Carlos Hernández

Wanna make this a "project"?

https://github.com/msmbuilder/msmbuilder/projects

> When would the column names have value? If you have ergodic trimming, you can keep the original cluster labels rather than having to do extra state mapping. > How...

Hey @MTZimmer, I noticed you're using Python 2.7. Is that necessary for your workflow? If not, it might be worth upgrading to Python 3.4+.

> Note that the MSMBuilder tutorial does not state that it requires py3.4+; consider adding a note about it. Good point! > Should this be concerning, or would you attribute...

cc @peastman

lol I didn't even get a chance to look at Chapter 11....

Your math for the rate matrix case LGTM. As far as bootstrapping goes, I would be inclined to choose bootstrapping over discretized trajectories, since that's already how I'd be calculating...

> i wonder if we need to push all the features through a Normalizer before we can use some of these algorithms. We should be careful about that. The variance...

updated for pymc3: http://pymc-devs.github.io/pymc3/api/diagnostics.html