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201016DCNCmpdPaperDraft.pdf (1.29 MB)

Document Embedding Centroids: New and Versatile Semantic Descriptors for Compounds

preprint
submitted on 28.10.2020, 02:59 and posted on 09.11.2020, 20:43 by John Santa Maria, Scott Gleim, Eugen Lounkine, Jeremy Jenkins
We describe a novel algorithm for generating representational embeddings of chemical matter based on the biomedical literature/semantic contexts in which they occur. We then demonstrate that these chemical descriptors have utility in nearest neighbor retrieval for early drug discovery tasks such as mechanism of action and target activity predictions.
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History

Email Address of Submitting Author

johnsantamariajr@gmail.com

Institution

Novartis Institutes for Biomedical Research

Country

United States of America

ORCID For Submitting Author

0000-0001-9441-2521

Declaration of Conflict of Interest

No conflict of interest

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