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The stored pseudoeigenvalues in SparseTICA are different from those computed for GMRQ scores, so `stica.score_ != stica.score(X_train)`. I think this is because `stica.eigenvalues_` [are computed using deflated versions of the...

maxentile

Spectral Clustering error

8

Hello, When using SpectralClustering to cluster my data I'm running into an error. Other clusterers seem to work fine. The error is: ``` --------------------------------------------------------------------------- AttributeError Traceback (most recent call last)...

driesvr

could be interesting to add this to msmb: https://github.com/idiap/eakmeans

cxhernandez

msm.core._transition_counts large memory usage

4

Hi, I have a large dataset and when I tried to fit my data, I was running into MemoryErrors when building the transition counts matrix. When I looked in the...

ryjin

see https://en.wikipedia.org/wiki/Robust_measures_of_scale#IQR_and_MAD We can make this an online algorithm fairly easily as shown in this [post](http://stackoverflow.com/questions/1058813/on-line-iterator-algorithms-for-estimating-statistical-median-mode-skewnes)

cxhernandez

Pledge to drop support for python 2

21

http://python3statement.github.io/ We should sign this pledge!

mpharrigan

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...

msultan

Transition towards using Pandas DataFrames?

2

I wanted to gauge what the pros and cons are for using `pandas.DataFrame` objects as attributes rather than `numpy.ndarrays`. Personally, I think the switch would be useful to keep track...

cxhernandez

Use canonical links for docs

2

https://en.wikipedia.org/wiki/Canonical_link_element In addition to `msmbuilder.org/3.5/msm.html` have `msmbuilder.org/latest/msm.html` and use the canonical tag to point to that one

mpharrigan

[WIP] Add SymmetryRMSDFeaturizer

4

- [x] Implement feature / fix bug - [x] Add tests - [ ] Update changelog For homo-multi-mers, there's rotational or permutational symmetry. This featurizer takes the minimum distance from...

mpharrigan