{"id":"https://openalex.org/W4414943204","doi":"https://doi.org/10.1109/iccv51701.2025.02121","title":"Integrating Biological Knowledge for Robust Microscopy Image Profiling on De Novo Cell Lines","display_name":"Integrating Biological Knowledge for Robust Microscopy Image Profiling on De Novo Cell Lines","publication_year":2025,"publication_date":"2025-10-19","ids":{"openalex":"https://openalex.org/W4414943204","doi":"https://doi.org/10.1109/iccv51701.2025.02121"},"language":"en","primary_location":{"id":"doi:10.1109/iccv51701.2025.02121","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccv51701.2025.02121","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE/CVF International Conference on Computer Vision (ICCV)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2507.10737","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031618552","display_name":"Jiayuan Chen","orcid":"https://orcid.org/0000-0002-2581-951X"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiayuan Chen","raw_affiliation_strings":["The Ohio State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Ohio State University","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076650478","display_name":"Thai-Hoang Pham","orcid":"https://orcid.org/0000-0002-1733-6155"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thai-Hoang Pham","raw_affiliation_strings":["The Ohio State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Ohio State University","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101720890","display_name":"Yuanlong Wang","orcid":"https://orcid.org/0009-0009-1022-5581"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuanlong Wang","raw_affiliation_strings":["The Ohio State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Ohio State University","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000873881","display_name":"Ping Zhang","orcid":"https://orcid.org/0000-0002-9620-8193"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ping Zhang","raw_affiliation_strings":["The Ohio State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Ohio State University","institution_ids":["https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I52357470"],"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":"22846","last_page":"22856"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9970999956130981,"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":0.9970999956130981,"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/T13114","display_name":"Image Processing Techniques and Applications","score":0.9789000153541565,"subfield":{"id":"https://openalex.org/subfields/2214","display_name":"Media Technology"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.9218000173568726,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.7067999839782715},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.524399995803833},{"id":"https://openalex.org/keywords/biological-cell","display_name":"Biological cell","score":0.4456999897956848},{"id":"https://openalex.org/keywords/high-content-screening","display_name":"High-content screening","score":0.4009000062942505},{"id":"https://openalex.org/keywords/microscopy","display_name":"Microscopy","score":0.3910999894142151},{"id":"https://openalex.org/keywords/cell-culture","display_name":"Cell culture","score":0.359499990940094},{"id":"https://openalex.org/keywords/biological-imaging","display_name":"Biological imaging","score":0.35109999775886536},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.33169999718666077}],"concepts":[{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.7067999839782715},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5716999769210815},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5324000120162964},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.524399995803833},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5074999928474426},{"id":"https://openalex.org/C2983013280","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Biological cell","level":2,"score":0.4456999897956848},{"id":"https://openalex.org/C157044486","wikidata":"https://www.wikidata.org/wiki/Q5754482","display_name":"High-content screening","level":3,"score":0.4009000062942505},{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.3910999894142151},{"id":"https://openalex.org/C81885089","wikidata":"https://www.wikidata.org/wiki/Q189082","display_name":"Cell culture","level":2,"score":0.359499990940094},{"id":"https://openalex.org/C2779884411","wikidata":"https://www.wikidata.org/wiki/Q4914995","display_name":"Biological imaging","level":3,"score":0.35109999775886536},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.33169999718666077},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.3142000138759613},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.31349998712539673},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3133000135421753},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30309998989105225},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.2962000072002411},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.29429998993873596},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.29420000314712524},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.2797999978065491},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.27379998564720154},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.27239999175071716},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.2721000015735626},{"id":"https://openalex.org/C15526883","wikidata":"https://www.wikidata.org/wiki/Q6657126","display_name":"Live cell imaging","level":3,"score":0.26899999380111694},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26339998841285706},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2574000060558319},{"id":"https://openalex.org/C2993684226","wikidata":"https://www.wikidata.org/wiki/Q2662727","display_name":"Human cell","level":3,"score":0.2565999925136566},{"id":"https://openalex.org/C147905033","wikidata":"https://www.wikidata.org/wiki/Q1378887","display_name":"Primary cell","level":3,"score":0.2538999915122986}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/iccv51701.2025.02121","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccv51701.2025.02121","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE/CVF International Conference on Computer Vision (ICCV)","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:2507.10737","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2507.10737","pdf_url":"https://arxiv.org/pdf/2507.10737","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":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2507.10737","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2507.10737","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":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2507.10737","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2507.10737","pdf_url":"https://arxiv.org/pdf/2507.10737","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":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2681174601","display_name":null,"funder_award_id":"R01AI188576","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5936910705","display_name":null,"funder_award_id":"R01GM141279","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7620595296","display_name":"CAREER: Developing Actionable Methods for Observational Health Data","funder_award_id":"2145625","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"High-throughput":[0],"screening":[1,28],"techniques,":[2],"such":[3],"as":[4],"microscopy":[5,66,171],"imaging":[6,131],"of":[7,130],"cellular":[8],"responses":[9],"to":[10,37,64,98,115,133],"genetic":[11],"and":[12,22,41,75,95,154],"chemical":[13],"perturbations,":[14],"play":[15],"a":[16,52,86],"crucial":[17],"role":[18],"in":[19,182],"drug":[20,185],"discovery":[21,186],"biomedical":[23],"research.":[24],"However,":[25],"robust":[26],"perturbation":[27],"for":[29,174],"\\textit{de":[30,134,175],"novo}":[31,135,176],"cell":[32,45,76,117,136,152,158,177],"lines":[33,159],"remains":[34],"challenging":[35],"due":[36],"the":[38,128,143,161],"significant":[39],"morphological":[40],"biological":[42,58,81],"heterogeneity":[43],"across":[44],"lines.":[46,137],"To":[47],"address":[48],"this,":[49],"we":[50,84,107],"propose":[51],"novel":[53],"framework":[54,141],"that":[55,167],"integrates":[56],"external":[57,80],"knowledge":[59,87],"into":[60],"existing":[61],"pretraining":[62],"strategies":[63],"enhance":[65],"image":[67,172],"profiling":[68,173],"models.":[69],"Our":[70],"approach":[71],"explicitly":[72],"disentangles":[73],"perturbation-specific":[74,102],"line-specific":[77,118],"representations":[78],"using":[79],"information.":[82],"Specifically,":[83],"construct":[85],"graph":[88],"leveraging":[89],"protein":[90],"interaction":[91],"data":[92],"from":[93,111,160],"STRING":[94],"Hetionet":[96],"databases":[97],"guide":[99],"models":[100,114,132],"toward":[101],"features":[103,110],"during":[104],"pretraining.":[105],"Additionally,":[106],"incorporate":[108],"transcriptomic":[109],"single-cell":[112],"foundation":[113],"capture":[116],"representations.":[119],"By":[120],"learning":[121],"these":[122],"disentangled":[123],"features,":[124],"our":[125,140,168],"method":[126,169],"improves":[127],"generalization":[129],"We":[138],"evaluate":[139],"on":[142,149,157],"RxRx":[144],"database":[145],"through":[146],"one-shot":[147],"fine-tuning":[148,156],"an":[150],"RxRx1":[151],"line":[153],"few-shot":[155],"RxRx19a":[162],"dataset.":[163],"Experimental":[164],"results":[165],"demonstrate":[166],"enhances":[170],"lines,":[178],"highlighting":[179],"its":[180],"effectiveness":[181],"real-world":[183],"phenotype-based":[184],"applications.":[187]},"counts_by_year":[],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
