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Efficiently predicting high resolution mass spectra with graph neural networks

Michael Murphy · Stefanie Jegelka · Ernest Fraenkel · Tobias Kind · David Healey · Thomas Butler

Exhibit Hall 1 #217
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Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a large database of chemical structures. However, current approaches to spectrum prediction model the output space in ways that force a tradeoff between capturing high resolution mass information and tractable learning. We resolve this tradeoff by casting spectrum prediction as a mapping from an input molecular graph to a probability distribution over chemical formulas. We further discover that a large corpus of mass spectra can be closely approximated using a fixed vocabulary constituting only 2% of all observed formulas. This enables efficient spectrum prediction using an architecture similar to graph classification - GrAFF-MS - achieving significantly lower prediction error and greater retrieval accuracy than previous approaches.

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