List of deep learning implementations in biology

Thank you for the great content! Just what i was looking for!

Follow the Data

I’m going to start collecting papers on, and implementations of, deep learning in biology (mostly genomics, but other areas as well) on this page. It’s starting to get hard to keep up! For the purposes of this list, I’ll consider things like single-layer autoencoders, although not literally “deep”, to qualify for inclusion. The categorizations will by necessity be arbitrary and might be changed around from time to time.

In parallel, I’ll try to post some of these on gitxiv as well under the tag bioinformatics plus other appropriate tags.

Please let me know about the stuff I missed!

Cheminformatics

Neural graph fingerprints [github][gitxiv]

A convolutional net that can learn features which are useful for predicting properties of novel molecules; “molecular fingerprints”. The net works on a graph where atoms are nodes and bonds are edges. Developed by the group of Ryan Adams, who co-hosts the very…

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