x3cflux.HopsyModel

class x3cflux.HopsyModel(simulator)

Bases: object

Wrapper to pass ILE sampling problem to hopsy.

Methods

log_curvature(x)

Compute the expected Fisher information.

log_density(x)

Compute the log likelihood up to a constant.

log_gradient(x)

Compute the gradient of the log likelihood.

log_density(x)

Compute the log likelihood up to a constant.

This is equal to

\[-\frac{1}{2} SSR(\boldsymbol \theta)\]
Parameters:

x (numpy.ndarray) – Metabolic parameters.

Returns:

Log-likelihood value.

Return type:

float

log_gradient(x)

Compute the gradient of the log likelihood.

This is equal to

\[\frac{\partial}{\partial \boldsymbol \theta} \left(-\frac{1}{2} SSR(\boldsymbol \theta)\right)\]
Parameters:

x (numpy.ndarray) – Metabolic parameters.

Returns:

Log-likelihood gradient.

Return type:

numpy.ndarray

log_curvature(x)

Compute the expected Fisher information.

This is the second moment of the score and is equal to the linearized local Hessian of the SSR.

Parameters:

x (numpy.ndarray) – Metabolic parameters.

Returns:

Local Fisher information matrix.

Return type:

numpy.ndarray