17.1.1.6.1.1. cobra.sampling.achr

Provide the ACHR sampler class.

17.1.1.6.1.1.1. Module Contents

17.1.1.6.1.1.1.1. Classes

ACHRSampler

Artificial Centering Hit-and-Run sampler.

class cobra.sampling.achr.ACHRSampler(model: Model, thinning: int = 100, nproj: Optional[int] = None, seed: Optional[int] = None, **kwargs)

Bases: cobra.sampling.hr_sampler.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).

n_samples

The total number of samples that have been generated by this sampler instance.

Type

int

problem

A NamedTuple whose attributes define the entire sampling problem in matrix form.

Type

typing.NamedTuple

warmup

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.

Type

numpy.matrix

retries

The overall of sampling retries the sampler has observed. Larger values indicate numerical instabilities.

Type

int

fwd_idx

A numpy array having one entry for each reaction in the model, containing the index of the respective forward variable.

Type

numpy.array

rev_idx

A numpy array having one entry for each reaction in the model, containing the index of the respective reverse variable.

Type

numpy.array

prev

The current/last flux sample generated.

Type

numpy.array

center

The center of the sampling space as estimated by the mean of all previously generated samples.

Type

numpy.array

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

__single_iteration(self) → None

Run a single iteration of the sampling.

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

Returns a pandas DataFrame with n rows, each containing a flux sample.

Return type

pandas.DataFrame

Notes

Performance of this function linearly depends on the number of reactions in your model and the thinning factor.