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DrugEx Version 3.4.0
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@martin-sicho martin-sicho released this 20 Feb 15:20
· 322 commits to master since this release
v3.4.0
ec9f350

Change Log

From v3.3.0 to v3.4.0

Fixes

None.

Changes

Major refactoring of drugex.training

  • Moving generators from drugex.training.models to drugex.training.generators, and harmonizing and renaming them

    • RNN -> SequenceRNN
    • GPT2Model -> SequenceTransformer
    • GraphModel -> GraphTransformer

  • Moving explorers from drugex.training.models to drugex.training.explorers, harmonizing and renaming them

    • SmilesExplorerNoFrag -> SequenceExplorer
    • SmilesExplorer -> FragSequenceExplorer
    • GraphExplorer -> FragGraphExplorer

  • Removal of all obsolete modules related to the two discontinued fragment-based LSTM models from DrugEx v3.

  • The generators' sample_smiles() has been replaced by a generate() function

  • Clafification of the terms qualifying the generated molecules to have the following unique and constant definitions (replacing ambigous VALID and DESIRE terms)

    • Valid : molecule can be parsed with rdkit
    • Accurate : molecule contains given input fragments
    • Desired : molecule fulfils all given objectives

  • Revise implementation of Tanimoto distance-based Pareto ranking scheme(SimilarityRanking) to correspond to the method described in DrugEx v2. Add option to use minimum Tanimoto distance between molecules in a front instead the mean distance.

  • Remove all references to NN-based RAscore (already discontinued)

Refactoring of CLI

  • Refactoring dataset.py and train.py to object based
  • Writting a single .txt.vocab file per dataset preprocessing instead of separate (duplicate) files for each subset in dataset.py

Removed

  • --save_voc argument in dataset.py as redundant
  • --pretrained_model argment in train.py (merged with --agent_path)
  • memory parameter and all associated code from in SequenceRNN

New Features

  • GRU-based RNN added to the CLI
  • added another possible implementation of similarity ranking (MutualSimilaritySortRanking), this is based on the code in the original repository of DrugEx
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