deeptime.markov.tools.analysis.pcca_memberships

deeptime.markov.tools.analysis.pcca_memberships(T, m)

Compute meta-stable sets using PCCA++. [1] Returns the membership of all states to these sets.

Parameters:

• T ((n, n) ndarray or scipy.sparse matrix) – Transition matrix

• m (int) – Number of metastable sets

Returns:

clusters – Membership vectors. clusters[i, j] contains the membership of state i to metastable state j

Return type:

(n, m) ndarray

Notes

Perron cluster center analysis assigns each microstate a vector of membership probabilities. This assignement is performed using the right eigenvectors of the transition matrix. Membership probabilities are computed via numerical optimization of the entries of a membership matrix.

References

[1]

Susanna Röblitz and Marcus Weber. Fuzzy spectral clustering by pcca+: application to markov state models and data classification. Advances in Data Analysis and Classification, 7(2):147–179, 2013.