[estimation] some corrections and improvements for the rate matrix estimator

markovmodel / msmtools

Tools for estimating and analyzing Markov state models

GNU Lesser General Public License v3.0

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Closed fabian-paul closed 7 years ago

fabian-paul commented 7 years ago

implemented missing initialization of rate matrix estimator from user-specified guess.
Added regularization hack for the gradient of the KL algorithm as described in McGibbon et al 10.1063/1.4926516 (seems to work better than not doing anything)
maxiter isn't applied anymore to internal transition matrix estimations. (This caused more harm than good.)

franknoe commented 7 years ago

Thank you!