Implementation of bio embeddings

jcapels / PlantsSM

A package to expose Secondary Metabolism of plants with Machine Learning and Systems Biology

MIT License

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Closed jcapels closed 2 years ago

jcapels commented 2 years ago

This pull request includes the following implementations:

Refactor of propythia wrappers. This closes issue #7.
Change "Dataset" signature to cope with 3d datasets. This closes issue #10.
Add ProtBERT, ESM-1b, UniRep, Word2vec, PlusRNN, one hot, blosum, NLF and z-scale encodings.
Add sequence paddings
Add one hot encodings
Add compounds SmilesPE tokenizers