Austria

This paper presents a pipeline for mitigating gender bias in large language models (LLMs) used in medical literature by neutralizing gendered occupational pronouns. A set of 379,000 PubMed abstracts from 1965-1980 was processed to identify and modify pronouns tied to professions. We developed a BERT-based model, &quot;Modern Occupational Bias Elimination with Refined Training,&quot; or &quot;MOBERT,&quot; trained on these neutralized abstracts, and compared it with &quot;1965BERT,&quot; trained on the original dataset. MOBERT achieved a 70% inclusive replacement rate, while 1965BERT reached only 4%. A further analysis of MOBERT revealed that pronoun replacement accuracy correlated with the frequency of occupational terms in the training data. We propose expanding the dataset and refining the pipeline to improve performance and ensure more equitable language modeling in medical applications.

ACL 2025

Gender-Neutral Large Language Models for Medical Applications: Reducing Bias in PubMed Abstracts

This paper presents a pipeline for mitigating gender bias in large language models (LLMs) used in medical literature by neutralizing gendered occupational pronouns. A set of 379,000 PubMed abstracts from 1965-1980 was processed to identify and modify pronouns tied to professions. We developed a BERT-based model, "Modern Occupational Bias Elimination with Refined Training," or "MOBERT," trained on these neutralized abstracts, and compared it with "1965BERT," trained on the original dataset. MOBERT achieved a 70% inclusive replacement rate, while 1965BERT reached only 4%. A further analysis of MOBERT revealed that pronoun replacement accuracy correlated with the frequency of occupational terms in the training data. We propose expanding the dataset and refining the pipeline to improve performance and ensure more equitable language modeling in medical applications.

workshop paper

### Welcome to The 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025)

Message from the General Chair: 
*It is my great pleasure and honor to welcome you to the 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025), held in beautiful Vienna, Austria, from July 27 to August 1, 2025. ACL2025continues our field’s tradition of excellence in scholarship, innovation, and inclusivity, and I am deeply grateful to the many volunteers who have worked tirelessly to bring this event to life.* 
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Welcome to The 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025)

Large Language Models (LLMs) have approached human-level performance in text generation and summarization, yet their application in clinical settings remains constrained by potential inaccuracies that could lead to serious consequences. This work addresses the critical safety weaknesses in medical documentation systems by focusing on detecting subtle errors that require specialized medical expertise. We introduce a novel multi-agent debating framework that achieves 78.8\% accuracy on medical error detection, significantly outperforming both single-agent approaches and previous multi-agent systems. Our framework leverages specialized LLM agents with asymmetric access to complementary medical knowledge sources (Mayo Clinic and WebMD), engaging them in structured debate to identify inaccuracies in clinical notes. A judge agent evaluates these arguments based solely on their medical reasoning quality, with agent-specific performance metrics incorporated as feedback for developing situation-specific trust models.

Error Detection in Medical Note through Multi Agent Debate

Biomedical entity linking models disambiguate mentions in text by matching them with unique biomedical concepts. This problem is commonly addressed using a two-stage pipeline comprising an inexpensive candidate generator, which filters a subset of suitable entities for a mention, and a costly but precise reranker that provides the final matching between the mention and the concept. With the goal of applying two-stage entity linking at scale, we explore the construction of effective cross-encoder reranker models, capable of scoring multiple mention-entity pairs simultaneously. Through experiments on four entity linking datasets, we show that our cross-encoder models provide between 2.7 to 36.97 times faster training speeds and 3.42 to 26.47 times faster inference speeds than a base cross-encoder model capable of scoring only one entity, while achieving similar accuracy (differences between -3.42% to 2.76% Acc@1).

Accelerating Cross-Encoders in Biomedical Entity Linking

In this work, we propose a structured four-step prompting strategy that explicitly guides large language models (LLMs) through (1) claim comprehension, (2) evidence analysis, (3) intermediate conclusion, and (4) entailment decision-making to improve the accuracy of biomedical claim verification. This strategy leverages compositional and human-like reasoning to enhance logical consistency and factual grounding to reduce reliance on memorizing few-Shot exemplars and help LLMs generalize reasoning patterns across different biomedical claim verification tasks. Through extensive evaluation on biomedical NLI benchmarks, we analyze the individual contributions of each reasoning step. Our findings demonstrate that comprehension, evidence analysis, and intermediate conclusion each play distinct yet complementary roles. Systematic prompting and carefully designed step-wise instructions not only unlock the latent cognitive abilities of LLMs but also enhance interpretability by making it easier to trace errors and understand the model's reasoning process. Our research aims to improve the reliability of AI-driven biomedical claim verification.

Advancing Biomedical Claim Verification by Using Large Language Models with Better Structured Prompting Strategies

Accurately mapping medical procedure names from healthcare providers to standardized terminology used by insurance companies is a crucial yet complex task. Inconsistencies in naming conventions lead to missclasified procedures, causing administrative inefficiencies and insurance claim problems in private healthcare settings. Many companies still use human resources for manual mapping, while there is a clear opportunity for automation. This paper proposes a retrieval-based architecture leveraging sentence embeddings for medical name matching in the Romanian healthcare system. This challenge is significantly more difficult in underrepresented languages such as Romanian, where existing pretrained language models lack domain-specific adaptation to medical text. We evaluate multiple embedding models, including Romanian, multilingual, and medical-domain-specific representations, to identify the most effective solution for this task. Our findings contribute to the broader field of medical NLP for low-resource languages such as Romanian.

A Retrieval-Based Approach to Medical Procedure Matching in Romanian

Gastroenterology (GI) cancer surveillance scheduling relies on extracting structured data from unstructured clinical texts, such as endoscopy and pathology reports. Traditional Natural Language Processing (NLP) models have been employed for this task, but recent advancements in Large Language Models (LLMs) present a new opportunity for automation without requiring extensive labeled datasets. In this study, we propose an LLM-based entity extraction and rule-based decision support framework for Barrett's Oesophagus (BO) surveillance timing prediction. Our approach processes endoscopy and pathology reports to extract clinically relevant information and structures it into a standardised format, which is then used to determine appropriate surveillance intervals. We evaluate multiple state-of-the-art LLMs on real-world clinical datasets from two hospitals, assessing their performance in accuracy and running time cost. The results demonstrate that LLMs, particularly Phi-4 and (DeepSeek distilled) Qwen-2.5, can effectively automate the extraction of BO surveillance-related information with high accuracy, while Phi-4 is also efficient during inference. We also compared the trade-offs between LLMs and fine-tuned non-LLMs. Our findings indicate that LLM extraction based methods can support clinical decision-making by providing justifications from report extractions, reducing manual workload, and improving guideline adherence in BO surveillance scheduling.

Improving Barrett's Oesophagus Surveillance Scheduling with Large Language Models: A Structured Extraction Approach

Large Language Models (LLMs) have significantly impacted medical Natural Language Processing (NLP), enabling automated information extraction from unstructured clinical texts. However, selecting the most suitable approach requires careful evaluation of different model architectures, such as generative LLMs and BERT-based models, along with appropriate adaptation strategies, including prompting techniques, or fine-tuning.

Prompting Large Language Models for Italian Clinical Reports: A Benchmark Study

Several studies explored different LLM implementations, highlighting their effectiveness in medical domain, including complex diagnostics patterns as for example in rheumatology. However, their application to Italian remains limited, serving as a key example of the broader gap in non-English language research. In this study, we present a task-specific benchmark analysis comparing generative LLMs and BERT-based models, on real-world Italian clinical reports. We evaluated zero-shot prompting, in-context learning (ICL), and fine-tuning across eight diagnostic categories in the rheumatology area. Results show that ICL improves performance over zero-shot-prompting, particularly for Mixtral and Gemma models. Overall, BERT fine-tuning present the highest performance, while ICL outperforms BERT in specific diagnoses, such as renal and systemic, suggesting that prompting can be a potential alternative when labeled data is scarce."

QoLAS: A Reddit Corpus of Health-Related Quality of Life Aspects of Mental Disorders

Biomedical Named Entity Recognition presents significant challenges due to the complexity of biomedical terminology and inconsistencies in annotation across datasets. This paper introduces SRU-NER (Slot-based Recurrent Unit NER), a novel approach designed to handle nested named entities while integrating multiple datasets through an effective multi-task learning strategy. SRU-NER mitigates annotation gaps by dynamically adjusting loss computation to avoid penalizing predictions of entity types absent in a given dataset. Through extensive experiments, including a cross-corpus evaluation and human assessment of the model's predictions, SRU-NER achieves competitive performance in biomedical and general-domain NER tasks, while improving cross-domain generalization.

Effective Multi-Task Learning for Biomedical Named Entity Recognition

This study explores the application of generative Large Language Models (LLMs) in DNA sequence analysis, highlighting their advantages over encoder-based models like DNABERT2 and Nucleotide Transformer. While encoder models excel in classification, they struggle to integrate external textual information. In contrast, generative LLMs can incorporate domain knowledge, such as BLASTn annotations, to improve classification accuracy even without fine-tuning. We evaluate this capability on antimicrobial resistance (AMR) gene classification, comparing generative LLMs with encoder-based baselines. Results show that LLMs significantly enhance classification when supplemented with textual information. Additionally, we demonstrate their potential in DNA sequence generation, further expanding their applicability. Our findings suggest that LLMs offer a novel paradigm for integrating biological sequences with external knowledge, bridging gaps in traditional classification methods.

Can Large Language Models Classify and Generate Antimicrobial Resistance Genes?

Case reports provide critical insights into rare and atypical diseases, but extracting structured knowledge remains challenging due to unstructured text and domain-specific terminology. We introduce CaseReportCollective, an LLM-extracted dataset of 85,961 open-access case reports spanning 37 years across 14 medical domains, validated through programmatic and human evaluation. Our dataset reveals key publication and demographic trends, including a significant increase in open-access case reports over the past decade, shifts in focus from oncology to COVID-19, and sex disparities in reporting across different medical conditions. Over time, the gap between male and female case reports has narrowed, suggesting greater equity in case reporting. Using \textbf{CaseReportCollective}, we further explore embedding-based retrieval for similar medical topics through accumulated similarity scores across extracted structured information. We also conducted detailed error analyses on the retrieval ranking, finding that high-reported topics dominate retrieval. Such retrieval is driven by lexical overlap rather than underlying clinical relevance, often failing to distinguish between semantically similar yet mechanistically distinct conditions. Future work should focus on clinical-aware embeddings adjusted for long-tailed case distributions to improve retrieval accuracy.

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Error Detection in Medical Note through Multi Agent Debate

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