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23rd BioNLP@ACL 2024: Bangkok, Thailand
- Dina Demner-Fushman, Sophia Ananiadou, Makoto Miwa, Kirk Roberts, Junichi Tsujii:
Proceedings of the 23rd Workshop on Biomedical Natural Language Processing, BioNLP@ACL 2024, Bangkok, Thailand, August 16, 2024. Association for Computational Linguistics 2024, ISBN 979-8-89176-130-8 - Seiji Shimizu, Shuntaro Yada, Lisa Raithel, Eiji Aramaki:
Improving Self-training with Prototypical Learning for Source-Free Domain Adaptation on Clinical Text. 1-13 - Agathe Zecevic, Xinyue Zhang, Sebastian S. Zeki, Angus Roberts:
Generation and Evaluation of Synthetic Endoscopy Free-Text Reports with Differential Privacy. 14-24 - Dorothea MacPhail, David Harbecke, Lisa Raithel, Sebastian Möller:
Evaluating the Robustness of Adverse Drug Event Classification Models using Templates. 25-38 - Himanshu Pandey, Akhil Amod, Shivang Kumar:
Advancing Healthcare Automation: Multi-Agent System for Medical Necessity Justification. 39-49 - Alberto Mario Ceballos-Arroyo, Monica Munnangi, Jiuding Sun, Karen Y. C. Zhang, Denis Jered McInerney, Byron C. Wallace, Silvio Amir:
Open (Clinical) LLMs are Sensitive to Instruction Phrasings. 50-71 - Vasiliki Kougia, Anastasiia Sedova, Andreas Stephan, Klim Zaporojets, Benjamin Roth:
Analysing zero-shot temporal relation extraction on clinical notes using temporal consistency. 72-84 - Justin Xu, Zhihong Chen, Andrew Johnston, Louis Blankemeier, Maya Varma, Jason Hom, William J. Collins, Ankit Modi, Robert Lloyd, Benjamin Hopkins, Curtis P. Langlotz, Jean-Benoit Delbrouck:
Overview of the First Shared Task on Clinical Text Generation: RRG24 and "Discharge Me!". 85-98 - Aaron Nicolson, Jinghui Liu, Jason Dowling, Anthony N. Nguyen, Bevan Koopman:
e-Health CSIRO at RRG24: Entropy-Augmented Self-Critical Sequence Training for Radiology Report Generation. 99-104 - Hendrik Damm
, Tabea Margareta Grace Pakull, Bahadir Eryilmaz, Helmut Becker, Ahmad Idrissi-Yaghir, Henning Schäfer, Sergej Schultenkämper, Christoph M. Friedrich:
WisPerMed at "Discharge Me!": Advancing Text Generation in Healthcare with Large Language Models, Dynamic Expert Selection, and Priming Techniques on MIMIC-IV. 105-121 - Tomas Goldsack, Carolina Scarton, Matthew Shardlow, Chenghua Lin:
Overview of the BioLaySumm 2024 Shared Task on the Lay Summarization of Biomedical Research Articles. 122-131 - Zhiwen You, Shruthan Radhakrishna, Shufan Ming, Halil Kilicoglu:
UIUC_BioNLP at BioLaySumm: An Extract-then-Summarize Approach Augmented with Wikipedia Knowledge for Biomedical Lay Summarization. 132-143 - Ferran Gonzalez Hernandez, Victoria Smith, Quang Nguyen
End-to-End Relation Extraction of Pharmacokinetic Estimates from the Scientific Literature. 144-154 - Rui Yang, Haoran Liu, Edison Marrese-Taylor, Qingcheng Zeng, Yuhe Ke, Wanxin Li, Lechao Cheng, Qingyu Chen, James Caverlee, Yutaka Matsuo, Irene Li:
KG-Rank: Enhancing Large Language Models for Medical QA with Knowledge Graphs and Ranking Techniques. 155-166 - Yunsoo Kim, Jinge Wu, Yusuf Abdulle, Honghan Wu:
MedExQA: Medical Question Answering Benchmark with Multiple Explanations. 167-181 - Zonghai Yao, Ahmed Jaafar, Beining Wang, Zhichao Yang, Hong Yu:
Do Clinicians Know How to Prompt? The Need for Automatic Prompt Optimization Help in Clinical Note Generation. 182-201 - Aman Sinha, Timothee Mickus, Marianne Clausel, Mathieu Constant, Xavier Coubez:
Domain-specific or Uncertainty-aware models: Does it really make a difference for biomedical text classification? 202-211 - Panagiotis Fytas, Anna Breger, Ian Selby, Simon Baker, Shahab Shahipasand, Anna Korhonen:
Can Rule-Based Insights Enhance LLMs for Radiology Report Classification? Introducing the RadPrompt Methodology. 212-235 - Hashem Hijazi, Diego Mollá, Vincent Nguyen, Sarvnaz Karimi:
Using Large Language Models to Evaluate Biomedical Query-Focused Summarisation. 236-242 - Mireia Hernandez Caralt, Clarence Boon Liang Ng, Marek Rei:
Continuous Predictive Modeling of Clinical Notes and ICD Codes in Patient Health Records. 243-255 - Shubham Vatsal, Ayush Singh:
Can GPT Redefine Medical Understanding? Evaluating GPT on Biomedical Machine Reading Comprehension. 256-265 - Saeed Farzi, Soumitra Ghosh, Alberto Lavelli, Bernardo Magnini:
Get the Best out of 1B LLMs: Insights from Information Extraction on Clinical Documents. 266-276 - Itay Manes, Naama Ronn, David Cohen, Ran Ilan Ber, Zehavi Horowitz-Kugler, Gabriel Stanovsky:
K-QA: A Real-World Medical Q&A Benchmark. 277-294 - Vahan Arsenyan, Spartak Bughdaryan, Fadi Shaya, Kent Wilson Small, Davit Shahnazaryan:
Large Language Models for Biomedical Knowledge Graph Construction: Information extraction from EMR notes. 295-317 - Kriti Bhattarai, Inez Y. Oh, Zachary B. Abrams, Albert M. Lai:
Document-level Clinical Entity and Relation extraction via Knowledge Base-Guided Generation. 318-327 - Tianyi Wu, Jingqing Zhang, Wenjia Bai, Kai Sun:
BiCAL: Bi-directional Contrastive Active Learning for Clinical Report Generation. 328-341 - Sanjeet Singh, Shreya Gupta, Niralee Gupta, Naimish Sharma
Generation and De-Identification of Indian Clinical Discharge Summaries using LLMs. 342-362 - Mathieu Lai-king
Pre-training data selection for biomedical domain adaptation using journal impact metrics. 363-369 - Gilchan Park, Vivek Mutalik, Christopher Neely, Carlos Soto, Shinjae Yoo, Paramvir Dehal:
Leveraging LLMs and Web-based Visualizations for Profiling Bacterial Host Organisms and Genetic Toolboxes. 370-379 - Darya Shlyk, Tudor Groza, Marco Mesiti, Stefano Montanelli, Emanuele Cavalleri:
REAL: A Retrieval-Augmented Entity Linking Approach for Biomedical Concept Recognition. 380-389 - Brian Hur, Lucy Lu Wang, Laura Hardefeldt, Meliha Yetisgen:
Is That the Right Dose? Investigating Generative Language Model Performance on Veterinary Prescription Text Analysis. 390-397 - William P. Hogan, Andrew Bartko, Jingbo Shang, Chun-Nan Hsu:
MiDRED: An Annotated Corpus for Microbiome Knowledge Base Construction. 398-408 - Rahmad Mahendra, Damiano Spina, Lawrence Cavedon, Karin Verspoor:
Do Numbers Matter? Types and Prevalence of Numbers in Clinical Texts. 409-415 - Yuan Liang, Massimo Poesio, Roonak Rezvani:
A Fine-grained citation graph for biomedical academic papers: the finding-citation graph. 416-426 - Ryan Engel, Gilchan Park:
Evaluating Large Language Models for Predicting Protein Behavior under Radiation Exposure and Disease Conditions. 427-439 - Omkar Chakradhar Thawakar, Abdelrahman M. Shaker, Sahal Shaji Mullappilly, Hisham Cholakkal, Rao Muhammad Anwer, Salman H. Khan, Jorma Laaksonen, Fahad Shahbaz Khan:
XrayGPT: Chest Radiographs Summarization using Large Medical Vision-Language Models. 440-448 - Vicente Iván Sánchez Carmona, Shanshan Jiang, Takeshi Suzuki, Bin Dong:
Multilevel Analysis of Biomedical Domain Adaptation of Llama 2: What Matters the Most? A Case Study. 449-456 - Oumaima El Khettari, Noriki Nishida, Shanshan Liu, Rumana Ferdous Munne, Yuki Yamagata, Solen Quiniou, Samuel Chaffron, Yuji Matsumoto:
Mention-Agnostic Information Extraction for Ontological Annotation of Biomedical Articles. 457-473 - Maxim Rubchinsky, Ella Rabinovich, Adi Shribman, Netanel Golan, Tali Sahar, Dorit Shweiki:
Automatic Extraction of Disease Risk Factors from Medical Publications. 474-485 - Yiyuan Pu, Kaitlyn Hair, Daniel Beck, Mike Conway, Malcolm MacLeod, Karin Verspoor:
Intervention extraction in preclinical animal studies of Alzheimer's Disease: Enhancing regex performance with language model-based filtering. 486-492 - Akshit Achara, Sanand Sasidharan, Gagan N:
Efficient Biomedical Entity Linking: Clinical Text Standardization with Low-Resource Techniques. 493-505 - Ajay Madhavan Ravichandran, Julianna Grune, Nils Feldhus, Aljoscha Burchardt, Roland Roller, Sebastian Möller:
XAI for Better Exploitation of Text in Medical Decision Support. 506-513 - Daniel Cabrera Lozoya, Jiahe Liu, Simon D'Alfonso, Mike Conway:
Optimizing Multimodal Large Language Models for Detection of Alcohol Advertisements via Adaptive Prompting. 514-525 - Ben Holgate, Shichao Fang, Anthony Shek, Matthew McWilliam, Pedro F. Viana, Joel S. Winston, James T. Teo, Mark P. Richardson:
Extracting Epilepsy Patient Data with Llama 2. 526-535 - Bojana Basaragin, Adela Ljajic, Darija Medvecki, Lorenzo Cassano, Milos Kosprdic, Nikola Milosevic:
How do you know that? Teaching Generative Language Models to Reference Answers to Biomedical Questions. 536-547 - Ashton Williamson, David de Hilster, Amnon Meyers, Nina C. Hubig, Amy Apon:
Low Resource ICD Coding of Hospital Discharge Summaries. 548-558 - Faraz Maschhur, Klaus Netter, Sven Schmeier, Katrin Ostermann, Rimantas Palunis, Tobias Strapatsas, Roland Roller:
Towards ML-supported Triage Prediction in Real-World Emergency Room Scenarios. 559-569 - Johann Frei, Frank Kramer:
Creating Ontology-annotated Corpora from Wikipedia for Medical Named-entity Recognition. 570-579 - Vojtech Lanz, Pavel Pecina:
Paragraph Retrieval for Enhanced Question Answering in Clinical Documents. 580-590 - Yuxiang Liao
CID at RRG24: Attempting in a Conditionally Initiated Decoding of Radiology Report Generation with Clinical Entities. 591-596 - Shaury Srivastav, Mercy Ranjit, Fernando Pérez-García, Kenza Bouzid, Shruthi Bannur, Daniel C. Castro, Anton Schwaighofer, Harshita Sharma, Maximilian Ilse, Valentina Salvatelli, Sam Bond-Taylor, Fabian Falck, Anja Thieme, Hannah Richardson, Matthew P. Lungren, Stephanie L. Hyland, Javier Alvarez-Valle:
MAIRA at RRG24: A specialised large multimodal model for radiology report generation. 597-602 - Marina Munkhoeva, Dmitry Umerenkov, Valentin Samokhin:
AIRI at RRG24: LLaVa with specialised encoder and decoder. 603-607 - Diego Campanini, Oscar Loch, Pablo Messina, Rafael Elberg, Denis Parra:
iHealth-Chile-1 at RRG24: In-context Learning and Finetuning of a Large Multimodal Model for Radiology Report Generation. 608-613 - Oscar Loch, Pablo Messina, Rafael Elberg, Diego Campanini, Álvaro Soto, René Vidal, Denis Parra:
iHealth-Chile-3&2 at RRG24: Template Based Report Generation. 614-623 - Xi Zhang, Zaiqiao Meng, Jake Lever, Edmond S. L. Ho:
Gla-AI4BioMed at RRG24: Visual Instruction-tuned Adaptation for Radiology Report Generation. 624-634 - Kiartnarin Udomlapsakul, Parinthapat Pengpun, Tossaporn Saengja, Kanyakorn Veerakanjana, Krittamate Tiankanon, Pitikorn Khlaisamniang, Pasit Supholkhan, Amrest Chinkamol, Pubordee Aussavavirojekul, Hirunkul Phimsiri, Tara Sripo, Chiraphat Boonnag, Trongtum Tongdee, Thanongchai Siriapisith, Pairash Saiviroonporn, Jiramet Kinchagawat, Piyalitt Ittichaiwong:
SICAR at RRG2024: GPU Poor's Guide to Radiology Report Generation. 635-644 - Yunzhen He, Hiroaki Yamagiwa, Hidetoshi Shimodaira:
Shimo Lab at "Discharge Me!": Discharge Summarization by Prompt-Driven Concatenation of Electronic Health Record Sections. 645-657 - Jordan Koontz, Maite Oronoz, Alicia Pérez:
Ixa-Med at Discharge Me! Retrieval-Assisted Generation for Streamlining Discharge Documentation. 658-663 - Rui Guo, Greg Farnan, Niall McLaughlin, Barry Devereux:
QUB-Cirdan at "Discharge Me!": Zero shot discharge letter generation by open-source LLM. 664-674 - Jinghui Liu, Aaron Nicolson, Jason Dowling, Bevan Koopman, Anthony N. Nguyen:
e-Health CSIRO at "Discharge Me!" 2024: Generating Discharge Summary Sections with Fine-tuned Language Models. 675-684 - Mengxian Lyu, Cheng Peng, Daniel Paredes, Ziyi Chen, Aokun Chen, Jiang Bian, Yonghui Wu:
UF-HOBI at "Discharge Me!": A Hybrid Solution for Discharge Summary Generation Through Prompt-based Tuning of GatorTronGPT Models. 685-695 - Haotian Wu, Paul Boulenger, Antonin Faure, Berta Céspedes, Farouk Boukil, Nastasia Morel, Zeming Chen, Antoine Bosselut:
EPFL-MAKE at "Discharge Me!": An LLM System for Automatically Generating Discharge Summaries of Clinical Electronic Health Record. 696-711 - Erlend Frayling, Jake Lever, Graham McDonald:
UoG Siephers at "Discharge Me!": Exploring Ways to Generate Synthetic Patient Notes From Multi-Part Electronic Health Records. 712-718 - Suzanne Wendelken, Anson Antony, Rajashekar Korutla, Bhanu Pachipala, James Shanahan, Walid Saba:
Roux-lette at "Discharge Me!": Reducing EHR Chart Burden with a Simple, Scalable, Clinician-Driven AI Approach. 719-723 - Vimig Socrates, Thomas Huang, Xuguang Ai, Soraya Fereydooni, Qingyu Chen, R. Andrew Taylor, David Chartash:
Yale at "Discharge Me!": Evaluating Constrained Generation of Discharge Summaries with Unstructured and Structured Information. 724-730 - An Quang Tang, Xiuzhen Zhang, Minh Ngoc Dinh:
IgnitionInnovators at "Discharge Me!": Chain-of-Thought Instruction Finetuning Large Language Models for Discharge Summaries. 731-739 - Abir Naskar, Jane S. Hocking, Patty Chondros, Douglas Boyle, Mike Conway:
MLBMIKABR at "Discharge Me!": Concept Based Clinical Text Description Generation. 740-747 - Huy Quoc To, Ming Liu, Guangyan Huang:
DeakinNLP at BioLaySumm: Evaluating Fine-tuning Longformer and GPT-4 Prompting for Biomedical Lay Summarization. 748-754 - Vicent Ahuir, Diego Torres, Encarna Segarra, Lluís-F. Hurtado:
ELiRF-VRAIN at BioLaySumm: Boosting Lay Summarization Systems Performance with Ranking Models. 755-761 - Akanksha Karotia, Seba Susan:
BioLay_AK_SS at BioLaySumm: Domain Adaptation by Two-Stage Fine-Tuning of Large Language Models used for Biomedical Lay Summary Generation. 762-768 - Tabea Margareta Grace Pakull, Hendrik Damm
WisPerMed at BioLaySumm: Adapting Autoregressive Large Language Models for Lay Summarization of Scientific Articles. 769-779 - Adrian Gonzalez Sanchez, Paloma Martínez:
HULAT-UC3M at BiolaySumm: Adaptation of BioBART and Longformer models to summarizing biomedical documents. 780-785 - Hwanmun Kim, Kamal Raj Kanakarajan, Malaikannan Sankarasubbu:
Saama Technologies at BioLaySumm: Abstract based fine-tuned models with LoRA. 786-792 - Loukritia Stefanou, Tatiana Passali, Grigorios Tsoumakas:
AUTH at BioLaySumm 2024: Bringing Scientific Content to Kids. 793-803 - Mariia Chizhikova, Manuel Carlos Díaz-Galiano, Luis Alfonso Ureña López, María Teresa Martín Valdivia:
SINAI at BioLaySumm: Self-Play Fine-Tuning of Large Language Models for Biomedical Lay Summarisation. 804-809 - Yuelyu Ji, Zhuochun Li, Rui Meng, Sonish Sivarajkumar, Yanshan Wang, Zeshui Yu, Hui Ji, Yushui Han, Hanyu Zeng, Daqing He:
RAG-RLRC-LaySum at BioLaySumm: Integrating Retrieval-Augmented Generation and Readability Control for Layman Summarization of Biomedical Texts. 810-817 - Jieli Zhou, Cheng Ye, Pengcheng Xu, Hongyi Xin:
Team YXZ at BioLaySumm: Adapting Large Language Models for Biomedical Lay Summarization. 818-825 - Satyam Modi, T. Karthikeyan:
Eulerian at BioLaySumm: Preprocessing Over Abstract is All You Need. 826-830 - Hemang Malik, Gaurav Pradeep, Pratinav Seth:
HGP-NLP at BioLaySumm: Leveraging LoRA for Lay Summarization of Biomedical Research Articles using Seq2Seq Transformers. 831-836 - Siyu Bao, Ruijing Zhao, Siqin Zhang, Jinghui Zhang, Weiyin Wang, Yunian Ru:
Ctyun AI at BioLaySumm: Enhancing Lay Summaries of Biomedical Articles Through Large Language Models and Data Augmentation. 837-844
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