Enabling rapid COVID-19 small molecule drug design through scalable deep learning of generative models

Sam Ade Jacobs, Tim Moon, Kevin McLoughlin, Derek Jones, David Hysom, Dong H. Ahn, John Gyllenhaal, Pythagoras Watson, Felice C. Lightstone, Jonathan E. Allen, Ian Karlin, Brian Van Essen

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


We improved the quality and reduced the time to produce machine learned models for use in small molecule antiviral design. Our globally asynchronous multi-level parallel training approach strong scales to all of Sierra with up to 97.7% efficiency. We trained a novel, character-based Wasserstein autoencoder that produces a higher quality model trained on 1.613 billion compounds in 23 minutes while the previous state of the art takes a day on 1 million compounds. Reducing training time from a day to minutes shifts the model creation bottleneck from computer job turnaround time to human innovation time. Our implementation achieves 318 PFLOPs for 17.1% of half-precision peak. We will incorporate this model into our molecular design loop enabling the generation of more diverse compounds; searching for novel, candidate antiviral drugs improves and reduces the time to synthesize compounds to be tested in the lab.

Original languageEnglish (US)
JournalInternational Journal of High Performance Computing Applications
StateAccepted/In press - 2021


  • COVID 19
  • drug design
  • generative models
  • machine learning
  • scalable performance

ASJC Scopus subject areas

  • Software
  • Theoretical Computer Science
  • Hardware and Architecture


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