Comments (1)
clonker
commented on August 16, 2024
Hi, that's correct! Currently deeptime only contains native VAMP. It's probably pretty easy to implement a symmetrized version to enforce reversibility (same as for TICA), stochasticity constraints as in deep MSM and deep rev MSM are a bit more involved. An intermediate would be training a VAMPNet lobe and use that as feature function before applying TICA - potentially stacked with other (derived from eg intuition) feature functions.
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Related Issues (20)
- Units
- TrajectoriesDataset misleading error message
- Better error handling for custom_sde
- Cannot install deeptime. I have Python 3.10 (Windows 10) and trying to install using Visual Studio 2022 HOT 12
- Error when installing from local repo via pip HOT 4
- TICA fit-once transform-many HOT 6
- Automate generating bdist wheels HOT 1
- Allowing weights for VAMP dimensionality reduction HOT 6
- Error importing deeptime with scikit-learn 1.2.0 HOT 4
- About applying Deeptime to molecular dynamics simulation trajectories on protien HOT 3
- Handling parallel simulations HOT 1
- Implied timescales from deeptime.decomposition.TICA HOT 2
- [Bug] At least one of the given states is not contained in this model HOT 2
- VAMPnet gives highly fluctuating score results HOT 1
- Bayesian Markov models give different MFPT
- How to compute any actual quantity of the coarse-grained kinetics with employing the fuzzy memberships? HOT 7
- Installation without conda and pip HOT 3
- deeptime cannot be installed on Mac computers with Apple Silicon and Python 3.12.0. HOT 4
- Does one need identical features to compare between related systems? HOT 4
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