msmbuilder.msm.MarkovStateModel.score

MarkovStateModel.score(sequences, y=None)

Score the model on new data using the generalized matrix Rayleigh quotient

Parameters:

sequences : list of array-like

List of sequences, or a single sequence. Each sequence should be a 1D iterable of state labels. Labels can be integers, strings, or other orderable objects.

Returns:

gmrq : float

Generalized matrix Rayleigh quotient. This number indicates how well the top n_timescales+1 eigenvectors of this MSM perform as slowly decorrelating collective variables for the new data in sequences.

References

[R25]

McGibbon, R. T. and V. S. Pande, “Variational cross-validation of slow dynamical modes in molecular kinetics” J. Chem. Phys. 142, 124105 (2015)