{"id":"https://openalex.org/W4379919227","doi":"https://doi.org/10.48550/arxiv.2306.03228","title":"Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks","display_name":"Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks","publication_year":2023,"publication_date":"2023-06-05","ids":{"openalex":"https://openalex.org/W4379919227","doi":"https://doi.org/10.48550/arxiv.2306.03228"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2306.03228","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2306.03228","pdf_url":"https://arxiv.org/pdf/2306.03228","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2306.03228","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057416419","display_name":"Mohannad Elhamod","orcid":"https://orcid.org/0000-0002-2383-947X"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Elhamod, Mohannad","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059865613","display_name":"Mridul Khurana","orcid":"https://orcid.org/0009-0003-9346-3206"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Khurana, Mridul","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092118545","display_name":"Harish Babu Manogaran","orcid":"https://orcid.org/0000-0003-3709-4656"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Manogaran, Harish Babu","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075230839","display_name":"Josef C. Uyeda","orcid":"https://orcid.org/0000-0003-4624-9680"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Uyeda, Josef C.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079679005","display_name":"Meghan A. Balk","orcid":"https://orcid.org/0000-0003-2699-3066"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Balk, Meghan A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037935786","display_name":"Wasila Dahdul","orcid":"https://orcid.org/0000-0003-3162-7490"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dahdul, Wasila","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015961414","display_name":"Yasin Bak\u0131\u015f","orcid":"https://orcid.org/0000-0001-6144-9440"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bak\u0131\u015f, Yasin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049470689","display_name":"Henry L. Bart","orcid":"https://orcid.org/0000-0002-5662-9444"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bart, Henry L.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020099887","display_name":"Paula Mabee","orcid":"https://orcid.org/0000-0002-8455-3213"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mabee, Paula M.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005484581","display_name":"Hilmar Lapp","orcid":"https://orcid.org/0000-0001-9107-0714"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lapp, Hilmar","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021056529","display_name":"James P. Balhoff","orcid":"https://orcid.org/0000-0002-8688-6599"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Balhoff, James P.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065582956","display_name":"Caleb Charpentier","orcid":"https://orcid.org/0000-0002-9787-7081"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Charpentier, Caleb","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090386394","display_name":"David Carlyn","orcid":"https://orcid.org/0000-0002-8323-0359"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Carlyn, David","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101520942","display_name":"Wei\u2010Lun Chao","orcid":"https://orcid.org/0000-0003-1269-7231"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chao, Wei-Lun","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035964079","display_name":"Charles V. Stewart","orcid":"https://orcid.org/0000-0001-6532-6675"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Stewart, Charles V.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038947564","display_name":"Daniel I. Rubenstein","orcid":"https://orcid.org/0000-0001-9049-5219"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rubenstein, Daniel I.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060005215","display_name":"Tanya Berger\u2010Wolf","orcid":"https://orcid.org/0000-0001-7610-1412"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Berger-Wolf, Tanya","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5081622450","display_name":"Anuj Karpatne","orcid":"https://orcid.org/0000-0003-1647-3534"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Karpatne, Anuj","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":18,"corresponding_author_ids":["https://openalex.org/A5057416419"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.9922000169754028,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.9922000169754028,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9790999889373779,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12417","display_name":"Morphological variations and asymmetry","score":0.9714000225067139,"subfield":{"id":"https://openalex.org/subfields/2608","display_name":"Geometry and Topology"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7250065803527832},{"id":"https://openalex.org/keywords/tree-of-life","display_name":"Tree of life (biology)","score":0.6992198824882507},{"id":"https://openalex.org/keywords/trait","display_name":"Trait","score":0.6763619184494019},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.6300027370452881},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5612128973007202},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5573117136955261},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.5057909488677979},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.48564302921295166},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4678422212600708},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.453235387802124},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.44064226746559143},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.42289212346076965},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3170224726200104},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1176026463508606},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0932999849319458},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07605943083763123}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7250065803527832},{"id":"https://openalex.org/C124388736","wikidata":"https://www.wikidata.org/wiki/Q3247497","display_name":"Tree of life (biology)","level":4,"score":0.6992198824882507},{"id":"https://openalex.org/C106934330","wikidata":"https://www.wikidata.org/wiki/Q1971873","display_name":"Trait","level":2,"score":0.6763619184494019},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6300027370452881},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5612128973007202},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5573117136955261},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.5057909488677979},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.48564302921295166},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4678422212600708},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.453235387802124},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.44064226746559143},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.42289212346076965},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3170224726200104},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1176026463508606},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0932999849319458},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07605943083763123},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2306.03228","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2306.03228","pdf_url":"https://arxiv.org/pdf/2306.03228","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2306.03228","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2306.03228","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2306.03228","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2306.03228","pdf_url":"https://arxiv.org/pdf/2306.03228","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2763775416","https://openalex.org/W1977405831","https://openalex.org/W1979959438","https://openalex.org/W2174809885","https://openalex.org/W3100853633","https://openalex.org/W4210644918","https://openalex.org/W1474331782","https://openalex.org/W2057191541","https://openalex.org/W2949296710","https://openalex.org/W2883025420"],"abstract_inverted_index":{"Discovering":[0],"evolutionary":[1,59,97],"traits":[2,37,60],"that":[3],"are":[4],"heritable":[5],"across":[6],"species":[7,125,134],"on":[8,66],"the":[9,34,74,94,104,108],"tree":[10],"of":[11,21,36,76,82,93,110,121],"life":[12],"(also":[13],"referred":[14],"to":[15,24,26],"as":[16,135],"a":[17,40,48,54,80,119,136],"phylogenetic":[18],"tree)":[19],"is":[20,38],"great":[22],"interest":[23],"biologists":[25],"understand":[27],"how":[28],"organisms":[29],"diversify":[30],"and":[31,42,128],"evolve.":[32],"However,":[33],"measurement":[35],"often":[39],"subjective":[41],"labor-intensive":[43],"process,":[44],"making":[45],"trait":[46,67],"discovery":[47],"highly":[49],"label-scarce":[50],"problem.":[51],"We":[52,106],"present":[53],"novel":[55],"approach":[56,112],"for":[57],"discovering":[58],"directly":[61],"from":[62],"images":[63],"without":[64],"relying":[65],"labels.":[68],"Our":[69],"proposed":[70],"approach,":[71],"Phylo-NN,":[72],"encodes":[73],"image":[75,126,130],"an":[77],"organism":[78],"into":[79],"sequence":[81,95],"quantized":[83],"feature":[84],"vectors":[85],"--":[86,89],"or":[87],"codes":[88],"where":[90],"different":[91],"segments":[92],"capture":[96],"signals":[98],"at":[99],"varying":[100],"ancestry":[101],"levels":[102],"in":[103,113,118],"phylogeny.":[105],"demonstrate":[107],"effectiveness":[109],"our":[111],"producing":[114],"biologically":[115],"meaningful":[116],"results":[117],"number":[120],"downstream":[122],"tasks":[123],"including":[124],"generation":[127],"species-to-species":[129],"translation,":[131],"using":[132],"fish":[133],"target":[137],"example.":[138]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-02-09T09:26:11.010843","created_date":"2023-06-09T00:00:00"}
