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1.7.0 Release
Highlights
Adds the seed and random state and sampling features to AMPL. (#344) The features are:
Imbalance-learn sampling
Seed for Reproducibility
Changes to control model sparsity and improvements to MultitaskScaffoldSplitter (#331):
Sped up MultitaskScaffoldSplitter and changed its implementation to allow better optimization of validation & test set difference from training set.
Added split_diagnostic_plots module for visualizing aspects of split quality.
Added L1 and L2 penalty parameters to XGBoost models to control model sparsity.
Added hyperopt search domain parameters for NN and XGBoost model sparsity parameters.
Resolved a bug in Transformers fitting where the Transformers for normalizing inputs, outputs, and weights were trained on the entire dataset instead of only the training dataset, potentially causing data leakage. (#385)
Incorporates CodeCov into the CI/CD pipeline to generate code coverage reports for enhancing code quality. (#372, #373)
Enhancements
Fixed a bug when running predictions on classification models with balancing weight transformers requires MinimalDataset weights for the prediction data. Previously, get_multitask_perf_from_files_new returned NaN metrics for single-task models mixed with multitask models; now, both return correct metrics. (#387)
Allows the users to combine calculated features with embedded features from pre-trained models (#395)
Logs exceptions generated during a HyperOpt search. Previously they were swallowed, ignored (#392)
Add compute_drug_likeness function to the RDkit_easy module to compute various drug-likeness criteria for compounds in a data frame (Lipinski rule of 5, Ghose and Veber filters, QED), along with the descriptors used to derive them. (#384)
AD calculation improvements. Fixed an error in the calculation. Added the ability to query for the nearest training set neighbors of each compound running predictions for. (#378)
Integrates the MODAC unit tests and automates their execution on GitHub CI/CD Actions (#371)
Implemented unit tests for plotting packages using matplotcheck and the PlotTester API to perform plot validation. (#394)
Maintenance
System clean up:
Improved the CI test pipeline to eliminate duplicate job executions.
Added markers to indicate the resources used in certain tests.
Expanded the range of tests executed in the CI pipeline. Only exclude those that require LLNL resources. (#393)
Bug Fixes
Correct the AD index calculation for Mordred features containing NaN value (#390)