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]])