{"id":"https://openalex.org/W7134953382","doi":"https://doi.org/10.48550/arxiv.2603.08935","title":"PathoScribe: Transforming Pathology Data into a Living Library with a Unified LLM-Driven Framework for Semantic Retrieval and Clinical Integration","display_name":"PathoScribe: Transforming Pathology Data into a Living Library with a Unified LLM-Driven Framework for Semantic Retrieval and Clinical Integration","publication_year":2026,"publication_date":"2026-03-09","ids":{"openalex":"https://openalex.org/W7134953382","doi":"https://doi.org/10.48550/arxiv.2603.08935"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2603.08935","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.08935","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2603.08935","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062903400","display_name":"Abdul Akbar","orcid":"https://orcid.org/0009-0004-2352-6360"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Akbar, Abdul Rehman","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128787739","display_name":"Samuel Wales-McGrath","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wales-McGrath, Samuel","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128710551","display_name":"Alejadro Levya","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Levya, Alejadro","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128700982","display_name":"Lina Gokhale","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gokhale, Lina","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128785448","display_name":"Rajendra Singh","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Singh, Rajendra","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128702259","display_name":"Wei Chen","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chen, Wei","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128756677","display_name":"Anil Parwani","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Parwani, Anil","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5128759672","display_name":"Muhammad Khalid Khan Niazi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Niazi, Muhammad Khalid Khan","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/T10028","display_name":"Topic Modeling","score":0.2653000056743622,"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/T10028","display_name":"Topic Modeling","score":0.2653000056743622,"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"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.24529999494552612,"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/T10862","display_name":"AI in cancer detection","score":0.1527000069618225,"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/operationalization","display_name":"Operationalization","score":0.6446999907493591},{"id":"https://openalex.org/keywords/digital-pathology","display_name":"Digital pathology","score":0.6424999833106995},{"id":"https://openalex.org/keywords/snomed-ct","display_name":"SNOMED CT","score":0.5938000082969666},{"id":"https://openalex.org/keywords/natural-language","display_name":"Natural language","score":0.4196999967098236},{"id":"https://openalex.org/keywords/cohort","display_name":"Cohort","score":0.35690000653266907},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.34459999203681946},{"id":"https://openalex.org/keywords/surgical-pathology","display_name":"Surgical pathology","score":0.3264000117778778},{"id":"https://openalex.org/keywords/chart","display_name":"Chart","score":0.3163999915122986}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6467000246047974},{"id":"https://openalex.org/C9354725","wikidata":"https://www.wikidata.org/wiki/Q286017","display_name":"Operationalization","level":2,"score":0.6446999907493591},{"id":"https://openalex.org/C2777522853","wikidata":"https://www.wikidata.org/wiki/Q5276128","display_name":"Digital pathology","level":2,"score":0.6424999833106995},{"id":"https://openalex.org/C206497026","wikidata":"https://www.wikidata.org/wiki/Q1753883","display_name":"SNOMED CT","level":3,"score":0.5938000082969666},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5358999967575073},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4244000017642975},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.4196999967098236},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4011000096797943},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36340001225471497},{"id":"https://openalex.org/C72563966","wikidata":"https://www.wikidata.org/wiki/Q1303415","display_name":"Cohort","level":2,"score":0.35690000653266907},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.3564000129699707},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.34459999203681946},{"id":"https://openalex.org/C194495517","wikidata":"https://www.wikidata.org/wiki/Q7646222","display_name":"Surgical pathology","level":2,"score":0.3264000117778778},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.32409998774528503},{"id":"https://openalex.org/C190812933","wikidata":"https://www.wikidata.org/wiki/Q28923","display_name":"Chart","level":2,"score":0.3163999915122986},{"id":"https://openalex.org/C551230270","wikidata":"https://www.wikidata.org/wiki/Q4368942","display_name":"Data retrieval","level":2,"score":0.30790001153945923},{"id":"https://openalex.org/C180198813","wikidata":"https://www.wikidata.org/wiki/Q121182","display_name":"Information system","level":2,"score":0.3041999936103821},{"id":"https://openalex.org/C44291984","wikidata":"https://www.wikidata.org/wiki/Q1074173","display_name":"Question answering","level":2,"score":0.3027999997138977},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.299699991941452},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.2955999970436096},{"id":"https://openalex.org/C4438859","wikidata":"https://www.wikidata.org/wiki/Q186117","display_name":"Timeline","level":2,"score":0.29269999265670776},{"id":"https://openalex.org/C19527891","wikidata":"https://www.wikidata.org/wiki/Q1120908","display_name":"Medical physics","level":1,"score":0.2867000102996826},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.2854999899864197},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.2784999907016754},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.27810001373291016},{"id":"https://openalex.org/C144559511","wikidata":"https://www.wikidata.org/wiki/Q2986279","display_name":"Principal (computer security)","level":2,"score":0.260699987411499}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2603.08935","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.08935","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2603.08935","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.08935","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[{"score":0.7425705194473267,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Pathology":[0],"underpins":[1],"modern":[2],"diagnosis":[3],"and":[4,38,122,146,180,191],"cancer":[5],"care,":[6],"yet":[7],"its":[8],"most":[9],"valuable":[10],"asset,":[11],"the":[12,65,156],"accumulated":[13],"experience":[14],"encoded":[15],"in":[16,74,169,189],"millions":[17],"of":[18],"narrative":[19],"reports,":[20,136],"remains":[21],"largely":[22],"inaccessible.":[23],"Although":[24],"institutions":[25],"are":[26],"rapidly":[27],"digitizing":[28],"pathology":[29,98,135,208],"workflows,":[30],"storing":[31],"data":[32,46],"without":[33],"effective":[34],"mechanisms":[35],"for":[36,67,141,205],"retrieval":[37,145],"reasoning":[39,150],"risks":[40],"transforming":[41],"archives":[42,99,209],"into":[43,100,214],"a":[44,79,86,101,127,202],"passive":[45,211],"repository,":[47],"where":[48],"institutional":[49],"knowledge":[50],"exists":[51],"but":[52,64],"cannot":[53],"meaningfully":[54],"inform":[55],"patient":[56],"care.":[57],"True":[58],"progress":[59],"requires":[60],"not":[61],"only":[62],"digitization,":[63],"ability":[66],"pathologists":[68],"to":[69,95,177,194],"interrogate":[70],"prior":[71],"similar":[72],"cases":[73,183],"real":[75],"time":[76,190],"while":[77],"evaluating":[78],"new":[80],"diagnostic":[81],"dilemma.":[82],"We":[83],"present":[84],"PathoScribe,":[85],"unified":[87],"retrieval-augmented":[88],"large":[89],"language":[90,109,143],"model":[91],"(LLM)":[92],"framework":[93],"designed":[94],"transform":[96],"static":[97],"searchable,":[102],"reasoning-enabled":[103],"living":[104],"library.":[105],"PathoScribe":[106,137],"enables":[107],"natural":[108,142],"case":[110,144],"exploration,":[111],"automated":[112,159],"cohort":[113,160],"construction,":[114],"clinical":[115,216],"question":[116],"answering,":[117],"immunohistochemistry":[118],"(IHC)":[119],"panel":[120],"recommendation,":[121],"prompt-controlled":[123],"report":[124],"transformation":[125],"within":[126],"single":[128],"architecture.":[129],"Evaluated":[130],"on":[131],"70,000":[132],"multi-institutional":[133],"surgical":[134],"achieved":[138],"perfect":[139],"Recall@10":[140],"demonstrated":[147],"high-quality":[148],"retrieval-grounded":[149],"(mean":[151,171],"reviewer":[152],"score":[153],"4.56/5).":[154],"Critically,":[155],"system":[157],"operationalized":[158],"construction":[161],"from":[162,210],"free-text":[163],"eligibility":[164],"criteria,":[165],"assembling":[166],"research-ready":[167],"cohorts":[168],"minutes":[170],"9.2":[172],"minutes)":[173],"with":[174],"91.3%":[175],"agreement":[176],"human":[178],"reviewers":[179],"no":[181],"eligible":[182],"incorrectly":[184],"excluded,":[185],"representing":[186],"orders-of-magnitude":[187],"reductions":[188],"cost":[192],"compared":[193],"traditional":[195],"manual":[196],"chart":[197],"review.":[198],"This":[199],"work":[200],"establishes":[201],"scalable":[203],"foundation":[204],"converting":[206],"digital":[207],"storage":[212],"systems":[213],"active":[215],"intelligence":[217],"platforms.":[218]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2026-03-12T00:00:00"}
