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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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mfpt uncertainty #1532

Closed ccccclw closed 2 years ago

ccccclw commented 2 years ago

Hi, is there any api for getting the uncertainty of mean first passage time between two states? Thanks!

thempel commented 2 years ago

Yes, you can estimate a Bayesian MSM and get the posterior distribution of the MFPT between chosen sets of states. E.g.

bayesian_msm.sample_f('mfpt', list_of_states_A, list_of_states_B)

There's an example here: https://github.com/markovmodel/pyemma_tutorials/blob/master/notebooks/05-pcca-tpt.ipynb

ccccclw commented 2 years ago

Thank you!