relative entropy between two MSM matrices

markovmodel / PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂

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relative entropy between two MSM matrices #1367

Open euhruska opened 5 years ago

euhruska commented 5 years ago

feature request: calculation of the relative entropy between two MSM matrices of the same protein, like in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637129/

marscher commented 5 years ago

Do you need to have the same discretization for both matrices or does the method recover for slightly different state spaces?

euhruska commented 5 years ago

It will show a much higher relative entropy, but yes it will work. Just needs the same number of microstates. The easiest is to let the user specify which two MSM count matrices to compare. The reason to specify the count matrix instead of the transition matrix is the 1/N addition step.