Chemprop Files

We continue to enhance and improve the functionality and usability of Chemprop. If there are things you'd like to see addressed in a future update, please open an issue or PR.

Core code changes

We discovered that our Noam learning rate scheduler does not match what was originally proposed. The current scheduler does work well though, so it was decided to not change the definition. Instead the scheduler was renamed and refactored to be more clear. By @shihchengli in https://github.com/chemprop/chemprop/pull/975 Work on uncertainty quantification methods revealed that our previous prediction tensor return dimensions would cause difficulty down the line. Now we have placed uncertainty into a separate dimension. By @hwpang in https://github.com/chemprop/chemprop/pull/959 The BinaryDirichletFFN and MulticlassDirichletFFN predictors were added early in the v2 development, but not tested. Now they have been tested and corrected. By @shihchengli in https://github.com/chemprop/chemprop/pull/1017 The RDKit 2D molecular featurizer was added back by popular demand. The versions used in v1 are available as well as a version that uses all available molecular features in rdkit.Chem.Descriptors. By @KnathanM in https://github.com/chemprop/chemprop/pull/877

CLI changes

• Log statistical summary of training, validation, and test datasets by @donerancl in https://github.com/chemprop/chemprop/pull/882
• Change the default verbose level to INFO by @shihchengli in https://github.com/chemprop/chemprop/pull/953
• Save both probabilities and class label for multiclass classification by @shihchengli in https://github.com/chemprop/chemprop/pull/987
• Add --remove-checkpoints flag to opt out of saving checkpoints by @shihchengli in https://github.com/chemprop/chemprop/pull/1014
• Add --class-balance flag to train CLI by @shihchengli in https://github.com/chemprop/chemprop/pull/1011
• Save target column names in model for use at inference by @hwpang in https://github.com/chemprop/chemprop/pull/935
• Fix save-smiles-splits not working with rxn. columns as column header by @jonwzheng in https://github.com/chemprop/chemprop/pull/998

Transfer learning

• Add new example notebook for transfer learning by @joelnkn in https://github.com/chemprop/chemprop/pull/904
• Use pre-train output scaler to scale training data in CLI by @KnathanM in https://github.com/chemprop/chemprop/pull/1051
• Add --checkpoint and --freeze-encoder flags in train CLI for transfer learning by @shihchengli in https://github.com/chemprop/chemprop/pull/1007

Documentation

• Fixed typos in CLI reference and standardized formatting by @donerancl in https://github.com/chemprop/chemprop/pull/880
• Example Notebook for Classification by @twinbrian in https://github.com/chemprop/chemprop/pull/1047
• Improve frzn-ffn-layers description and update doc for transfer learning by @oscarwumit in https://github.com/chemprop/chemprop/pull/993
• add transform tests by @KnathanM in https://github.com/chemprop/chemprop/pull/955
• Add documentation for how to use a separate splits file (CLI) by @KnathanM in https://github.com/chemprop/chemprop/pull/1041

Other small bug fixes

• Convert v1 models trained on GPU by @KnathanM in https://github.com/chemprop/chemprop/pull/978
• Fix hpopting Notebook and CLI for Windows by @JacksonBurns in https://github.com/chemprop/chemprop/pull/1034
• Update multiclass data to be compatible with rdkit 2024.09.1 by @jonwzheng in https://github.com/chemprop/chemprop/pull/1037
• Define task_weights if it is None in MulticlassClassificationFFN by @shihchengli in https://github.com/chemprop/chemprop/pull/988
• change installed torch version on windows actions again by @KnathanM in https://github.com/chemprop/chemprop/pull/1016
• Update batch norm freezing to freeze running stats by @joelnkn in https://github.com/chemprop/chemprop/pull/952
• Pass map_location through load_submodules() to torch.load() by @shihchengli in https://github.com/chemprop/chemprop/pull/1029
• fix no-header-rows in predict command error by @sunhwan in https://github.com/chemprop/chemprop/pull/1001

New Contributors

• @sunhwan made their first contribution in https://github.com/chemprop/chemprop/pull/1001
• @twinbrian made his first contribution in https://github.com/chemprop/chemprop/pull/1047

Full Changelog: https://github.com/chemprop/chemprop/compare/v2.0.4...v2.0.5