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to reduce time necessary for TICA:
1) try calculating covariances on each node in parallel and the on one node calculate the TICA
https://github.com/markovmodel/PyEMMA/issues/1351
2) alternative:…
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Hi, I was going through DeepTime documentation, Like in pyEmma I could source my data instead of loading and using the source object for TICA, but I couldn't use the same source object for TICA in D…
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So there's a file docs/tICA/tICA.pdf that shares a lot in common with http://msmbuilder.s3-website-us-east-1.amazonaws.com/theory/tICA.html
However, there are several key differences:
1. HTML versio…
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As I know, the first step of tICA-Metadynamics is to run some MD simulations starting from all available crystal structures and then analyze these trajectories by tICA. Muneeb told me I don't have to …
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http://people.brandeis.edu/~berkes/data/papers/BlasBerkWisk_NeurComp2006.pdf
Linear SFA is formally equivalent to tICA with time-delay one.
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Learning a global linear transformation with high autocorrelation doesn't necessarily help. Example potential: "X," or blobs on a hypercube-- no linear transformation will achieve high autocorrelation…
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Hi, is there a method in Deeptime similar to Pyemma's " pyemma.coordinates.save_traj" which can be used to extract pdb structures representing macrostates after coarse-graining using PCCA+
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`File "pipeline.py", line 72, in run_pipeline`
`cPickle.dump(tica, f)`
`cPickle.PicklingError: Can't pickle : attribute lookup pyemma._base.progress.reporter.dummy failed`
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Hello, I am following some tutorials for the implementation of TICA, to do a dimension reduction, but I have the following problem;
AttributeError: module 'numpy' has no attribute 'bool'.
`np.bo…
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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-heatm…