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BioNLP 2026: all accepted papers

124 papers · page 1 of 2 · the most cited first · ← BioNLP 2026

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  1. Operation-Mechanism Alignment for Reliable Clinical Reasoning over Electronic Health RecordsGuanyu Tao, Siyao Wang, Yong Xue et al.1 citation · our summary
  2. PromptRad: Knowledge-Enhanced Multi-Label Prompt-Tuning for Low-Resource Radiology Report Labeling ↗Ying-Jia Lin, Tzu-Chin Lo, Ping-Chien Li et al.1 citation
  3. A Comparative Analysis of In-Context Learning and Fine-Tuning for Biomedical Information Retrieval and Sentence Extraction Using Research Domain Criteria ↗Athlene Jones, Khanh Lieu, Indika Kahanda
  4. A Deterministic Multi-Stage Retrieval Pipeline for Longitudinal EHR Question Answering ↗Shubham Agarwal, Thomas Searle, Richard Dobson et al.
  5. A Multi-Agent Open-Source LLM for Structured Cancer Registry Information Extraction from Pathology and Medical Reports ↗Abdulrahman Aal Abdulsalam, Adhari Al Zaabi, Riham Jeeballah et al.
  6. A Multi-View Framework for Cross-Domain Nutrition Misinformation Detection in Social MediaVishwaa Shah, Indika Kahanda, Andrea Arikawa et al.our summary
  7. AAbAAC: An Annotated Corpus for Autoimmunity Information ExtractionFabien Maury, Solène Grosdidier, Maud de Dieuleveult et al.our summary
  8. Agentic AI Architectures for SOAP Note Generation ↗Keno Hanken
  9. Agentic Feature Selection via LLM for Epileptic Seizure Detection ↗Aizierjiang Aiersilan, Xiaodong Qu
  10. AlienAnnotators at PsyDefDetect: What Lies Between the Lines: Probing Lightweight Open-Source LLMs for Psychological Defense Mechanism Detection ↗Siam Rahman Karip, Nahid Hossain
  11. Analyzing Prompt Design Choices in Biomedical Information Extraction for Low-Resource Languages ↗Ayesha Khatun, Kadir Bulut Ozler, Steven Bethard et al.
  12. Beyond Knowledge Graphs: PubMedBERT Embeddings as a Competitive Standalone Modality for Drug Re-purposing ↗Rishik Kondadadi, John E. Ortega
  13. BioConflict: A Benchmark for Evaluating Large Language Models in Biomedical Contradiction Detection and Consensus Synthesis ↗Ashwin Kirubakaran, Henry Gagnier
  14. BioCoref: Benchmarking Biomedical Coreference Resolution with LLMs ↗Nourah Salem, Elizabeth White, Michael Bada et al.
  15. BioRAG: A Systematic Ablation Study of Retrieval Strategies for Biomedical Question Answering ↗Krushil Bhojani, Mayank Waghmare, Hima Bindu Nandyala
  16. BioTopicXplor: A Web Tool for Interactive Exploration of PubMed Literature through Reproducible Topics. ↗Lana Yeganova, Donald Comeau, Won Kim et al.
  17. Bridging the Version Gap: Multi-version Training Improves ICD Code Prediction, Especially for Rare Codes ↗Jinghui Liu, Anthony Nguyen
  18. CAP: A Source-Grounded Proposition Scaffold for Faithful Clinical Dialogue-to-Note Generation ↗Hyunkyung Lee, Jisoo Jung, Jeonguk Lee et al.
  19. CASPAR: A Context-Aware Span Refinement Approach for Decision SupportJing Tao, Amir Eskandari, Farhana Zulkernineour summary
  20. CENT: Context Engineering Framework for Normalization of Clinical Trial ProceduresSanya Taneja, Ziqing Ji, Hans Verstraete et al.our summary
  21. CS_Metro at PsyDefDetect: Detecting Psychological Defense Mechanisms in Mental Health Dialogues with Summarization-Enhanced Transformer EnsemblesOarisa Rebayet, Radiul Walee, Symom Hossain Shohan et al.our summary
  22. CUAMC @ MedExACT 2026: Robust Ensemble Voting for Fair Medical Decision Extraction ↗William Baumgartner, Lisa Schilling
  23. Can NLP Models Detect When One Publication Outweighs Twenty? Predicting Systematic Review Conclusion Changes ↗Ebrahim Alharbi, Mark Stevenson
  24. Citation-Aware Continual Pre-Training for Biomedical Language Models ↗Masaki Asada, Tomoki Tsujimura, Tatsuya Ishigaki et al.
  25. Clinical Evidence and Patient Reviews: A Linked Dataset for Antidepressant Side Effects ↗Steven Au
  26. CoreELM: An Open-Source Framework for Aligning Large Language Models to Embedding SpacesBrian Ondov, Chia-Hsuan Chang, Yujia Zhou et al.our summary
  27. CrossDDI: Cross-Source Evidence-Grounded Drug-Drug Interaction VerificationHui Wang, Bohao Chu, Norbert Fuhrour summary
  28. DAL Team at PsyDefDetect: From Supervised Encoders to Hierarchical LLM-RAG for Psychological Defense DetectionDuc-Luong Tran, Phuong-Anh Chu, Hoang-Dat Do et al.our summary
  29. DLNLP at ClinicalSkillQA: EvidenceFlow for Structured Zero-Shot Clinical Keyframe Ordering ↗Kexin Li, Zhekun Wang, Yiran Wang et al.
  30. Developing Literature Annotation Guidelines for Representing Normal Physiology in Biolink-Compatible Knowledge Graphs ↗Madeline Bittner, Willie Rogers, Dina Demner-Fushman et al.
  31. Diagnosable ColBERT: Debugging Late-Interaction Retrieval Models Using a Learned Latent Space as ReferenceFrançois Remyour summary
  32. Diagnosing Lower Extremity Arteriovenous Diseases Using Agentic LLMs ↗Zicen Liao, Yunhao Sun, Matthew Purver
  33. Discharge Instructions are not One Task: Grounding Differences Between Surgical and Non-Surgical Admissions ↗Mayank Jobanputra, Justin Xu, Samarth Oza et al.
  34. Diverse Transformer Ensemble with Majority Voting for Medical Decision Extraction at MedExACT 2026 ↗Rishik Kondadadi
  35. Divide-Prompt-Refine: a Training-Free, Structure-Aware Framework for Biomedical Abstract Generation ↗Sylvey Lin, Joseph Menke, Shufan Ming et al.
  36. Do Syntactic Features Help Biomedical Relation Extraction? An Empirical Study of Verb Token and Dependency Graph AugmentationMustafa Sikder, Ernest Kwegyir-Affulour summary
  37. ELiRF-UPV@MedExACT 2026: Dynamic Section Conditioning for Medical Decision Span Detection in Discharge Summaries ↗Vicent Ahuir, Lluís Hurtado, María Castro-Bleda
  38. Effects of Adaptive Pretraining in Specialized Domains for Named Entity RecognitionJack Lynam, Sam Henryour summary
  39. EmCellLLM: Human Peri-Implantation Embryonic Cell Annotation Based on Large Language Models ↗Xiaorui Guo, Zhiwei Liu, Qianqian Xie et al.
  40. Eraserhead at PsyDefDetect: Prompt Design and Class Rebalancing for Psychological Defense Mechanism Detection ↗Muhammad Abu Horaira, Mehreen Rahman, Nahian Chowdhury
  41. Evaluating LLM-as-a-Judge for Medical Term Simplification ↗Ioana Buhnila, Aman Sinha, Rohit Agarwal et al.
  42. Evaluation of Multilingual Text Simplification for the Mental Health Domain: Exploring Small Language ModelsOlga Pelloni, Sandra Just, Lars Bongoour summary
  43. Expert-Guided Schema-Based Structured Extraction from CONSORT Diagrams Using Vision-Language ModelsDamian Stachura, Bartosz Przechera, Monika Opałek et al.our summary
  44. Explainators at PsyDefDetect: Hierarchical Prompting and Representation-Based Classification for Psychological Defenses ↗Liudmila Babakova, Christopher Luongo-Vazquez, Ilia Stepin
  45. Exploring Novel Drug Research Area using Large Language Models Based on Research Trends in Biomedical Literature ↗Afnan Afnan, Michael Van Supranes, Tomohiro Nishiyama et al.
  46. FACT: Functional Group Alignment and Consistency in Token Space for Structure-aware Molecular Representation LearningHyeonyeong Nam, Woojae Choi, Deok-Joong Lee et al.our summary
  47. FBK-NLP at ClinSkill QA 2026: Improving Temporal Reasoning via Keypoint-Augmented Inputs ↗Pedro Gabriel Campana, Alberto Lavelli, Bernardo Magnini
  48. FHexchange: Resources for Family Health History Extraction and Normalization From Consumer Dialog SourcesMichelle Nguyen, Nidhi Soley, Ayah Zirikly et al.our summary
  49. Fast, Accurate, and Local Conversion of MIMIC-IV to OMOP with DBTAdam Sutton, Niko Moller-Grell, Thomas Searle et al.our summary
  50. Forgotten Words: Benchmarking NeoBERT for Dementia Detection in Low-Resource Conversational Filipino and English Speech ↗Rez Samantha Floresca, Edric Castel Hao, Hannah Grachiella Buñales et al.
  51. From Rules to Predictions: Federated Tabular Learning with LLM ReasoningAfsaneh Mahanipour, Hana Khamfroushour summary
  52. GRAFT: Gated Retrieval-Augmented Fine-Tuning for Relation Extraction ↗Yuhang Jiang, Ramakanth Kavuluru
  53. Gold Label Errors in the SciFact Benchmark: An LLM-Assisted Annotation AuditJulien Sylvestreour summary
  54. Hierarchy-Aware Hyperbolic and Semantic Reranking for Ontology-Based Phenotype Linking ↗Thomas Labbe, Moussa Baddour, Axel Bonesteve et al.
  55. IndicMedDialog: A Parallel Multi-Turn Medical Dialogue Dataset for Accessible Healthcare in Indic LanguagesShubham Kumar Nigam, Suparnojit Sarkar, Piyush Patelour summary
  56. Interpretable ICD Code Classification with Faithful Sentence ExtractionYichen Wang, Lian Hong, Masato Mizogaki et al.our summary
  57. Investigating Stigmatizing Language in Clinical Documentation with Open-Source Large Language Models ↗Rajashree Dahal, Pardis Hossein Pour, Pranathi Kamisetty et al.
  58. KALIMBA: Knowledge-Assisted Literature Mining for Biological Interaction Analysis ↗Niloofar Arazkhani, Maciej Kotecki, Brent Cochran et al.
  59. KCL-Cogstack at PsyDefDetect: A Hierarchical Approach to Detecting Defense Mechanisms in Supportive Dialogue ↗Shubham Agarwal, Thomas Searle, Richard Dobson
  60. KGRxn-LLM: Knowledge Graph Enhanced Large Language Models for Molecular Reaction ReasoningWeichen Liu, Qiyao Xue, Yuyang Wu et al.our summary
  61. LAMAR at MedExACT 2026: Agreement-Driven Large Language Model Ensembles for Clinical Decision Extraction from Discharge Summaries ↗Monrada Chiewhawan, Keetawan Limaroon, Titipat Achakulvisut
  62. LAMAR-2 at MedGenVidQA 2026: Visual Answer Localization in Medical Videos via Multimodal LLM and Context-Augmented PromptingWatcharitpol Sermsrisuwan, Nopporn Lekuthai, Seksan Yoadsanit et al.our summary
  63. Learning to Combine AI Annotations for Improved Biomedical Relevance Labeling ↗Won Gyu Kim, Lana Yeganova, Shubo Tian et al.
  64. LinguIUTics at PsyDefDetect: Iterative Imbalance-Aware Fine-tuning of Qwen3-8B for Psychological Defense Mechanism Classification ↗Shefayat E Shams Adib, Ahmed Alfey Sani, Md Hasibur Rahman Alif et al.
  65. MAX-EVAL-11: A Large Scale Benchmark for Evaluating Large Language Models on Full-Spectrum ICD-11 Medical CodingUjjwal Singh, Sarthak Deshwal, Nitish Dube et al.our summary
  66. MeSHClass-ES and AnatEM-ES: Open Resources for Spanish Biomedical NLPSantiago Martinez Novoa, Lina Gomez Mesa, Juan Prieto et al.our summary
  67. MedBench: Deliberative Evaluation of Medical Language Models ↗Pratik Jalan, Mukul Joshi, Akhilesh Magotra et al.
  68. MedCAT v2: a modular, extensible architecture for clinical named entity recognition and linking under real-world privacy and compute constraintsMart Ratas, Thomas Searle, Adam Sutton et al.our summary
  69. Medical Context Variation: A source of impairment for Event classificationAman Sinha, Marianne Clausel, Mathieu Constant et al.our summary
  70. NJUST-KMG at MedGenVidQA 2026: Cascade Multi-modal Alignment with Gaussian Soft Priors for Medical Visual Answer Localization ↗Jinglong Li, Yang Yang
  71. NM at CRF Filling 2026: A Two-Stage LLM Pipeline for Clinical CRF PopulationNiccolò Morabitoour summary
  72. Neural Nexus at PsyDefDetect: Fine-Tuning RoBERTa with Focal Loss and Role-Tagged Dialogue History for Defense Level Detection ↗Subhrajyoti Basu
  73. Nürnberg NLP at PsyDefDetect: Multi-Axis Voter Ensembles for Psychological Defence Mechanism ClassificationPhilipp Steigerwald, Eric Rudolph, Jens Albrechtour summary
  74. Ontological Validation of Biomedical Topic Models: SNOMED CT Hierarchy Distance as an Automated Evaluation Metric ↗Ilan Rubinfeld, Sami Zaidi, Milosh Djuric et al.
  75. Otter at MedExAct2026: Diverse Encoder Ensemble for Medical Decision Span DetectionLalita Lowphansirikul, Piyalitt Ittichaiwongour summary
  76. Overview of the ClinicalSkillQA 2026 Shared Task on Continuous Perception and Procedural Reasoning in Clinical Skill Assessment ↗Xiyang Huang, Renxiong Wei, Yihuai Xu et al.
  77. Overview of the MedGenVidQA 2026 Shared Task on Medical Generative Video Question Answering ↗Deepak Gupta, Collin Campbell, Pedram Golnari et al.
  78. Overview of the Medical Decision Extraction, Analysis, and Classification Task (MedExACT) of BioNLP 2026 ↗Mohamed Elgaar, Jiali Cheng, Nidhi Vakil et al.
  79. Overview of the PsyDefDetect Shared Task at BioNLP 2026: Detecting Levels of Psychological Defense Mechanisms in Supportive ConversationsHongbin Na, Zimu Wang, Zhaoming Chen et al.our summary
  80. PerceptionLab at PsyDefDetect: Overcoming Extreme Response Bias in LLMs via Rubric-Grounded Retrieval and Supervised Clinical Reasoning Distillation for Fine-Grained Ordinal Classification ↗Tamjid Hasan Fahim, Syed Asif Johan, Saad Bin Maksud
  81. Post Hoc Agentic Refinement for Improving Precision in Multilingual Clinical Text De-identification ↗Justin Xu, Alistair Johnson, Thomas Lin et al.
  82. Pride-Boiler at MedGenVidQA 2026: LLM-Augmented BM25 Retrieval with Corrective Self-Verification for Biomedical Evidence Retrieval ↗Basil Ebinesar, Keyuan Jiang, Charansai Maddineni et al.
  83. PrionNER: A Named Entity Recognition Dataset for Prion Disease Biomedical Literature ↗An Dao, Nhan Ly, Thao Tran et al.
  84. Probing and Steering Uncertainty in Biomedical Language Models: Representational Structure and Behavioral LimitsDebmalya Palour summary
  85. Randomized Controlled Trials as the Gold-Standard for Evaluating LLMs: A Primer for Biomedical NLP Researchers ↗Vicente Ivan Sanchez Carmona, Shanshan Jiang, Bin Dong
  86. Reading Between the Lines: Toward Translating Verbose Patient-authored Messages into Clinician-Formulated QuestionsSarvesh Soni, Madeline Bittner, Dina Demner-Fushmanour summary
  87. Relations of Linguistic Features and Medical Text Preferences are Nontrivial ↗Davis Bartels, Brandon Colelough, Dina Demner-Fushman
  88. Reliable Automated Triage in Spanish Clinical Notes: A Hybrid Framework for Risk-Aware HIV Suspicion IdentificationRodrigo Morales-Sánchez, Soto Montalvo, Raquel Martínezour summary
  89. SCoPE: Planning for Hybrid Querying over Clinical Trial Data ↗Suparno Chowdhury, Manan Choudhury, Tejas Anvekar et al.
  90. Seahawk at MedGenVidQA 2026: LLM Segment-Range Selection for Medical Visual Answer LocalizationXiaotian Tian, Gulustan Doganour summary
  91. Segmentation Matters: Exploring LLM-Based Strategies for Temporal Clinical Event Identification in Oncology Reports ↗Cristiano Bellucci, Francesco Madeddu, Chiara Iacomini et al.
  92. Small LLMs for Biomedical Claim Verification: Cost-Effective Fine-Tuning, Structural Dataset Shortcuts, and Cross-Domain Generalization ↗Gaurav Kumar
  93. Sparse Category Routing and Fairness-Aware Optimization for Medical Decision Extraction ↗Ahmed Elshehaby, Mohamed Abdalla, Youssef Mohamed
  94. Systematic Evaluation of the Quality of Synthetic Clinical Notes Rephrased by LLMs at Million-Note ScaleJinghui Liu, Sarvesh Soni, Anthony Nguyenour summary
  95. TONI-NLP at PsyDefDetect: Defense Mechanism Detection via LLM-based Ensemble MethodsDurjoy Paul, Arshitha Basavaraj, Callum Chan et al.our summary
  96. Team Aurum at MedExACT 2026@ACL: Data Augmentation and Clinical Longformer Fine-Tuning for Medical Decision Extraction ↗Jyoti Kumari, Vinay Ulli, Anindita Mondal
  97. The Divergence Hypothesis: Unmasking Lexical Interference and Label Bias in Mental Health NLP ↗Moustafa Yehia Hassan
  98. Tokenization Granularity and Medical Term Representations in Language Models ↗Vojtech Lanz, Pavel Pecina
  99. Towards Grounded Hallucination Definitions for Biomedical Question Answering with Reproducible Examples from ClinIQLink ↗Brandon Colelough, Davis Bartels, Madeline Bittner et al.
  100. Towards Unified Factuality Evaluation for Biomedical QA and Summarization: Aligning Metrics with Clinical Use-CasesMahule Roy, Subhas Royour summary

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