# Source code for cobra.sampling.optgp

```
# -*- coding: utf-8 -*-
"""Provide OptGP sampler."""
from __future__ import absolute_import, division
from multiprocessing import Pool
import numpy as np
import pandas
from cobra.core.configuration import Configuration
from cobra.sampling.hr_sampler import HRSampler, shared_np_array, step
__all__ = ("OptGPSampler",)
CONFIGURATION = Configuration()
def mp_init(obj):
"""Initialize the multiprocessing pool."""
global sampler
sampler = obj
# Unfortunately this has to be outside the class to be usable with
# multiprocessing :()
def _sample_chain(args):
"""Sample a single chain for OptGPSampler.
center and n_samples are updated locally and forgotten afterwards.
"""
n, idx = args # has to be this way to work in Python 2.7
center = sampler.center
np.random.seed((sampler._seed + idx) % np.iinfo(np.int32).max)
pi = np.random.randint(sampler.n_warmup)
prev = sampler.warmup[pi, :]
prev = step(sampler, center, prev - center, 0.95)
n_samples = max(sampler.n_samples, 1)
samples = np.zeros((n, center.shape[0]))
for i in range(1, sampler.thinning * n + 1):
pi = np.random.randint(sampler.n_warmup)
delta = sampler.warmup[pi, :] - center
prev = step(sampler, prev, delta)
if sampler.problem.homogeneous and (
n_samples * sampler.thinning % sampler.nproj == 0
):
prev = sampler._reproject(prev)
center = sampler._reproject(center)
if i % sampler.thinning == 0:
samples[i // sampler.thinning - 1, :] = prev
center = (n_samples * center) / (n_samples + 1) + prev / (n_samples + 1)
n_samples += 1
return (sampler.retries, samples)
[docs]class OptGPSampler(HRSampler):
"""A parallel optimized sampler.
A parallel sampler with fast convergence and parallel execution. See [1]_
for details.
Parameters
----------
model : cobra.Model
The cobra model from which to generate samples.
processes: int, optional (default Configuration.processes)
The number of processes used during sampling.
thinning : int, optional
The thinning factor of the generated sampling chain. A thinning of 10
means samples are returned every 10 steps.
nproj : int > 0, optional
How often to reproject the sampling point into the feasibility space.
Avoids numerical issues at the cost of lower sampling. If you observe
many equality constraint violations with `sampler.validate` you should
lower this number.
seed : int > 0, optional
Sets the random number seed. Initialized to the current time stamp if
None.
Attributes
----------
model : cobra.Model
The cobra model from which the samples get generated.
thinning : int
The currently used thinning factor.
n_samples : int
The total number of samples that have been generated by this
sampler instance.
problem : collections.namedtuple
A python object whose attributes define the entire sampling problem in
matrix form. See docstring of `Problem`.
warmup : numpy.matrix
A matrix of with as many columns as reactions in the model and more
than 3 rows containing a warmup sample in each row. None if no warmup
points have been generated yet.
retries : int
The overall of sampling retries the sampler has observed. Larger
values indicate numerical instabilities.
seed : int > 0, optional
Sets the random number seed. Initialized to the current time stamp if
None.
nproj : int
How often to reproject the sampling point into the feasibility space.
fwd_idx : numpy.array
Has one entry for each reaction in the model containing the index of
the respective forward variable.
rev_idx : numpy.array
Has one entry for each reaction in the model containing the index of
the respective reverse variable.
prev : numpy.array
The current/last flux sample generated.
center : numpy.array
The center of the sampling space as estimated by the mean of all
previously generated samples.
Notes
-----
The sampler is very similar to artificial centering where each process
samples its own chain. Initial points are chosen randomly from the warmup
points followed by a linear transformation that pulls the points a little
bit towards the center of the sampling space.
If the number of processes used is larger than the one requested,
number of samples is adjusted to the smallest multiple of the number of
processes larger than the requested sample number. For instance, if you
have 3 processes and request 8 samples you will receive 9.
Memory usage is roughly in the order of (2 * number reactions)^2
due to the required nullspace matrices and warmup points. So large
models easily take up a few GB of RAM. However, most of the large matrices
are kept in shared memory. So the RAM usage is independent of the number
of processes.
References
----------
.. [1] Megchelenbrink W, Huynen M, Marchiori E (2014)
optGpSampler: An Improved Tool for Uniformly Sampling the Solution-Space
of Genome-Scale Metabolic Networks.
PLoS ONE 9(2): e86587.
https://doi.org/10.1371/journal.pone.0086587
"""
def __init__(self, model, processes=None, thinning=100, nproj=None, seed=None):
"""Initialize a new OptGPSampler."""
super(OptGPSampler, self).__init__(model, thinning, seed=seed)
self.generate_fva_warmup()
if processes is None:
self.processes = CONFIGURATION.processes
else:
self.processes = processes
# This maps our saved center into shared memory,
# meaning they are synchronized across processes
self.center = shared_np_array(
(len(self.model.variables),), self.warmup.mean(axis=0)
)
[docs] def sample(self, n, fluxes=True):
"""Generate a set of samples.
This is the basic sampling function for all hit-and-run samplers.
Parameters
----------
n : int
The minimum number of samples that are generated at once
(see Notes).
fluxes : boolean
Whether to return fluxes or the internal solver variables. If set
to False will return a variable for each forward and backward flux
as well as all additional variables you might have defined in the
model.
Returns
-------
numpy.matrix
Returns a matrix with `n` rows, each containing a flux sample.
Notes
-----
Performance of this function linearly depends on the number
of reactions in your model and the thinning factor.
If the number of processes is larger than one, computation is split
across as the CPUs of your machine. This may shorten computation time.
However, there is also overhead in setting up parallel computation so
we recommend to calculate large numbers of samples at once
(`n` > 1000).
"""
if self.processes > 1:
n_process = np.ceil(n / self.processes).astype(int)
n = n_process * self.processes
# The cast to list is weird but not doing it gives recursion
# limit errors, something weird going on with multiprocessing
args = list(zip([n_process] * self.processes, range(self.processes)))
# No with statement or starmap here since Python 2.x
# does not support it :(
mp = Pool(self.processes, initializer=mp_init, initargs=(self,))
results = mp.map(_sample_chain, args, chunksize=1)
mp.close()
mp.join()
chains = np.vstack([r[1] for r in results])
self.retries += sum(r[0] for r in results)
else:
mp_init(self)
results = _sample_chain((n, 0))
chains = results[1]
# Update the global center
self.center = (self.n_samples * self.center + np.atleast_2d(chains).sum(0)) / (
self.n_samples + n
)
self.n_samples += n
if fluxes:
names = [r.id for r in self.model.reactions]
return pandas.DataFrame(
chains[:, self.fwd_idx] - chains[:, self.rev_idx],
columns=names,
)
else:
names = [v.name for v in self.model.variables]
return pandas.DataFrame(chains, columns=names)
# Models can be large so don't pass them around during multiprocessing
[docs] def __getstate__(self):
"""Return the object for serialization."""
d = dict(self.__dict__)
del d["model"]
return d
```