msultan

Default learning rate and other hyper params.

1

Based upon some testing, I am starting to think that the default learning rate of 1e-4 is probably too low for our applications and might be better to bump it...

retire the msmbuilder email list?

2

How do the @msmbuilder/developers feel about retiring the email list? I think the github issue tracker is probably a better way since the issues are indexed by google and easier...

Multisequence support

9

I think having ability to juggle multiple sequences within msmbuilder would be awesome. I have been writing some code to that effect in one of my [repos](https://github.com/msultan/kinase_msm) though it would...

Better error detections in trajectories

7

So this is based off my experiences earlier today working with a large dataset. Basically, I was trying to run tICA on a set of contacts and kept getting e-15...

Trajectory finder module.

2

One of the things that i have been struggling with in everyday work is identifying cross over trajectories that go from one region of phase space to another. Ideally i...

implement MAP estimate for the bayesian models.

1

We need to be able to get the MAP estimate from the set of models being sampled from posteriors by all the Bayesian models to make the analysis somewhat tractable....

It would be nice to get a Transfomer class with the capability to parallelize over the input set of seq. Ideally it should be capable of parallelizing over ipython cluster...

It would be nice to be able to limit the template crystallographic resolution when making models for a particular target.