msmbuilder.MSMLib.estimate_rate_matrix¶

msmbuilder.MSMLib.estimate_rate_matrix(count_matrix, assignments)[source]¶

MLE Rate Matrix given transition counts and dwell times

Parameters:

count_matrix : sparse or dense matrix

transition counts

assignments : ndarray

2D assignments array used to compute average dwell times

Returns:

K : csr_matrix

Rate matrix

See also

estimate_transition_matrix

Notes

The correct likelihood function to use for estimating the rate matrix when the data is sampled at a discrete frequency is open for debate. This likelihood function doesn’t take into account the error in the lifetime estimates from the discrete sampling. Other methods are currently under development (RTM 6/27)

References

[R5]	Buchete NV, Hummer G. “Coarse master equaions for peptide folding dynamics.” J Phys Chem B 112:6057-6069.