msmbuilder

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- This function is slow. See https://mailman.stanford.edu/pipermail/msmbuilder-user/2015-April/000070.html - For many trajectory formats like `xtc`, `seek` is not an O(1) operation, so repeatedly calling `load_frame()` to load a single frame (random...

rmcgibbo

Reorganize _ratematrix.sigma_X to not require matrix inverse

1

It should be possible to reorganize the loops in `sigma_timescales`, `sigma_K`, and `sigma_K` to use the cholesky of the hessian instead of its inverse. For sigma_pi, it's pretty obvious, since...

rmcgibbo

[ENH] Speed up calculation of MSM count matrix

6

@mpharrigan: you mentioned at lunch that you thought calculating the count matrix from the sequences was slow. Do you have any benchmarks / timing on that. If so, I can...

rmcgibbo

See https://github.com/rmcgibbo/mixtape/pull/149#issuecomment-43017061

rmcgibbo

- BFGS optimization over the lagrange multipliers on the constraints. Not clear that it can be hot-started any better. - Stochastic gradient descent? - Profile the performance of the objective...

rmcgibbo

Desired GMRQ behavior when scoring discrete trajectories?

8

Hi! If I ask a `MarkovStateModel` to score discrete trajectories that never enter its largest strongly connected component, MSMBuilder raises an error instead of returning `0`. ``` python import numpy...

maxentile

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...

msultan

tICA plot command?

1

Might be useful to make a command for making scatter plots of transformed coordinates that are in a vector space. We have a example notebook like http://msmbuilder.org/latest/examples/plot-tica-heatmap.html, but it would...

rmcgibbo

I found [this](https://github.com/fkling/JSNetworkX) awesome javascript port of NetworkX. Maybe we can implement a webview of networks generated by mixtape?

cxhernandez

[FR] Minimum traj length in ConvertChunkedProject

1

So back in the day, ConvertDataToHDF had the ability to specify the minimum number of frames you wanted in a trajectory. That doesn't appear to be an option in msmb...

sryckbos