deeptime.markov.tools.estimation.prior_neighbor

deeptime.markov.tools.estimation.prior_neighbor(C, alpha=0.001)

Neighbor prior for the given count matrix.

Parameters:

• C ((M, M) ndarray or scipy.sparse matrix) – Count matrix

• alpha (float (optional)) – Value of prior counts

Returns:

B – Prior count matrix

Return type:

(M, M) ndarray or scipy.sparse matrix

Notes

The neighbor prior $b_{ij}$ is defined as

$$b_{ij}=\left \{ \begin{array}{rl} \alpha & c_{ij}+c_{ji}>0 \\ 0 & \text{else} \end{array} \right .$$

Examples

>>> import numpy as np
>>> from deeptime.markov.tools.estimation import prior_neighbor

>>> C = np.array([[10, 1, 0], [2, 0, 3], [0, 1, 4]])
>>> B = prior_neighbor(C)
>>> B
array([[0.001, 0.001, 0.   ],
       [0.001, 0.   , 0.001],
       [0.   , 0.001, 0.001]])