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Recapitulation and Retrospective Prediction of Biomedical Associations Using Temporally-enabled Word Embeddings

Jiho Park, Agustin Lopez Marquez, Arjun Puranik, Ajit Rajasekharan, Murali Aravamudan, View ORCID ProfileEnrique Garcia-Rivera
doi: https://doi.org/10.1101/627513
Jiho Park
1nference, Cambridge, MA, 02142, USA
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Agustin Lopez Marquez
1nference, Cambridge, MA, 02142, USA
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Arjun Puranik
1nference, Cambridge, MA, 02142, USA
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Ajit Rajasekharan
1nference, Cambridge, MA, 02142, USA
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Murali Aravamudan
1nference, Cambridge, MA, 02142, USA
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Enrique Garcia-Rivera
1nference, Cambridge, MA, 02142, USA
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  • ORCID record for Enrique Garcia-Rivera
  • For correspondence: enrique@nference.net
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Abstract

The recent explosion of biomedical knowledge presents both a major opportunity and challenge for scientists tackling complex problems in healthcare. Here we present an approach for synthesizing biomedical knowledge based on a combination of word-embeddings and select cooccurrences. We evaluated our ability to recapitulate and retrospectively predict disease-gene associations from the Online Mendelian Inheritance in Man (OMIM) resource. Our metrics achieved an area under the curve (AUC) value of 0.981 at the recapitulation task for 2,400 disease-gene associations. At the most stringent cutoff, our metrics predicted 13.89% of these associations before their first cooccurrence in the literature, with a median time of 4 years between prediction and first cooccurrence. Finally, our literature metrics can be combined with human genetics data to retrospectively predict disease-gene associations, IL-6 and Giant Cell Arteritis provided as an example. We believe this framework can provide robust biomedical hypotheses at a much faster pace than current standard practices.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 07, 2019.
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Recapitulation and Retrospective Prediction of Biomedical Associations Using Temporally-enabled Word Embeddings
Jiho Park, Agustin Lopez Marquez, Arjun Puranik, Ajit Rajasekharan, Murali Aravamudan, Enrique Garcia-Rivera
bioRxiv 627513; doi: https://doi.org/10.1101/627513
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Recapitulation and Retrospective Prediction of Biomedical Associations Using Temporally-enabled Word Embeddings
Jiho Park, Agustin Lopez Marquez, Arjun Puranik, Ajit Rajasekharan, Murali Aravamudan, Enrique Garcia-Rivera
bioRxiv 627513; doi: https://doi.org/10.1101/627513

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