{"id":"https://openalex.org/W4403160027","doi":"https://doi.org/10.48550/arxiv.2409.02335","title":"What Do You See in Common? Learning Hierarchical Prototypes over Tree-of-Life to Discover Evolutionary Traits","display_name":"What Do You See in Common? Learning Hierarchical Prototypes over Tree-of-Life to Discover Evolutionary Traits","publication_year":2024,"publication_date":"2024-09-03","ids":{"openalex":"https://openalex.org/W4403160027","doi":"https://doi.org/10.48550/arxiv.2409.02335"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2409.02335","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2409.02335","pdf_url":"https://arxiv.org/pdf/2409.02335","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2409.02335","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061217350","display_name":"M. Maruf","orcid":"https://orcid.org/0000-0003-0637-1753"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Maruf, M.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076598286","display_name":"Arka Daw","orcid":"https://orcid.org/0009-0006-3319-1271"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Daw, Arka","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053418777","display_name":"Kazi Sajeed Mehrab","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mehrab, Kazi Sajeed","raw_affiliation_strings":[],"raw_orcid":null,"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 Patrick","raw_affiliation_strings":[],"raw_orcid":null,"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":[],"raw_orcid":null,"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":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083711010","display_name":"Matthew J Thompson","orcid":"https://orcid.org/0000-0003-0583-8585"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Thompson, Matthew J","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093402845","display_name":"Elizabeth G Campolongo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Campolongo, Elizabeth G","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086009284","display_name":"Kaiya L. Provost","orcid":"https://orcid.org/0000-0002-5865-7238"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Provost, Kaiya L","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Chao, Wei-Lun","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chao, Wei-Lun","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Berger-Wolf, Tanya","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Berger-Wolf, Tanya","raw_affiliation_strings":[],"raw_orcid":null,"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":[],"raw_orcid":null,"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":[],"raw_orcid":null,"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":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9916999936103821,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9916999936103821,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/tree-of-life","display_name":"Tree of life (biology)","score":0.6395393013954163},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5278387069702148},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.40045076608657837},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3341619670391083},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2972646951675415},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14592954516410828},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.12822431325912476},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.08814963698387146},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07706379890441895}],"concepts":[{"id":"https://openalex.org/C124388736","wikidata":"https://www.wikidata.org/wiki/Q3247497","display_name":"Tree of life (biology)","level":4,"score":0.6395393013954163},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5278387069702148},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.40045076608657837},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3341619670391083},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2972646951675415},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14592954516410828},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.12822431325912476},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.08814963698387146},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07706379890441895},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2409.02335","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2409.02335","pdf_url":"https://arxiv.org/pdf/2409.02335","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2409.02335","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2409.02335","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2409.02335","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2409.02335","pdf_url":"https://arxiv.org/pdf/2409.02335","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2004270443","https://openalex.org/W2207720026","https://openalex.org/W1766380752","https://openalex.org/W2901347066","https://openalex.org/W2146536773","https://openalex.org/W2011419188","https://openalex.org/W1976078150","https://openalex.org/W4205212613","https://openalex.org/W3047355839","https://openalex.org/W1923231248"],"abstract_inverted_index":{"A":[0],"grand":[1],"challenge":[2],"in":[3,24,42,56,83,116,141,190],"biology":[4],"is":[5,45],"to":[6,15,31,49,71,123,132,155,187,192],"discover":[7,50],"evolutionary":[8,51],"traits":[9,52],"-":[10],"features":[11],"of":[12,18,27,39,59,62,77,90,105,145,160,166],"organisms":[13],"common":[14],"a":[16,21,46,60,74,119,128,151],"group":[17],"species":[19,146,189],"with":[20,147],"shared":[22],"ancestor":[23],"the":[25,36,57,88,103,142,158,167],"tree":[26,168],"life":[28],"(also":[29],"referred":[30],"as":[32],"phylogenetic":[33],"tree).":[34],"With":[35],"growing":[37],"availability":[38],"image":[40],"repositories":[41],"biology,":[43],"there":[44],"tremendous":[47],"opportunity":[48],"directly":[53],"from":[54],"images":[55],"form":[58],"hierarchy":[61],"prototypes.":[63],"However,":[64],"current":[65],"prototype-based":[66],"methods":[67],"are":[68,139,181],"mostly":[69],"designed":[70],"operate":[72],"over":[73],"flat":[75],"structure":[76],"classes":[78],"and":[79,150,185],"face":[80],"several":[81],"challenges":[82],"discovering":[84],"hierarchical":[85],"prototypes,":[86,127],"including":[87],"issue":[89],"learning":[91,125],"over-specific":[92,126,161],"prototypes":[93,134,162,179],"at":[94,135,163],"internal":[95,137],"nodes.":[96],"To":[97],"overcome":[98],"these":[99],"challenges,":[100],"we":[101],"introduce":[102],"framework":[104],"Hierarchy":[106],"aligned":[107],"Commonality":[108],"through":[109],"Prototypical":[110],"Networks":[111],"(HComP-Net).":[112],"The":[113],"key":[114],"novelties":[115],"HComP-Net":[117,177],"include":[118],"novel":[120,129,152],"over-specificity":[121],"loss":[122,131],"avoid":[124],"discriminative":[130],"ensure":[133],"an":[136],"node":[138],"absent":[140],"contrasting":[143],"set":[144],"different":[148],"ancestry,":[149],"masking":[153],"module":[154],"allow":[156],"for":[157],"exclusion":[159],"higher":[164],"levels":[165],"without":[169],"hampering":[170],"classification":[171],"performance.":[172],"We":[173],"empirically":[174],"show":[175],"that":[176,180],"learns":[178],"accurate,":[182],"semantically":[183],"consistent,":[184],"generalizable":[186],"unseen":[188],"comparison":[191],"baselines.":[193]},"counts_by_year":[],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
