Which version of VAMPNets is there?

deeptime-ml / deeptime

Python library for analysis of time series data including dimensionality reduction, clustering, and Markov model estimation

https://deeptime-ml.github.io/

GNU Lesser General Public License v3.0

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Which version of VAMPNets is there? #282

Open palominohernandez opened 1 year ago

palominohernandez commented 1 year ago

Dear all,

I was having a look at the code for VampNets that is in deeptime, and it seems that it is the one from mardt2018vampnets, right? Thus, it does not implement the reversibility and stochasticity constraints from _Deep_revmsm, right? I just wanted to know if I am right.

Thanks a lot!

clonker commented 1 year ago

Hi, that's correct! Currently deeptime only contains native VAMP. It's probably pretty easy to implement a symmetrized version to enforce reversibility (same as for TICA), stochasticity constraints as in deep MSM and deep rev MSM are a bit more involved. An intermediate would be training a VAMPNet lobe and use that as feature function before applying TICA - potentially stacked with other (derived from eg intuition) feature functions.