Chemprop Files

The v2.1 release adds the uncertainty quantification modules, including estimation, calibration, and evaluation (#937). For more details on uncertainty quantification in Chemprop, please refer to the documentation and the example notebook. Additionally, we switched the loss functions and metrics to torchmetrics (#1022). With this change we also changed the "val_loss" reported to be calculated the same as the training loss to make them comparable (#1020). We also changed Chemprop to use replicates instead of cross validation (#994) and batch normalization is now disabled by default (#1058).

Core code changes

• The validation_loss_function is removed in [#1023].
• The batch norm is disabled by default in [#1058]
• An new predictor, quantile QuantileFFN, is added in [#963]
• BinaryDirichletLoss and MulticlassDirichletLoss are integrated into DirichletLoss in [#1066]
• The split type of CV and CV_NO_VAL are removed in [#994]
• A models list of metric is now registered as children modules in [#1020]

CLI changes

• Disable batch norm by default, and it can be turned on by --batch-norm [#1058]
• Many CLI flags related to uncertainty quantification are added [#1010]
• Quantile regression is now supported via -t regression-quantile [#963]
• The cross validation (CV) is replaced with replicates. The number of replicates can be specified via --num-replicates and the flag --num-folds is deprecated [#994]
• --tracking-metric is added which is the metric to track for early stopping and checkpointing [#1020]

New notebooks

• An notebook showing interoperability of Chemprop featurizer w/ other libraries (DGL and PyG) [#1063]
• Active learning [#910]
• Uncertainty quantification [#1071]

CI/CD

• Ray can be tested on Python 3.12 [#1064]
• USE_LIBUV: 0 is added into the CI workflow [#1065]

Backwards Compatibility Note

Models trained with v2.0 will not load properly in v2.1 due to the loss functions file being moved. A conversion script is provided to convert a v2.0 model to one compatible with v2.1. Its usage is python chemprop/utils/v2_0_to_v2_1.py <v2_0.pt> <v2_1.pt>

What's Changed

• change installed torch version on windows actions again by @shihchengli in https://github.com/chemprop/chemprop/pull/1062
• .pt instead of .ckpt by @twinbrian in https://github.com/chemprop/chemprop/pull/1060
• add ModelCheckpointing to training.ipynb so best model is used automatically by @donerancl in https://github.com/chemprop/chemprop/pull/1059
• Add ray to tests on python 3.12 by @KnathanM in https://github.com/chemprop/chemprop/pull/1064
• v2.1 Feature: Replicates Instead of Cross Validation Folds by @JacksonBurns in https://github.com/chemprop/chemprop/pull/994
• disable libuv with env var rather than avoiding latest torch by @JacksonBurns in https://github.com/chemprop/chemprop/pull/1065
• Add new example notebook for active learning by @joelnkn in https://github.com/chemprop/chemprop/pull/910
• Fix: splits column is a string not a list by @KnathanM in https://github.com/chemprop/chemprop/pull/1074
• Update chemprop to v2.1 in https://github.com/chemprop/chemprop/pull/1038
  • This PR included the following PRs:
  • Rerun notebooks for v2.1 by @KnathanM in #1067
  • Refactor with torchmetrics by @KnathanM in #1022
  • update train docs for v2.1 by @KnathanM in #1069
  • Disable batch norm by default by @jonwzheng in #1058
  • Add notebook showing interoperability of Chemprop featurizer w/other libraries by @jonwzheng in #1063
  • Add tracking metric options; make metrics ModuleList; other improvements by @KnathanM in #1020
  • Remove old validate-loss-function function by @KnathanM in #1023
  • V2: Uncertainty implementation in #1058
    • This PR included the following PRs:
    • Improve the docstring for uncertainty modules by @shihchengli in #986
    • Add Platt calibrator by @KnathanM in #961
    • Add dropout and ensemble predictors by @joelnkn in #970
    • Add NLL and Spearman Uncertainty Evaluators by @am2145 in #984
    • Add quantile regression by @shihchengli in #963
    • Add miscalibration area and ence evaluators by @shihchengli in #1012
    • Add isotonic calibrators by @KnathanM in #1053
    • V2 conformal calibrators by @shihchengli in #989
    • V2 conformal evaluators by @shihchengli in #1005
    • Uncertainty regression calibrators (non-conformal) by @shihchengli in #1055
    • Adding Evidential, MVE, and Binary Dirichlet Uncertainty Predictors by @akshatzalte in #1061
    • Cleanup the uncertainty modules by @shihchengli in #1072
    • Multiclass dirichlet give uncertainty by @KnathanM in #1066
    • Rename uncertainty estimator by @KnathanM in #1070
    • Update uncertainty notebook by @shihchengli in #1071
    • Add uncertainty quantification to the predict CLI by @shihchengli in #1010

Full Changelog: https://github.com/chemprop/chemprop/compare/v2.0.5...v2.1.0