msmbuilder

msmbuilder copied to clipboard

RMSD clustering segfault?

4

@jchodera reports on pyemma issue that they want to do rmsd clustering but: > @maxentile can't actually cluster our data with MSMBuilder without it throwing a segfault Can you provide...

mpharrigan

PCCA+ doesn't work with continuous MSMs

1

Where `msm_mdl` is a continuous time MSM, upon running `pcca = PCCAPlus.from_msm(msm_mdl, 3)`, I get: ``` TypeError Traceback (most recent call last) in () 1 from msmbuilder.lumping import PCCAPlus ---->...

brookehus

Might speed up our workflow for larger datasets: http://arxiv.org/pdf/1502.03167v3.pdf

cxhernandez

Add Feature Selection Algorithms

2

We can start by: - [x] porting from [sklearn](http://scikit-learn.org/stable/modules/feature_selection.html) - [ ] adding a few from [this resource](http://featureselection.asu.edu/algorithms.php) (esp the decision tree-based approaches) - [ ] implementing [Gradient Boosted Feature...

cxhernandez

GaussianFusionHMM.draw_samples

1

`GaussianFusionHMM.draw_samples()` does not return `sample_features` as advertised by the docstring

mpharrigan

PCCA from command line

1

1. The lumping code is missing from the command line API. We should add this feature. 2. We should also add a lumping example to the docs. 3. What about...

rmcgibbo

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....

msultan

This could help out with larger datasets?

cxhernandez

[ENH] Calculating uncertainty in MFPT

6

Could probably be useful.

cxhernandez

cc msmbuilder-user mailing list

mpharrigan