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bioRxiv · 10.1101/2020.05.11.088344

Reimplementing Unirep in JAX

Ma, E.·Kummer, A.
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Abstract

UniRep is a recurrent neural network model trained on 24 million protein sequences, and has shown utility in protein engineering. The original model, however, has rough spots in its implementation, and a convenient API is not available for certain tasks. To rectify this, we reimplemented the model in JAX/NumPy, achieving near-100X speedups in forward pass performance, and implemented a convenient API for specialized tasks. In this article, we wish to document our model reimplementation process with the goal of educating others interested in learning how to dissect a deep learning model, and engineer it for robustness and ease of use.

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Ma, E., Kummer, A.. 2020-05-13. Reimplementing Unirep in JAX. https://doi.org/10.1101/2020.05.11.088344

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