Deep Review Versions Save

This is the git commit associated with the manuscript version accepted to the Journal of the Royal Society Interface. Changes include:

• Clarifications to the abstract, introduction, glossary table, and augmented training discussion
• A few additional references
• Updates to the build process, including versioned webpages

The HTML permalink is here.

This is the git commit associated with the journal resubmission and the second submission to bioRxiv (webpage, pdf). Major changes include:

• New sections on protein-protein interactions, MHC-peptide binding, graph convolutions, neuroscience, model uncertainty, natural language processing in healthcare, and cryo-electron microscopy.
• Major revisions to the transcription factor, promoter and enhancer, chemical representation, and evaluation sections.
• A table and figures to introduce neural network architectures.
• 9 new authors and over 100 new references.
• Manubot upgrades.
• Typo, grammar, and formatting corrections.

A complete diff is available on bioRxiv as a supplementary file and the HTML permalink is here.

This is the git commit associated with the first submission to bioRxiv (webpage, pdf). The bioRxiv preprint has DOI 10.1101/142760 and the HTML permalink is here.