deeptime-ml / deeptime

Python library for analysis of time series data including dimensionality reduction, clustering, and Markov model estimation

https://deeptime-ml.github.io/

deeptime-ml/deeptime Issues

Cross Validation score for MaximumLikelihoodMSMs and BayesianMSMs
Closed 2 months ago2
Does one need identical features to compare between related systems?
Closed 6 months ago4
Applying TICA to ragged feature vectors
Closed 6 months ago2
Example/tutorial for dealing with MD trajectories
Updated 6 months ago1
deeptime cannot be installed on Mac computers with Apple Silicon and Python 3.12.0.
Updated 8 months ago4
Which version of VAMPNets is there?
Updated a year ago1
Installation without conda and pip
Updated a year ago3
About applying Deeptime to molecular dynamics simulation trajectories on protien
Closed a year ago3
[Bug] At least one of the given states is not contained in this model
Closed a year ago2
How to compute any actual quantity of the coarse-grained kinetics with employing the fuzzy memberships?
Updated a year ago7
VAMPnet gives highly fluctuating score results
Closed a year ago1
Bayesian Markov models give different MFPT
Closed a year ago
Handling parallel simulations
Closed a year ago1
Implied timescales from deeptime.decomposition.TICA
Closed a year ago2
Feauture request - Tcorex covariance matrix
Closed a year ago2
Automate generating bdist wheels
Closed a year ago1
Error importing deeptime with scikit-learn 1.2.0
Closed 2 years ago4
Allowing weights for VAMP dimensionality reduction
Updated 2 years ago6
Cannot install deeptime. I have Python 3.10 (Windows 10) and trying to install using Visual Studio 2022
Closed 2 years ago12
Error when installing from local repo via pip
Closed 2 years ago4
TICA fit-once transform-many
Closed 2 years ago6
Different VAMPNET results from CPU/GPU training
Closed 2 years ago11
Sort Markov matrix
Updated 2 years ago21
Installation runs into CUDA problem
Closed 2 years ago13
TrajectoriesDataset misleading error message
Closed 2 years ago
Better error handling for custom_sde
Closed 2 years ago
Units
Updated 2 years ago
Build fails suddenly
Closed 2 years ago3
Chapman-Kolmogorov test for Koopman models
Updated 2 years ago
Docs: Add k3d-jupyter support and transform some of the animations with it
Updated 3 years ago
Largest connected set returns a state when it should return an empty set
Closed 3 years ago10
Use mamba build instead of conda build in CI
Closed 3 years ago1
TransitionCountModel.states_to_symbols incorrectly handles negative indices
Closed 3 years ago1
Problem with ck test for VAMP models based on VAMPnet
Closed 3 years ago2
serialization
Updated 3 years ago1
Mention the Arxiv article in readme or docs
Closed 3 years ago
HMM sampling for out-of-sample data bug
Closed 3 years ago2
ModuleNotFoundError: No module named 'deeptime.util.data'
Closed 3 years ago3
Fail to install through conda or pip
Closed 3 years ago3
VAMPNet manage multiple trajectories
Closed 3 years ago3
Adding Koopman operator evaluation, ITS evaluation and CK test to VAMPnet module
Closed 3 years ago10
VAMPnet partial fit
Closed 3 years ago14
How to pass arguments in the method gather_stats of deeptime.markov.hmm.BayesianHMMPosterior
Closed 4 years ago1
The link in the README is broken
Closed 4 years ago2
Default random engine might be linear congruential
Closed 4 years ago2
vamp model expectation
Closed 4 years ago1
test oom
Closed 4 years ago
online covariance - example
Closed 5 years ago14
submodels
Closed 5 years ago1
submodels of msms
Closed 5 years ago1