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Poster
Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network
Wengong Jin · Connor Coley · Regina Barzilay · Tommi Jaakkola

Tue Dec 05 06:30 PM -- 10:30 PM (PST) @ Pacific Ballroom #135
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The prediction of organic reaction outcomes is a fundamental problem in computational chemistry. Since a reaction may involve hundreds of atoms, fully exploring the space of possible transformations is intractable. The current solution utilizes reaction templates to limit the space, but it suffers from coverage and efficiency issues. In this paper, we propose a template-free approach to efficiently explore the space of product molecules by first pinpointing the reaction center -- the set of nodes and edges where graph edits occur. Since only a small number of atoms contribute to reaction center, we can directly enumerate candidate products. The generated candidates are scored by a Weisfeiler-Lehman Difference Network that models high-order interactions between changes occurring at nodes across the molecule. Our framework outperforms the top-performing template-based approach with a 10% margin, while running orders of magnitude faster. Finally, we demonstrate that the model accuracy rivals the performance of domain experts.

Keywords: Deep Learning · Supervised Deep Networks · Representation Learning · Applications
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Author Information

Wengong Jin (MIT CSAIL)
Connor Coley (MIT)
Regina Barzilay (Massachusetts Institute of Technology)
Tommi Jaakkola (MIT)

Tommi Jaakkola is a professor of Electrical Engineering and Computer Science at MIT. He received an M.Sc. degree in theoretical physics from Helsinki University of Technology, and Ph.D. from MIT in computational neuroscience. Following a Sloan postdoctoral fellowship in computational molecular biology, he joined the MIT faculty in 1998. His research interests include statistical inference, graphical models, and large scale modern estimation problems with predominantly incomplete data.

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