Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks

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dc.contributor.authorElhamod, Mohannaden
dc.contributor.authorKhurana, Mridulen
dc.contributor.authorManogaran, Harish Babuen
dc.contributor.authorUyeda, Josef C.en
dc.contributor.authorBalk, Meghan A.en
dc.contributor.authorDahdul, Wasilaen
dc.contributor.authorBakış, Yasinen
dc.contributor.authorBart, Henry L. Jr.en
dc.contributor.authorMabee, Paula M.en
dc.contributor.authorLapp, Hilmaren
dc.contributor.authorBalhoff, James P.en
dc.contributor.authorCharpentier, Caleben
dc.contributor.authorCarlyn, Daviden
dc.contributor.authorChao, Wei-Lunen
dc.contributor.authorStewart, Charles V.en
dc.contributor.authorRubenstein, Daniel I.en
dc.contributor.authorBerger-Wolf, Tanyaen
dc.contributor.authorKarpatne, Anujen
dc.date.accessioned2023-09-05T13:39:48Zen
dc.date.available2023-09-05T13:39:48Zen
dc.date.issued2023-08-06en
dc.date.updated2023-09-01T07:49:39Zen
dc.description.abstractDiscovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our proposed approach, <i>Phylo-NN</i>, encodes the image of an organism into a sequence of quantized feature vectors–or codes–where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example.en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1145/3580305.3599808en
dc.identifier.urihttp://hdl.handle.net/10919/116207en
dc.language.isoenen
dc.publisherACMen
dc.rightsIn Copyrighten
dc.rights.holderThe author(s)en
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.titleDiscovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networksen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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