{"id":"https://openalex.org/W7148885380","doi":"https://doi.org/10.48550/arxiv.2604.01619","title":"Automatic Image-Level Morphological Trait Annotation for Organismal Images","display_name":"Automatic Image-Level Morphological Trait Annotation for Organismal Images","publication_year":2026,"publication_date":"2026-04-02","ids":{"openalex":"https://openalex.org/W7148885380","doi":"https://doi.org/10.48550/arxiv.2604.01619"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2604.01619","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.01619","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":false,"raw_source_name":null,"raw_type":"article"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2604.01619","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102752724","display_name":"Vardaan Pahuja","orcid":"https://orcid.org/0000-0001-7538-8474"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Pahuja, Vardaan","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5132872400","display_name":"Samuel Stevens","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Stevens, Samuel","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024095643","display_name":"Alyson East","orcid":"https://orcid.org/0000-0003-1143-1255"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"East, Alyson","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5132919592","display_name":"Sydne Record","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Record, Sydne","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5132867174","display_name":"Yu Su","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Su, Yu","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5102752724"],"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.7095999717712402,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.7095999717712402,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.030500000342726707,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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/T10895","display_name":"Species Distribution and Climate Change","score":0.026799999177455902,"subfield":{"id":"https://openalex.org/subfields/2302","display_name":"Ecological Modeling"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/trait","display_name":"Trait","score":0.718500018119812},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.670799970626831},{"id":"https://openalex.org/keywords/salient","display_name":"Salient","score":0.6281999945640564},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.6276999711990356},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5839999914169312},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.4810999929904938},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.4641999900341034},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.42829999327659607},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.36579999327659607}],"concepts":[{"id":"https://openalex.org/C106934330","wikidata":"https://www.wikidata.org/wiki/Q1971873","display_name":"Trait","level":2,"score":0.718500018119812},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.670799970626831},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6305000185966492},{"id":"https://openalex.org/C2780719617","wikidata":"https://www.wikidata.org/wiki/Q1030752","display_name":"Salient","level":2,"score":0.6281999945640564},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.6276999711990356},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5839999914169312},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5636000037193298},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.4810999929904938},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.4641999900341034},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.42829999327659607},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.36579999327659607},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.361299991607666},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.35100001096725464},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.3449000120162964},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.325300008058548},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.3098999857902527},{"id":"https://openalex.org/C177606310","wikidata":"https://www.wikidata.org/wiki/Q5674297","display_name":"Adaptability","level":2,"score":0.30820000171661377},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.26910001039505005},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2687000036239624},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.2678999900817871},{"id":"https://openalex.org/C16345878","wikidata":"https://www.wikidata.org/wiki/Q107472979","display_name":"Orientation (vector space)","level":2,"score":0.2667999863624573},{"id":"https://openalex.org/C130073038","wikidata":"https://www.wikidata.org/wiki/Q1211967","display_name":"Phenotypic trait","level":4,"score":0.26420000195503235},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.25679999589920044},{"id":"https://openalex.org/C63882131","wikidata":"https://www.wikidata.org/wiki/Q17122954","display_name":"Strengths and weaknesses","level":2,"score":0.25209999084472656},{"id":"https://openalex.org/C2776502983","wikidata":"https://www.wikidata.org/wiki/Q690182","display_name":"Contrast (vision)","level":2,"score":0.2500999867916107}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2604.01619","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.01619","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":"doi:10.48550/arxiv.2604.01619","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.01619","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":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Morphological":[0],"traits":[1,22,153],"are":[2],"physical":[3],"characteristics":[4],"of":[5,41,104,120,146],"biological":[6,45,118],"organisms":[7,14],"that":[8,55,67,83],"provide":[9],"vital":[10],"clues":[11],"on":[12,59,70,143],"how":[13],"interact":[15],"with":[16,154],"their":[17,29,141],"environment.":[18],"Yet":[19],"extracting":[20],"these":[21],"remains":[23],"a":[24,79,102,130,155,166],"slow,":[25],"expert-driven":[26],"process,":[27],"limiting":[28],"use":[30],"in":[31],"large-scale":[32,178],"ecological":[33,186],"studies.":[34],"A":[35],"major":[36],"bottleneck":[37],"is":[38],"the":[39,117,121,144,147,183],"absence":[40],"high-quality":[42],"datasets":[43],"linking":[44],"images":[46,111],"to":[47,91,169],"trait-level":[48],"annotations.":[49],"In":[50],"this":[51,75,97],"work,":[52],"we":[53,77,99,164],"demonstrate":[54],"sparse":[56],"autoencoders":[57],"trained":[58],"foundation-model":[60],"features":[61],"yield":[62],"monosemantic,":[63],"spatially":[64],"grounded":[65],"neurons":[66],"consistently":[68],"activate":[69],"meaningful":[71,172],"morphological":[72,123,179],"parts.":[73],"Leveraging":[74],"property,":[76],"introduce":[78],"trait":[80,94,106,149],"annotation":[81],"pipeline":[82,157],"localizes":[84],"salient":[85],"regions":[86],"and":[87,139,181,188],"uses":[88],"vision-language":[89],"prompting":[90],"generate":[92],"interpretable":[93],"descriptions.":[95,124,150],"Using":[96],"approach,":[98],"construct":[100],"Bioscan-Traits,":[101],"dataset":[103],"80K":[105],"annotations":[107],"spanning":[108],"19K":[109],"insect":[110],"from":[112],"BIOSCAN-5M.":[113],"Human":[114],"evaluation":[115],"confirms":[116],"plausibility":[119],"generated":[122],"We":[125],"assess":[126],"design":[127,137],"sensitivity":[128],"through":[129],"comprehensive":[131],"ablation":[132],"study,":[133],"systematically":[134],"varying":[135],"key":[136],"choices":[138],"measuring":[140],"impact":[142],"quality":[145],"resulting":[148],"By":[151],"annotating":[152],"modular":[156],"rather":[158],"than":[159],"prohibitively":[160],"expensive":[161],"manual":[162],"efforts,":[163],"offer":[165],"scalable":[167],"way":[168],"inject":[170],"biologically":[171],"supervision":[173],"into":[174],"foundation":[175],"models,":[176],"enable":[177],"analyses,":[180],"bridge":[182],"gap":[184],"between":[185],"relevance":[187],"machine-learning":[189],"practicality.":[190]},"counts_by_year":[],"updated_date":"2026-04-04T06:15:33.020886","created_date":"2026-04-04T00:00:00"}
