{"id":"https://openalex.org/W4416037197","doi":"https://doi.org/10.18653/v1/2025.emnlp-industry.159","title":"BIOPSY - Biomarkers In Oncology: Pipeline for Structured Yielding","display_name":"BIOPSY - Biomarkers In Oncology: Pipeline for Structured Yielding","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4416037197","doi":"https://doi.org/10.18653/v1/2025.emnlp-industry.159"},"language":null,"primary_location":{"id":"doi:10.18653/v1/2025.emnlp-industry.159","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2025.emnlp-industry.159","pdf_url":"https://aclanthology.org/2025.emnlp-industry.159.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing: Industry Track","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://aclanthology.org/2025.emnlp-industry.159.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063037019","display_name":"Sanya A. Chetwani","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sanya A. Chetwani","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5120309189","display_name":"Jaseem Mahmmdla","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jaseem Mahmmdla","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":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.29618768,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"2313","last_page":"2321"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10183","display_name":"Breast Cancer Treatment Studies","score":0.062300000339746475,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10183","display_name":"Breast Cancer Treatment Studies","score":0.062300000339746475,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10755","display_name":"HER2/EGFR in Cancer Research","score":0.05909999832510948,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10336","display_name":"Cancer Cells and Metastasis","score":0.04879999905824661,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.599399983882904},{"id":"https://openalex.org/keywords/biopsy","display_name":"Biopsy","score":0.3174999952316284},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.2581000030040741},{"id":"https://openalex.org/keywords/medical-imaging","display_name":"Medical imaging","score":0.21629999577999115}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.599399983882904},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.47870001196861267},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4043000042438507},{"id":"https://openalex.org/C126838900","wikidata":"https://www.wikidata.org/wiki/Q77604","display_name":"Radiology","level":1,"score":0.35830000042915344},{"id":"https://openalex.org/C2775934546","wikidata":"https://www.wikidata.org/wiki/Q179991","display_name":"Biopsy","level":2,"score":0.3174999952316284},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2969000041484833},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.2581000030040741},{"id":"https://openalex.org/C136229726","wikidata":"https://www.wikidata.org/wiki/Q327092","display_name":"Biomedical engineering","level":1,"score":0.23929999768733978},{"id":"https://openalex.org/C31601959","wikidata":"https://www.wikidata.org/wiki/Q931309","display_name":"Medical imaging","level":2,"score":0.21629999577999115},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2134999930858612}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.18653/v1/2025.emnlp-industry.159","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2025.emnlp-industry.159","pdf_url":"https://aclanthology.org/2025.emnlp-industry.159.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing: Industry Track","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.18653/v1/2025.emnlp-industry.159","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2025.emnlp-industry.159","pdf_url":"https://aclanthology.org/2025.emnlp-industry.159.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing: Industry Track","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4416037197.pdf","grobid_xml":"https://content.openalex.org/works/W4416037197.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"In":[0],"clinical":[1,24,80,108,131],"science,":[2],"biomarkers":[3,19,59],"are":[4],"crucial":[5],"indicators":[6],"for":[7,91,95,123],"early":[8],"cancer":[9],"detection,":[10],"prognosis,":[11],"and":[12,20,29,67,93,115,128],"guiding":[13],"personalized":[14],"treatment":[15],"decisions.Although":[16],"critical,":[17],"extracting":[18],"their":[21,61],"levels":[22],"from":[23],"texts":[25],"remains":[26],"a":[27,47,53,64,69],"complex":[28],"underexplored":[30],"problem":[31],"in":[32,130],"natural":[33],"language":[34],"processing":[35],"research.In":[36],"this":[37],"paper,":[38],"we":[39],"present":[40],"BIOPSY,":[41],"an":[42,85],"end-to-end":[43],"pipeline":[44,103],"that":[45],"integrates":[46],"domain-adapted":[48],"biomarker":[49,74,126],"entity":[50],"recognition":[51],"model,":[52],"relation":[54],"extraction":[55,127],"model":[56],"to":[57,60,72,104],"link":[58],"respective":[62],"mutations,":[63],"biomarker-type":[65],"classifier,":[66],"finally,":[68],"tailored":[70],"algorithm":[71],"capture":[73],"expression":[75],"levels.Evaluated":[76],"on":[77],"5,000":[78],"real-world":[79],"texts,":[81],"our":[82],"system":[83],"achieved":[84],"overall":[86],"F1":[87],"score":[88],"of":[89,101],"0.86":[90],"oncology":[92],"0.87":[94],"neuroscience":[96],"domains.This":[97],"reveals":[98],"the":[99,102,119],"ability":[100],"adapt":[105],"across":[106],"various":[107],"sources,":[109],"including":[110],"trial":[111],"records,":[112],"research":[113],"papers,":[114],"medical":[116],"notes,":[117],"offering":[118],"first":[120],"comprehensive":[121],"solution":[122],"end-to-end,":[124],"contextaware":[125],"interpretation":[129],"research.":[132]},"counts_by_year":[],"updated_date":"2026-08-25T07:29:55.448023","created_date":"2025-11-08T00:00:00"}
