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markovmodel / PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂
http://pyemma.org
GNU Lesser General Public License v3.0
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Unclear documentation for attribute active_state_indexes of pyemma.msm.MaximumLikelihoodMSM #1473

Closed pl992 closed 4 years ago

pl992 commented 4 years ago

The output is a list of 2D-arrays where is unclear what the second column represents. My guess is that the first column are the cluster indices but I'm not entirely sure. Moreover the core_set attribute doesn't return anything... this has been tested also with your notebooks for tutorials (like 03-msm-estimation-validation)

clonker commented 4 years ago

For each state, active_state_indexes contains all trajectory and time indexes where this state occurs. Each matrix has a number of rows equal to the number of occurrences of the corresponding state, with rows consisting of a tuple (i, t), where i is the index of the trajectory and t is the time index within the trajectory.

core_set is only relevant if you are using milestoning.