Software
scipr
An extensible API for learning transformation functions to align batches of scRNA-seq data.
sparsely-connected-keras
A new layer class for Keras models that allows static zero-weighted connections between neurons in adjacent layers (sparsely connecting layers instead of typical dense connections). Useful for VNN architectures.
tied-autoencoder-keras
Autoencoder layer classes (with tied encode and decode weights) for Keras.
Open source contributions
Keras
Added code to prevent programming-error. The bug would result in hard-to-decipher error messages for users. With this fix, we catch this error much earlier, and provide an error message that plainly states the issue. Merged into Keras 2.2.0 (PR)
Armatus
Used detailed knowledge of C++11 STL to remove an unnecessary binary search through a std::map. (PR)
Apple WebKit (web engine used by Safari)
Discovered and fixed a bug with the storage of cookies from third party origins. Fixing this closes a potential cookie policy loophole, improving security. Resulted in the two bug reports below, and my patches for each: