll()
# r.resetToOrigin()
self.setParameterVector(param_values, exponential=False)
s = self.r.simulate(0, 25., 100, ['time', quantity_id])
import tellurium as te
# te.plot(sim[:,0], reference_data, scatter=True,
# name=quantity_id+' data', show=False,
# title=quantity_id,
# error_y_pos=maximum(residuals,0),
# error_y_neg=-minimum(residuals,0))
print(quantity_id + ' sim')
te.plot(s[:, 0], s[:, 1], name=quantity_id + ' sim')
def getParameterValue(self, param_index):
from params import param_index_to_name_map
try:
return self.r[param_index_to_name_map[param_index]]
except KeyError:
raise KeyError(
'No such parameter for index {}, must be 0-1758 inclusive'.
format(param_index))
class TimecourseModel(Evaluator):
''' Class that performs a timecourse simulation
and calculates the residuals for b4.'''
def __init__(self, sbml, data_quantities, measurement_map):
'''
Constructor.
:param measurement_map: A dictionary that maps the names of quantities to measurements to their respective (numpy) arrays.
'''
self.sbml = sbml
self.r = RoadRunner(sbml)
self.residuals = []
#print(self.r.getFloatingSpeciesIds())
self.timepoints = unique(hstack(a[:, 0] for a in data_quantities))
self.reset()
self.measurement_map = measurement_map
# keep track of the number of times a measurement is used
# (check correct number of residuals)
self.measurement_count = OrderedDict(
(quantity, 0) for quantity in self.measurement_map)
self.quantity_residuals = dict(
(quantity, list()) for quantity in self.measurement_map)
def calcResiduals(self, t):
''' Try to calculate residuals at the current time t
and add them to self.residuals.
If they do not exist for certain datasets at time t,
just pass over the dataset.'''
self.usage_map = dict((q, False) for q in self.measurement_map)
for quantity in self.measurement_map.keys():
self.tryAddResidual(t, self.r[quantity], quantity)
def tryAddResidual(self, t, predicted_value, identifier):
''' Append a residual to the list of residuals.
Call with a single value from a simulation and pass
array of measurements for that quantity.
If there is no measurement at this time point (t), do nothing.'''
a = self.measurement_map[identifier]
try:
# if there is a measurement a this timepoint, append to list
r = predicted_value - valueAtTime(a, t)
self.residuals.append(r)
self.quantity_residuals[identifier].append(r)
# increment the residual use count (check all measurements are used exactly once)
self.measurement_count[identifier] += 1
self.usage_map[identifier] = True
except MissingValue:
# no measurement at this timepoint, do nothing
return
def plotQuantity(self, identifier, bars=True):
''' Plot a simulated quantity vs its data points using Tellurium.
The residuals should already be calculated.'''
data = self.measurement_map[identifier]
# data contains one column of time and one column of values
import tellurium as te
te.plot(data[:, 0],
data[:, 1],
scatter=True,
name=identifier + ' data',
show=False,
error_y_pos=maximum(array(self.quantity_residuals[identifier]),
0),
error_y_neg=-minimum(
array(self.quantity_residuals[identifier]), 0))
# simulate and plot the model
r = RoadRunner(self.sbml)
s = r.simulate(0, self.timepoints[-1], 1000, ['time', identifier])
te.plot(s[:, 0], s[:, 1], name=identifier + ' sim')
def MSE(self):
''' Calc the MSE for all residuals.
Call this after calculating all residuals.'''
r = array(self.residuals)
return (r**2).mean()
def simulateToNextTime(self):
t_begin = self.t
t_end = self.timepoints[self.next_ti]
delta = t_end - t_begin
stepsize = 0.1
steps = int(max(100, delta / stepsize))
self.r.simulate(t_begin, t_end, steps)
return t_end
def reset(self):
self.r.resetAll()
self.t = self.timepoints[0]
# next time index
self.next_ti = 0
def buildResidualList(self):
# simulate to the first timepoint (not necessarily zero)
delta = self.timepoints[0]
stepsize = 0.1
steps = int(max(100, delta / stepsize))
self.r.simulate(0, delta, steps)
self.next_ti = 1
if len(self.timepoints) < 2:
raise RuntimeError('Expected at least two timepoints')
# calculate the residuals
self.calcResiduals(self.t)
# simulate to the rest of the timepoints
while self.next_ti < self.timepoints.shape[0]:
self.t = self.simulateToNextTime()
self.calcResiduals(self.t)
self.next_ti += 1
def setParameterVector(self, x, param_list):
# type: (array, List) -> None
# TODO: sample in log space
expect(
len(x) == len(param_list),
'Wrong length for parameter vector - expected {} but got {}'.
format(len(param_list), len(x)))
for i, v in enumerate(x):
self.r[param_list[i]] = v
def evaluate(self, x):
# type: (array) -> SupportsFloat
"""
Evaluate and return the objective function.
"""
self.reset()
self.setParameterVector(x)
try:
self.buildResidualList()
except RuntimeError:
# if convergence fails, use a penalty score
return 1e9
return self.MSE()
def getUsageByQuantity(self):
'''
Calculates the number of times a given quantity is used.
Should be equal to the number of datap oints for that quantity
if all goes well.
'''
total = 0
total_used = 0
usage_for_quantity = OrderedDict()
for q in self.measurement_count:
a = self.measurement_map[q]
used = self.measurement_count[q]
usage_for_quantity[q] = used
n = a.shape[0]
total += n
total_used += used
return (total, total_used, usage_for_quantity)
def printDatapointUsage(self):
''' For debugging. Make sure every data point is
used.'''
total, total_used, usage_for_quantity = self.getUsageByQuantity()
for q, used in usage_for_quantity.keys():
a = self.measurement_map[q]
n = a.shape[0]
print('Usage for {}: {}/{}'.format(q, used, n))
print('*** Total usage: {}/{} ({:.1f}%)'.format(
total_used, total, 100. * total_used / total))
class TimecourseSimIrreg(TimecourseSimBase):
''' Performs a timecourse simulation on an irregular grid.'''
def __init__(self, sbml, data_quantities, measurement_map):
'''
Constructor.
:param measurement_map: A dictionary that maps the names of quantities to measurements to their respective (numpy) arrays.
'''
self.sbml = sbml
self.r = RoadRunner(sbml)
# self.r.integrator.stiff = False
# self.r.integrator.minimum_time_step = 0.0001
# self.r.integrator.maximum_time_step = 1.
# self.residuals = []
#print(self.r.getFloatingSpeciesIds())
self.timepoints = unique(hstack(a[:, 0] for a in data_quantities))
self.reset()
self.measurement_map = measurement_map
# map a quantity to its mean measured value
self.mean_measurement_map = {
quantity: mean(values[:, 1])
for quantity, values in self.measurement_map.items()
}
# keep track of the number of times a measurement is used
# (check correct number of residuals)
self.measurement_count = OrderedDict(
(quantity, 0) for quantity in self.measurement_map)
self.penalty_scale = 1.
def plotQuantity(self, identifier, param_values, bars=True):
''' Plot a simulated quantity vs its data points using Tellurium.
The residuals should already be calculated.'''
data = self.measurement_map[identifier]
# data contains one column of time and one column of values
import tellurium as te
te.plot(data[:, 0],
data[:, 1],
scatter=True,
name=identifier + ' data',
show=False,
error_y_pos=maximum(array(self.quantity_residuals[identifier]),
0),
error_y_neg=-minimum(
array(self.quantity_residuals[identifier]), 0))
# simulate and plot the model
r = RoadRunner(self.sbml)
if param_values is not None:
self._setParameterVector(param_values, self.param_list, r)
s = r.simulate(0, self.timepoints[-1], 1000, ['time', identifier])
te.plot(s[:, 0], s[:, 1], name=identifier + ' sim')
def calcResiduals(self, t):
''' Try to calculate residuals at the current time t
and add them to self.residuals.
If they do not exist for certain datasets at time t,
just pass over the dataset.'''
self.usage_map = dict((q, False) for q in self.measurement_map)
for quantity in self.measurement_map.keys():
self.tryAddResidual(t, self.r[quantity], quantity)
def tryAddResidual(self, t, predicted_value, identifier):
''' Append a residual to the list of residuals.
Call with a single value from a simulation and pass
array of measurements for that quantity.
If there is no measurement at this time point (t), do nothing.'''
a = self.measurement_map[identifier]
try:
# if there is a measurement a this timepoint, append to list
r = predicted_value - valueAtTime(a, t)
# self.residuals.append(r)
self.quantity_residuals[identifier].append(r)
# increment the residual use count (check all measurements are used exactly once)
self.measurement_count[identifier] += 1
self.usage_map[identifier] = True
except MissingValue:
# no measurement at this timepoint, do nothing
return
def simulateToNextTime(self):
t_begin = self.t
t_end = self.timepoints[self.next_ti]
delta = t_end - t_begin
stepsize = 0.1
steps = int(max(100, delta / stepsize))
self.r.simulate(t_begin, t_end, steps)
return t_end
def reset(self):
self.r.resetAll()
self.t = self.timepoints[0]
# next time index
self.next_ti = 0
def buildResidualList(self):
# simulate to the first timepoint (not necessarily zero)
delta = self.timepoints[0]
stepsize = 0.1
steps = int(max(100, delta / stepsize))
self.r.simulate(0, delta, steps)
if self.divergent():
raise RuntimeError('Diverged at first time step')
self.next_ti = 1
if len(self.timepoints) < 2:
raise RuntimeError('Expected at least two timepoints')
# calculate the residuals
self.calcResiduals(self.t)
# simulate to the rest of the timepoints
while self.next_ti < self.timepoints.shape[0]:
self.t = self.simulateToNextTime()
if self.divergent():
raise RuntimeError('Diverged at time step {}'.format(
self.next_ti))
self.calcResiduals(self.t)
self.next_ti += 1
def evaluate(self, x):
# type: (array) -> SupportsFloat
"""
Evaluate and return the objective function.
"""
from interruptingcow import timeout
self.reset()
self.setParameterVector(x)
self.quantity_residuals = dict(
(quantity, list()) for quantity in self.measurement_map)
def worker():
self.buildResidualList()
if self.divergent():
return 1e9 * self.penalty_scale
try:
with timeout(10, StalledSimulation):
worker()
except (RuntimeError, StalledSimulation):
# if convergence fails, use a penalty score
return 1e9 * self.penalty_scale
print('evaluate')
# for quantity,residuals in self.quantity_residuals.items():
# print(quantity,mean(array(residuals)**2.),self.mean_measurement_map[quantity])
return sqrt(mean(array([
mean(array(residuals)**2.)/self.mean_measurement_map[quantity]**2. \
for quantity,residuals in self.quantity_residuals.items() \
])))
def getUsageByQuantity(self):
'''
Calculates the number of times a given quantity is used.
Should be equal to the number of datap oints for that quantity
if all goes well.
'''
total = 0
total_used = 0
usage_for_quantity = OrderedDict()
for q in self.measurement_count:
a = self.measurement_map[q]
used = self.measurement_count[q]
usage_for_quantity[q] = used
n = a.shape[0]
total += n
total_used += used
return (total, total_used, usage_for_quantity)
def printDatapointUsage(self):
''' For debugging. Make sure every data point is
used.'''
total, total_used, usage_for_quantity = self.getUsageByQuantity()
for q, used in usage_for_quantity.keys():
a = self.measurement_map[q]
n = a.shape[0]
print('Usage for {}: {}/{}'.format(q, used, n))
print('*** Total usage: {}/{} ({:.1f}%)'.format(
total_used, total, 100. * total_used / total))
def RMSE_quantity(self, identifier):
''' Calc the RMSE of a quantity.'''
from math import sqrt
return sqrt(
float((array(self.quantity_residuals[identifier])**
2).mean())) / self.mean_measurement_map[identifier]