BioNLP 2026

BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor 2026-07 Association for Computational Linguistics San Diego, California text conference publication 979-8-89176-434-7 bionlp-2026-1 https://aclanthology.org/2026.bionlp-1.0/ The Divergence Hypothesis: Unmasking Lexical Interference and Label Bias in Mental Health NLP Moustafa Hassan author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 hassan-2026-divergence https://aclanthology.org/2026.bionlp-1.1/ 2026-07 1 14 Towards Unified Factuality Evaluation for Biomedical QA and Summarization: Aligning Metrics with Clinical Use-Cases Mahule Roy author Subhas Roy author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 roy-roy-2026-towards https://aclanthology.org/2026.bionlp-1.2/ 2026-07 15 19 Using Synthetic Records to Improve Automated Identification of Seizure Freedom in Clinical Text about People with Epilepsy Stephen Barlow author Yujian Gan author Joe Davies author Joel Winston author James Teo author Mark Richardson author Ben Holgate author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 barlow-etal-2026-using https://aclanthology.org/2026.bionlp-1.3/ 2026-07 20 30 Analyzing Prompt Design Choices in Biomedical Information Extraction for Low-Resource Languages Ayesha Khatun author Kadir Bulut Ozler author Steven Bethard author Egoitz Laparra author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 khatun-etal-2026-analyzing https://aclanthology.org/2026.bionlp-1.4/ 2026-07 31 44 Hierarchy-Aware Hyperbolic and Semantic Reranking for Ontology-Based Phenotype Linking Thomas Labbe author Moussa Baddour author Axel Bonesteve author Paul Rollier author Marie De Tayrac author Olivier Dameron author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 labbe-etal-2026-hierarchy https://aclanthology.org/2026.bionlp-1.5/ 2026-07 45 63 Agentic Feature Selection via LLM for Epileptic Seizure Detection Aizierjiang Aiersilan author Xiaodong Qu author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 aiersilan-qu-2026-agentic https://aclanthology.org/2026.bionlp-1.6/ 2026-07 64 74 Training Biomedical Retrievers From Large-Scale Citation Contexts Xing David Wang author Duy Le Thanh author Ulf Leser author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 wang-etal-2026-training-biomedical https://aclanthology.org/2026.bionlp-1.7/ 2026-07 75 83 Reliable Automated Triage in Spanish Clinical Notes: A Hybrid Framework for Risk-Aware HIV Suspicion Identification Rodrigo Morales-Sánchez author Soto Montalvo author Raquel Martínez author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 morales-sanchez-etal-2026-reliable https://aclanthology.org/2026.bionlp-1.8/ 2026-07 84 96 Gold Label Errors in the SciFact Benchmark: An LLM-Assisted Annotation Audit Julien Sylvestre author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 sylvestre-2026-gold https://aclanthology.org/2026.bionlp-1.9/ 2026-07 97 103 BioRAG: A Systematic Ablation Study of Retrieval Strategies for Biomedical Question Answering Krushil Bhojani author Mayank Waghmare author Hima Bindu Nandyala author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 bhojani-etal-2026-biorag https://aclanthology.org/2026.bionlp-1.10/ 2026-07 104 114 Post Hoc Agentic Refinement for Improving Precision in Multilingual Clinical Text De-identification Justin Xu author Alistair Johnson author Thomas Lin author David Eyre author Rodolfo Quispe author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 xu-etal-2026-post https://aclanthology.org/2026.bionlp-1.11/ 2026-07 115 127 Do Syntactic Features Help Biomedical Relation Extraction? An Empirical Study of Verb Token and Dependency Graph Augmentation Mustafa Sikder author Ernest Kwegyir-Afful author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 sikder-kwegyir-afful-2026-syntactic https://aclanthology.org/2026.bionlp-1.12/ 2026-07 128 134 Beyond Knowledge Graphs: PubMedBERT Embeddings as a Competitive Standalone Modality for Drug Re-purposing Rishik Kondadadi author John E Ortega author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 kondadadi-ortega-2026-beyond https://aclanthology.org/2026.bionlp-1.13/ 2026-07 135 140 When Demographic Sensitivity Isn’t What It Seems: Baseline-Aware Counterfactual Audits for Clinical NLP Hyunwoo Yoo author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 yoo-2026-demographic https://aclanthology.org/2026.bionlp-1.14/ 2026-07 141 155 CoreELM: An Open-Source Framework for Aligning Large Language Models to Embedding Spaces Brian Ondov author Chia-Hsuan Chang author Yujia Zhou author Mauro Giuffrè author Hua Xu author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 ondov-etal-2026-coreelm https://aclanthology.org/2026.bionlp-1.15/ 2026-07 156 180 Uncertainty-Aware Multi-Label Routing of Clinical Text to Surveillance Pathways Agathe Zecevic author Sebastian Zeki author Angus Roberts author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 zecevic-etal-2026-uncertainty https://aclanthology.org/2026.bionlp-1.16/ 2026-07 181 190 MedCAT v2: a modular, extensible architecture for clinical named entity recognition and linking under real-world privacy and compute constraints Mart Ratas author Thomas Searle author Adam Sutton author Richard Dobson author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 ratas-etal-2026-medcat https://aclanthology.org/2026.bionlp-1.17/ 2026-07 191 198 Effects of Adaptive Pretraining in Specialized Domains for Named Entity Recognition Jack Lynam author Sam Henry author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 lynam-henry-2026-effects https://aclanthology.org/2026.bionlp-1.18/ 2026-07 199 208 Trade-offs in Medical LLM Adaptation: An Empirical Study in French QA Ikram Belmadani author Oumaima El Khettari author Carlos Ramisch author Frederic Bechet author Richard Dufour author Benoit Favre author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 belmadani-etal-2026-trade https://aclanthology.org/2026.bionlp-1.19/ 2026-07 209 234 PromptRad: Knowledge-Enhanced Multi-Label Prompt-Tuning for Low-Resource Radiology Report Labeling Ying-Jia Lin author Tzu-Chin Lo author Ping-Chien Li author Chi-Tung Cheng author Chien-Hung Liao author Hung-Yu Kao author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 lin-etal-2026-promptrad https://aclanthology.org/2026.bionlp-1.20/ 2026-07 235 249 Diagnosing Lower Extremity Arteriovenous Diseases Using Agentic LLMs Zicen Liao author Yunhao Sun author Matthew Purver author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 liao-etal-2026-diagnosing https://aclanthology.org/2026.bionlp-1.21/ 2026-07 250 267 KGRxn-LLM: Knowledge Graph Enhanced Large Language Models for Molecular Reaction Reasoning Weichen Liu author Qiyao Xue author Yuyang Wu author Olexandr Isayev author Natasa Miskov-Zivanov author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 liu-etal-2026-kgrxn https://aclanthology.org/2026.bionlp-1.22/ 2026-07 268 281 MAX-EVAL-11: A Large Scale Benchmark for Evaluating Large Language Models on Full-Spectrum ICD-11 Medical Coding Ujjwal Singh author Sarthak Deshwal author Nitish Dube author Arjun Sharma author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 singh-etal-2026-max https://aclanthology.org/2026.bionlp-1.23/ 2026-07 282 291 Trustworthy NLP for Low-Resource Languages: Agent-Based Uncertainty Modeling for Hebrew Radiology Report Structuring Hadas Ben Atya author Naama Gavrielov author Zvi Badash author Gili Focht author Ruth Cytter-Kuint author Talar Hagopian author Dan Turner author Moti Freiman author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 ben-atya-etal-2026-trustworthy https://aclanthology.org/2026.bionlp-1.24/ 2026-07 292 311 Treating Decoder-Only LLMs as Encoders: A Simple and Effective Fine-tuning Approach for Named Entity Recognition Ken Yano author Hiroya Takamura author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 yano-takamura-2026-treating https://aclanthology.org/2026.bionlp-1.25/ 2026-07 312 325 A Multi-View Framework for Cross-Domain Nutrition Misinformation Detection in Social Media Vishwaa Shah author Indika Kahanda author Andrea Arikawa author Asal Abbaszadeh author Richard Loftis author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 shah-etal-2026-multi https://aclanthology.org/2026.bionlp-1.26/ 2026-07 326 341 Ontological Validation of Biomedical Topic Models: SNOMED CT Hierarchy Distance as an Automated Evaluation Metric Ilan Rubinfeld author Sami Zaidi author Milosh Djuric author Loay Kabbani author Mouhammad Halabi author Alex Shepard author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 rubinfeld-etal-2026-ontological https://aclanthology.org/2026.bionlp-1.27/ 2026-07 342 352 Systematic Evaluation of the Quality of Synthetic Clinical Notes Rephrased by LLMs at Million-Note Scale Jinghui Liu author Sarvesh Soni author Anthony Nguyen author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 liu-etal-2026-systematic-evaluation https://aclanthology.org/2026.bionlp-1.28/ 2026-07 353 371 Bridging the Version Gap: Multi-version Training Improves ICD Code Prediction, Especially for Rare Codes Jinghui Liu author Anthony Nguyen author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 liu-nguyen-2026-bridging https://aclanthology.org/2026.bionlp-1.29/ 2026-07 372 381 EmCellLLM: Human Peri-Implantation Embryonic Cell Annotation Based on Large Language Models Xiaorui Guo author Zhiwei Liu author Qianqian Xie author Sophia Ananiadou author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 guo-etal-2026-emcellllm https://aclanthology.org/2026.bionlp-1.30/ 2026-07 382 391 Randomized Controlled Trials as the Gold-Standard for Evaluating LLMs: A Primer for Biomedical NLP Researchers Vicente Ivan Sanchez Carmona author Shanshan Jiang author Bin Dong author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 sanchez-carmona-etal-2026-randomized https://aclanthology.org/2026.bionlp-1.31/ 2026-07 392 406 Citation-Aware Continual Pre-Training for Biomedical Language Models Masaki Asada author Tomoki Tsujimura author Tatsuya Ishigaki author Shusaku Egami author Ken Fukuda author Hiroya Takamura author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 asada-etal-2026-citation https://aclanthology.org/2026.bionlp-1.32/ 2026-07 407 412 TrackList: Tracing Back Query Linguistic Diversity for Head and Tail Medical Knowledge in Open Large Language Models Ioana Buhnila author Aman Sinha author Mathieu Constant author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 buhnila-etal-2026-tracklist https://aclanthology.org/2026.bionlp-1.33/ 2026-07 413 425 Discharge Instructions are not One Task: Grounding Differences Between Surgical and Non-Surgical Admissions Mayank Jobanputra author Justin Xu author Samarth Oza author Hulma Naseer author Yifan Wang author Blerta Veseli author Chandralekha Kona author Haochen Cui author David Eyre author Vera Demberg author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 jobanputra-etal-2026-discharge https://aclanthology.org/2026.bionlp-1.34/ 2026-07 426 434 PrionNER: A Named Entity Recognition Dataset for Prion Disease Biomedical Literature An Dao author Nhan Ly author Thao Tran author Yuji Matsumoto author Akiko Aizawa author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 dao-etal-2026-prionner https://aclanthology.org/2026.bionlp-1.35/ 2026-07 435 463 Evaluation of Multilingual Text Simplification for the Mental Health Domain: Exploring Small Language Models Olga Pelloni author Sandra Just author Lars Bongo author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 pelloni-etal-2026-evaluation https://aclanthology.org/2026.bionlp-1.36/ 2026-07 464 474 BioTopicXplor: A Web Tool for Interactive Exploration of PubMed Literature through Reproducible Topics. Lana Yeganova author Donald Comeau author Won Kim author Natalie Xie author Shubo Tian author W John Wilbur author Zhiyong Lu author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 yeganova-etal-2026-biotopicxplor https://aclanthology.org/2026.bionlp-1.37/ 2026-07 475 480 Reading Between the Lines: Toward Translating Verbose Patient-authored Messages into Clinician-Formulated Questions Sarvesh Soni author Madeline Bittner author Dina Demner-Fushman author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 soni-etal-2026-reading https://aclanthology.org/2026.bionlp-1.38/ 2026-07 481 489 Investigating Stigmatizing Language in Clinical Documentation with Open-Source Large Language Models Rajashree Dahal author Pardis Hosseinpour author Pranithi Kamishetty author Satwik Pamulaparthy author Saeid Tizpaz-Niari author Natalie Parde author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 dahal-etal-2026-investigating https://aclanthology.org/2026.bionlp-1.39/ 2026-07 490 501 Learning to Combine AI Annotations for Improved Biomedical Relevance Labeling Won Gyu Kim author Lana Yeganova author Shubo Tian author Donald Comeau author W John Wilbur author Zhiyong Lu author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 kim-etal-2026-learning https://aclanthology.org/2026.bionlp-1.40/ 2026-07 502 507 When Does Retrieval Beat Direct LLM Diagnosis in Rare Disease? An Empirical Study of Ontology Coverage Mohamed Elmofty author Ulf Leser author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 elmofty-leser-2026-retrieval https://aclanthology.org/2026.bionlp-1.41/ 2026-07 508 518 BioCoref: Benchmarking Biomedical Coreference Resolution with LLMs Nourah Salem author Elizabeth White author Michael Bada author Lawrence Hunter author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 salem-etal-2026-biocoref https://aclanthology.org/2026.bionlp-1.42/ 2026-07 519 530 A Multi-Agent Open-Source LLM for Structured Cancer Registry Information Extraction from Pathology and Medical Reports Abdulrahman Aal Abdulsalam author Adhari Al Zaabi author Riham Jeeballah author Habiba El Keraby author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 aal-abdulsalam-etal-2026-multi https://aclanthology.org/2026.bionlp-1.43/ 2026-07 531 551 BioConflict: A Benchmark for Evaluating Large Language Models in Biomedical Contradiction Detection and Consensus Synthesis Ashwin Kirubakaran author Henry Gagnier author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 kirubakaran-gagnier-2026-bioconflict https://aclanthology.org/2026.bionlp-1.44/ 2026-07 552 558 Tokenization Granularity and Medical Term Representations in Language Models Vojtech Lanz author Pavel Pecina author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 lanz-pecina-2026-tokenization https://aclanthology.org/2026.bionlp-1.45/ 2026-07 559 571 CAP: A Source-Grounded Proposition Scaffold for Faithful Clinical Dialogue-to-Note Generation Hyunkyung Lee author Jisoo Jung author Jeonguk Lee author Jaehyo Yoo author Wooseok Han author Minkyu Kim author Gibaeg Kim author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 lee-etal-2026-cap https://aclanthology.org/2026.bionlp-1.46/ 2026-07 572 594 Segmentation Matters: Exploring LLM-Based Strategies for Temporal Clinical Event Identification in Oncology Reports Cristiano Bellucci author Francesco Madeddu author Chiara Iacomini author Carlotta Masciocchi author Stefano Patarnello author Massimo Bernaschi author Mario Santoro author Livia Lilli author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 bellucci-etal-2026-segmentation https://aclanthology.org/2026.bionlp-1.47/ 2026-07 595 604 Operation-Mechanism Alignment for Reliable Clinical Reasoning over Electronic Health Records Guanyu Tao author Siyao Wang author Yong Xue author Ashwani Tanwar author Yuting Ji author Kai Sun author Monica Mok author Marzana Chowdhury author Deepa Gupta author Ashok Gupta author Jingqing Zhang author Vibhor Gupta author Yike Guo author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 tao-etal-2026-operation https://aclanthology.org/2026.bionlp-1.48/ 2026-07 605 616 MeSHClass-ES and AnatEM-ES: Open Resources for Spanish Biomedical NLP Santiago Martinez Novoa author Lina Gomez Mesa author Juan Prieto author Ruben Manrique author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 martinez-novoa-etal-2026-meshclass https://aclanthology.org/2026.bionlp-1.49/ 2026-07 617 629 When Evidence Conflicts: Uncertainty and Order Effects in Retrieval-Augmented Biomedical Question Answering Yikun Han author Mengfei Lan author Halil Kilicoglu author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 han-etal-2026-evidence https://aclanthology.org/2026.bionlp-1.50/ 2026-07 630 643 A Comparative Analysis of In-Context Learning and Fine-Tuning for Biomedical Information Retrieval and Sentence Extraction Using Research Domain Criteria Athlene Jones author Khanh Lieu author Indika Kahanda author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 jones-etal-2026-comparative https://aclanthology.org/2026.bionlp-1.51/ 2026-07 644 655 Clinical Evidence and Patient Reviews: A Linked Dataset for Antidepressant Side Effects Steven Au author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 au-2026-clinical https://aclanthology.org/2026.bionlp-1.52/ 2026-07 656 664 A Deterministic Multi-Stage Retrieval Pipeline for Longitudinal EHR Question Answering Shubham Agarwal author Thomas Searle author Richard Dobson author Ninoslav Majkic author Niko Moller-Grell author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 agarwal-etal-2026-deterministic https://aclanthology.org/2026.bionlp-1.53/ 2026-07 665 678 Interpretable ICD Code Classification with Faithful Sentence Extraction Yichen Wang author Lian Hong author Masato Mizogaki author Shunnosuke Umeda author Toshimune Kenmotsu author Akihiro Tamura author Daniel Andrade author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 wang-etal-2026-interpretable-icd https://aclanthology.org/2026.bionlp-1.54/ 2026-07 679 686 Evaluating LLM-as-a-Judge for Medical Term Simplification Ioana Buhnila author Aman Sinha author Rohit Agarwal author Dilip K Prasad author Mathieu Constant author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 buhnila-etal-2026-evaluating https://aclanthology.org/2026.bionlp-1.55/ 2026-07 687 694 FACT: Functional Group Alignment and Consistency in Token Space for Structure-aware Molecular Representation Learning Hyeonyeong Nam author Woojae Choi author Deok-Joong Lee author Young-Han Son author Sangwoon Lee author Bogyeong Kang author Eunjung Jo author Tae-Eui Kam author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 nam-etal-2026-fact https://aclanthology.org/2026.bionlp-1.56/ 2026-07 695 703 Small LLMs for Biomedical Claim Verification: Cost-Effective Fine-Tuning, Structural Dataset Shortcuts, and Cross-Domain Generalization Gaurav Kumar author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 kumar-2026-small https://aclanthology.org/2026.bionlp-1.57/ 2026-07 704 712 Diagnosable ColBERT: Debugging Late-Interaction Retrieval Models Using a Learned Latent Space as Reference François Remy author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 remy-2026-diagnosable https://aclanthology.org/2026.bionlp-1.58/ 2026-07 713 717 Developing Literature Annotation Guidelines for Representing Normal Physiology in Biolink-Compatible Knowledge Graphs Madeline Bittner author Willie Rogers author Dina Demner-Fushman author Richard Scheuermann author Matthew Diller author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 bittner-etal-2026-developing https://aclanthology.org/2026.bionlp-1.59/ 2026-07 718 728 CENT: Context Engineering Framework for Normalization of Clinical Trial Procedures Sanya Taneja author Ziqing Ji author Hans Verstraete author Ali Samadani author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 taneja-etal-2026-cent https://aclanthology.org/2026.bionlp-1.60/ 2026-07 729 741 Agentic AI Architectures for SOAP Note Generation Keno Hanken author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 hanken-2026-agentic https://aclanthology.org/2026.bionlp-1.61/ 2026-07 742 752 VERICITE: Evaluating Sentence-Level Citation Faithfulness in Retrieval-Augmented Medical Question Answering Yixian Ma author Bohao Chu author Norbert Fuhr author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 ma-etal-2026-vericite https://aclanthology.org/2026.bionlp-1.62/ 2026-07 753 759 Overview of the Medical Decision Extraction, Analysis, and Classification Task (MedExACT) of BioNLP 2026 Mohamed Elgaar author Jiali Cheng author Nidhi Vakil author Mehrnaz Sadrolashrafi author Mitra Mohtarami author Adrian Wong author Hadi Amiri author Leo Celi author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 elgaar-etal-2026-overview https://aclanthology.org/2026.bionlp-1.63/ 2026-07 760 769 Divide-Prompt-Refine: a Training-Free, Structure-Aware Framework for Biomedical Abstract Generation Sylvey Lin author Joseph Menke author Shufan Ming author Dongin Nam author Neil Smalheiser author Halil Kilicoglu author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 lin-etal-2026-divide https://aclanthology.org/2026.bionlp-1.64/ 2026-07 770 790 AAbAAC: An Annotated Corpus for Autoimmunity Information Extraction Fabien Maury author Solène Grosdidier author Maud De Dieuleveult author Adrien Coulet author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 maury-etal-2026-aabaac https://aclanthology.org/2026.bionlp-1.65/ 2026-07 791 800 What Do Biomedical NER and Entity Linking Benchmarks Measure? A Corpus-Centric Diagnostic Framework Robert Leaman author Rezarta Islamaj author Zhiyong Lu author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 leaman-etal-2026-biomedical https://aclanthology.org/2026.bionlp-1.66/ 2026-07 801 811 Towards Grounded Hallucination Definitions for Biomedical Question Answering with Reproducible Examples from ClinIQLink Brandon Colelough author Davis Bartels author Madeline Bittner author Dina Demner-Fushman author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 colelough-etal-2026-towards https://aclanthology.org/2026.bionlp-1.67/ 2026-07 812 842 Can NLP Models Detect When One Publication Outweighs Twenty? Predicting Systematic Review Conclusion Changes Ebrahim Alharbi author Mark Stevenson author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 alharbi-stevenson-2026-nlp https://aclanthology.org/2026.bionlp-1.68/ 2026-07 843 852 VaxScope: Document-Level Structured Evidence Extraction from Immunization Systematic Reviews Bahar Ilgen author Ebenezer Awotoro author Georges Hattab author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 ilgen-etal-2026-vaxscope https://aclanthology.org/2026.bionlp-1.69/ 2026-07 853 863 Medical Context Variation: A source of impairment for Event classification Aman Sinha author Marianne Clausel author Mathieu Constant author Xavier Coubez author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 sinha-etal-2026-medical https://aclanthology.org/2026.bionlp-1.70/ 2026-07 864 879 KALIMBA: Knowledge-Assisted Literature Mining for Biological Interaction Analysis Niloofar Arazkhani author Maciej Kotecki author Brent Cochran author Natasa Miskov-Zivanov author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 arazkhani-etal-2026-kalimba https://aclanthology.org/2026.bionlp-1.71/ 2026-07 880 889 When Retrieval Doesn’t Help: A Large-Scale Study of Biomedical RAG Erfan Nourbakhsh author Rocky Slavin author Ke Yang author Anthony Rios author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 nourbakhsh-etal-2026-retrieval https://aclanthology.org/2026.bionlp-1.72/ 2026-07 890 910 CrossDDI: Cross-Source Evidence-Grounded Drug-Drug Interaction Verification Bohao Chu author Norbert Fuhr author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 chu-fuhr-2026-crossddi https://aclanthology.org/2026.bionlp-1.73/ 2026-07 911 919 GRAFT: Gated Retrieval-Augmented Fine-Tuning for Relation Extraction Yuhang Jiang author Ramakanth Kavuluru author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 jiang-kavuluru-2026-graft https://aclanthology.org/2026.bionlp-1.74/ 2026-07 920 931 Overview of the PsyDefDetect Shared Task at BioNLP 2026: Detecting Levels of Psychological Defense Mechanisms in Supportive Conversations Hongbin Na author Zimu Wang author Zhaoming Chen author Yining Hua author Rena Gao author Kailai Yang author Ling Chen author Wei Wang author Shaoxiong Ji author John Torous author Sophia Ananiadou author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 na-etal-2026-overview https://aclanthology.org/2026.bionlp-1.75/ 2026-07 932 943 SCoPE: Planning for Hybrid Querying over Clinical Trial Data Suparno Chowdhury author Manan Choudhury author Tejas Anvekar author Muhammed Khan author Kaneez Khakwani author Mohamad Sonbol author Irbaz Riaz author Vivek Gupta author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 chowdhury-etal-2026-scope https://aclanthology.org/2026.bionlp-1.76/ 2026-07 944 954 Expert-Guided Schema-Based Structured Extraction from CONSORT Diagrams Using Vision-Language Models Damian Stachura author Bartosz Przechera author Monika Opa?ek author Ewelina Sadowska author Ewa Borowiack author Artur Nowak author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 stachura-etal-2026-expert https://aclanthology.org/2026.bionlp-1.77/ 2026-07 955 969 From Rules to Predictions: Federated Tabular Learning with LLM Reasoning Afsaneh Mahanipour author Hana Khamfroush author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 mahanipour-khamfroush-2026-rules https://aclanthology.org/2026.bionlp-1.78/ 2026-07 970 980 MedBench: Deliberative Evaluation of Medical Language Models Pratik Jalan author Mukul Joshi author Akhilesh Magotra author Kshitij Jadhav author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 jalan-etal-2026-medbench https://aclanthology.org/2026.bionlp-1.79/ 2026-07 981 991 Fast, Accurate, and Local Conversion of MIMIC-IV to OMOP with DBT Adam Sutton author Niko Moller-Grell author Thomas Searle author Richard Dobson author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 sutton-etal-2026-fast https://aclanthology.org/2026.bionlp-1.80/ 2026-07 992 996 Exploring Novel Drug Research Area using Large Language Models Based on Research Trends in Biomedical Literature Afnan Afnan author Michael Van Supranes author Tomohiro Nishiyama author Shoko Wakamiya author Eiji Aramaki author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 afnan-etal-2026-exploring https://aclanthology.org/2026.bionlp-1.81/ 2026-07 997 1013 FHexchange: Resources for Family Health History Extraction and Normalization From Consumer Dialog Sources Michelle Nguyen author Nidhi Soley author Ayah Zirikly author João Sedoc author Casey Taylor author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 nguyen-etal-2026-fhexchange https://aclanthology.org/2026.bionlp-1.82/ 2026-07 1014 1028 Forgotten Words: Benchmarking NeoBERT for Dementia Detection in Low-Resource Conversational Filipino and English Speech Rez Samantha Floresca author Edric Castel Hao author Hannah Grachiella Buñales author Chelsea Dominique Temprosa author Georgianna Reyes author Kervin Gabriel Chua author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 floresca-etal-2026-forgotten https://aclanthology.org/2026.bionlp-1.83/ 2026-07 1029 1040 IndicMedDialog: A Parallel Multi-Turn Medical Dialogue Dataset for Accessible Healthcare in Indic Languages Shubham Nigam author Suparnojit Sarkar author Piyush Patel author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 nigam-etal-2026-indicmeddialog https://aclanthology.org/2026.bionlp-1.84/ 2026-07 1041 1055 Towards a Radiologist Imitation Framework for 3D CT Diagnosis with Multimodal LLMs Kaidi Zhang author Zhiyuan Yan author Gao Cheng author Zhenyang Cai author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 zhang-etal-2026-towards-radiologist https://aclanthology.org/2026.bionlp-1.85/ 2026-07 1056 1065 Probing and Steering Uncertainty in Biomedical Language Models: Representational Structure and Behavioral Limits Debmalya Pal author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 pal-2026-probing https://aclanthology.org/2026.bionlp-1.86/ 2026-07 1066 1079 Relations of Linguistic Features and Medical Text Preferences are Nontrivial Davis Bartels author Brandon Colelough author Dina Demner-Fushman author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 bartels-etal-2026-relations https://aclanthology.org/2026.bionlp-1.87/ 2026-07 1080 1088 Overview of the MedGenVidQA 2026 Shared Task on Medical Generative Video Question Answering Deepak Gupta author Collin Campbell author Pedram Golnari author Dina Demner-Fushman author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 gupta-etal-2026-overview https://aclanthology.org/2026.bionlp-1.88/ 2026-07 1089 1100 Overview of the ClinicalSkillQA 2026 Shared Task on Continuous Perception and Procedural Reasoning in Clinical Skill Assessment Xiyang Huang author Renxiong Wei author Yihuai Xu author Zhiyuan Chen author Keying Wu author Jiayi Xiang author Buzhou Tang author Yanqing Ye author Jinyu Chen author Cheng Zeng author Min Peng author Qianqian Xie author Sophia Ananiadou author 2026-07 text BioNLP 2026 Dina Demner-Fushman editor Sophia Ananiadou editor Kirk Roberts editor Junichi Tsujii editor Association for Computational Linguistics San Diego, California conference publication 979-8-89176-434-7 huang-etal-2026-overview https://aclanthology.org/2026.bionlp-1.89/ 2026-07 1101 1108