# Source code for cobra.sampling.achr

```
"""Provide the ACHR sampler class."""
from typing import TYPE_CHECKING, Optional
import numpy as np
import pandas as pd
from .hr_sampler import HRSampler, step
if TYPE_CHECKING:
from cobra import Model
[docs]class ACHRSampler(HRSampler):
"""
Artificial Centering Hit-and-Run sampler.
A sampler with low memory footprint and good convergence.
Parameters
----------
model : cobra.Model
The cobra model from which to generate samples.
thinning : int, optional
The thinning factor of the generated sampling chain. A thinning of
10 means samples are returned every 10 steps (default 100).
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 (default None).
seed : int > 0, optional
Sets the random number seed. Initialized to the current time stamp
if None (default None).
Attributes
----------
n_samples : int
The total number of samples that have been generated by this
sampler instance.
problem : typing.NamedTuple
A NamedTuple whose attributes define the entire sampling problem in
matrix form.
warmup : numpy.matrix
A numpy matrix 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.
fwd_idx : numpy.array
A numpy array having one entry for each reaction in the model,
containing the index of the respective forward variable.
rev_idx : numpy.array
A numpy array having 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
-----
ACHR generates samples by choosing new directions from the sampling
space's center and the warmup points. The implementation used here is
the same as in the MATLAB COBRA Toolbox [2]_ and uses only the initial
warmup points to generate new directions and not any other previous
iterations. This usually gives better mixing, since the startup points
are chosen to span the space in a wide manner. This also makes the
generated sampling chain quasi-Markovian since the center converges
rapidly.
Memory usage is roughly in the order of (2 * number of reactions) ^ 2
due to the required nullspace matrices and warmup points. So, large
models easily take up a few GBs of RAM.
References
----------
.. [1] Direction Choice for Accelerated Convergence in Hit-and-Run Sampling
David E. Kaufman, Robert L. Smith
Operations Research 199846:1 , 84-95
https://doi.org/10.1287/opre.46.1.84
.. [2] https://github.com/opencobra/cobratoolbox
"""
def __init__(
self,
model: "Model",
thinning: int = 100,
nproj: Optional[int] = None,
seed: Optional[int] = None,
**kwargs
) -> None:
"""Initialize a new ACHRSampler."""
super().__init__(model, thinning, nproj=nproj, seed=seed, **kwargs)
self.generate_fva_warmup()
self.prev = self.center = self.warmup.mean(axis=0)
np.random.seed(self._seed)
[docs] def __single_iteration(self) -> None:
"""Run a single iteration of the sampling."""
pi = np.random.randint(self.n_warmup)
# mix in the original warmup points to not get stuck
delta = self.warmup[pi, :] - self.center
self.prev = step(self, self.prev, delta)
if self.problem.homogeneous and (
self.n_samples * self.thinning % self.nproj == 0
):
self.prev = self._reproject(self.prev)
self.center = self._reproject(self.center)
self.center = (self.n_samples * self.center) / (
self.n_samples + 1
) + self.prev / (self.n_samples + 1)
self.n_samples += 1
[docs] def sample(self, n: int, fluxes: bool = True) -> pd.DataFrame:
"""Generate a set of samples.
This is the basic sampling function for all hit-and-run samplers.
Parameters
----------
n : int
The number of samples that are generated at once.
fluxes : bool, optional
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 (default True).
Returns
-------
pandas.DataFrame
Returns a pandas DataFrame 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.
"""
samples = np.zeros((n, self.warmup.shape[1]))
for i in range(1, self.thinning * n + 1):
self.__single_iteration()
if i % self.thinning == 0:
samples[i // self.thinning - 1, :] = self.prev
if fluxes:
names = [r.id for r in self.model.reactions]
return pd.DataFrame(
samples[:, self.fwd_idx] - samples[:, self.rev_idx],
columns=names,
)
else:
names = [v.name for v in self.model.variables]
return pd.DataFrame(samples, columns=names)
```