Recent Releases of mlcolvar
mlcolvar - v1.2.0
This version includes several bugfixes, improvements as well as new features: - Interpretability module - Committor CV via Kolmogorov’s variational principle
What's Changed
- Fix DeepLDA regularization by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/114
- Fix bug in lr scheduler configure by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/116
- Fix device issue checkpoint test by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/117
- Bug fix in nn.feedforward by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/119
- Remove scipy version requirement from pyproject by @andrrizzi in https://github.com/luigibonati/mlcolvar/pull/121
- Fix issues in CI by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/129
- Extension of transform module by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/124
- Add committor code by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/132
- Bug fix transform and committor by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/133
- Make last layer activation of committor an explicit block by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/135
- Interpretability module: sparse linear models via LASSO by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/120
- Register TDA target parameters as loss module buffers by @recisic in https://github.com/luigibonati/mlcolvar/pull/142
- Improvement committor module by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/145
- Test PyPI version via CI by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/146
- Add SequentialTransform by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/147
- Numpy 2 update temporary fixes by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/152
- Committor updates by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/151
- Fixed deltaF bug by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/156
- Doc minor fixes by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/157
- Improve transform tutorial coverage by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/158
- Committor tutorials update by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/159
- Fixed docs requirements by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/162
- Fixed markdown headers by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/163
- Fixed colab links by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/164
- Add cutoff on distances lists by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/165
New Contributors
- @recisic made their first contribution in https://github.com/luigibonati/mlcolvar/pull/142
Full Changelog: https://github.com/luigibonati/mlcolvar/compare/v1.1.0...v1.2.0
- Python
Published by luigibonati over 1 year ago
mlcolvar - v1.1.0
Bug fixes + sensitivity analysis
What's Changed
- Fix mamba commands migration issue by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/98
- Fix bug in CI badge by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/99
- general split_dataset functions by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/100
- Add installation info for main page by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/102
- change register_cmap to register by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/107
- remove version check on scipy by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/109
- Add sensitivity analysis by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/108
- add sensitivity tutorial to doc by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/112
- Fix bug unrepresented state. by @andrrizzi in https://github.com/luigibonati/mlcolvar/pull/110
- Fix #103: CVs cannot be loaded from checkpoint by @andrrizzi in https://github.com/luigibonati/mlcolvar/pull/113
- Add lr_scheduler options by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/111
Full Changelog: https://github.com/luigibonati/mlcolvar/compare/v1.0.1...v1.1.0
- Python
Published by luigibonati over 2 years ago
mlcolvar - v1.0.1
Bug fixes and doc improvements
What's Changed
- Fixed path to state file timelagged experiment by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/82
- added scipy version requirement by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/85
- Update doc and readme by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/86
- fix citation by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/87
- specify dependency version requirement by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/89
- Minor fixes by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/92
- Allow training without validation dataset by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/88
- Fix doc by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/93
Full Changelog: https://github.com/luigibonati/mlcolvar/compare/v1.0.0...v1.0.1
- Python
Published by luigibonati over 2 years ago
mlcolvar - v1.0.0
First stable release of mlcolvar package. Most of the changes with respect to 0.3.0 are related to documentation and notebooks illustrating tutorials and examples on how to use and expand the library, together with small fixes and enhancements.
What's Changed
- Support for multiple datasets of different size by @andrrizzi in https://github.com/luigibonati/mlcolvar/pull/59
- NormalizationInverse class by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/61
- Codecov_debug by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/64
- Codecov_improve by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/65
- Include notebook testing to codecov by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/70
- Fix AutoEncoder calling pre/postprocessing during training by @andrrizzi in https://github.com/luigibonati/mlcolvar/pull/69
- Colab interface for notebooks by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/71
- Tutorials_fix by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/62
- Moved notebook tests only to Ubuntu by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/76
- Chingolin example with TPI-Deep-TDA + minor fix in createdatasetfrom_file by @EnricoTrizio in https://github.com/luigibonati/mlcolvar/pull/77
- Update documentation with contributions and references by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/78
- Add section for examples notebooks by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/79
- Prepare for pypi release by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/80
- fix dependencies in pyproject by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/81
Full Changelog: https://github.com/luigibonati/mlcolvar/compare/v0.3.0...v1.0.0
- Python
Published by luigibonati about 3 years ago
mlcolvar - v0.3.0 (mlcolvar)
First mlcolvar release
The library went through a complete refactoring (including being renamed from mlcvs to mlcolvar) with new structure and APIs.
Main changes
- Pytorch lightning support
- Modular CV structure
- Dict-like datasets
- Many new CVs methods
Pull requests
Only the recent changes are shown in this list: * First implementation of a Variation Autoencoder CV by @andrrizzi in https://github.com/luigibonati/mlcolvar/pull/27 * Change base cv attributes by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/32 * change MSEloss signature from diff to input, target by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/37 * add option in ae/vae to compare output of the decoder with a different target by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/38 * Improve loaddataframe by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/41 * Implement Loss classes, some PEP8 fixes by @andrrizzi in https://github.com/luigibonati/mlcolvar/pull/42 * Switch from functional to class losses by @andrrizzi in https://github.com/luigibonati/mlcolvar/pull/43 * Add PCA method by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/44 * Support for multiple datasets by @andrrizzi in https://github.com/luigibonati/mlcolvar/pull/45 * Added reduced_rank to TICA by @Pietronvll in https://github.com/luigibonati/mlcolvar/pull/36 * Multi-task CV and various fixes by @andrrizzi in https://github.com/luigibonati/mlcolvar/pull/46 * rename library v2 by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/49 * Fix device loss by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/50 * Rename data objects by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/51 * Support for task-specific layers by @andrrizzi in https://github.com/luigibonati/mlcolvar/pull/53 * Merge lightning into main by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/55 * Add paper experiments by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/56 * Code fixes by @luigibonati in https://github.com/luigibonati/mlcolvar/pull/58
New Contributors
- @andrrizzi made their first contribution in https://github.com/luigibonati/mlcolvar/pull/27
- @Pietronvll made their first contribution in https://github.com/luigibonati/mlcolvar/pull/36
Full Changelog: https://github.com/luigibonati/mlcolvar/compare/v0.2.2...v0.3.0
- Python
Published by luigibonati about 3 years ago
mlcolvar - v0.2.2 (mlcvs)
What's Changed
- Fix bug in the logging for the tutorials (see #25)
Note that this is the last version that does not use the PyTorch Lightning high-level framework, and in which the module is named mlcvs.
Full Changelog: https://github.com/luigibonati/mlcvs/compare/v0.2.1...v0.2.2
- Python
Published by luigibonati about 3 years ago
mlcolvar - v0.2.1
What's Changed
- Prune the tree: move general functions to base class NNCV by @luigibonati in https://github.com/luigibonati/mlcvs/pull/18
- add autoencoder cv by @luigibonati in https://github.com/luigibonati/mlcvs/pull/22
- Add CodeQL workflow for GitHub code scanning by @lgtm-com in https://github.com/luigibonati/mlcvs/pull/21
New Contributors
- @lgtm-com made their first contribution in https://github.com/luigibonati/mlcvs/pull/21
Full Changelog: https://github.com/luigibonati/mlcvs/compare/v0.2.0...v0.2.1
- Python
Published by luigibonati over 3 years ago
mlcolvar - v0.2.0
Added DeepTDA cvs
What's Changed
- DeepTDA by @EnricoTrizio in https://github.com/luigibonati/mlcvs/pull/15
New Contributors
- @EnricoTrizio made their first contribution in https://github.com/luigibonati/mlcvs/pull/15
Full Changelog: https://github.com/luigibonati/mlcvs/compare/v0.1.1...v0.2.0
- Python
Published by luigibonati over 3 years ago
mlcolvar - v0.1.1
DeepTICA improvements and bugfixes
What's Changed
- Tprime evaluation and Solve TICA problem with not-symmetric Correlation Matrix by @nicolopedrani in https://github.com/luigibonati/mlcvs/pull/13
New Contributors
- @nicolopedrani made their first contribution in https://github.com/luigibonati/mlcvs/pull/13
Full Changelog: https://github.com/luigibonati/mlcvs/compare/v0.1.0...v0.1.1
- Python
Published by luigibonati over 3 years ago