Austria

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).

ACL 2025

Accelerating Cross-Encoders in Biomedical Entity Linking

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)

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

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A Retrieval-Based Approach to Medical Procedure Matching in Romanian

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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

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Can Large Language Models Classify and Generate Antimicrobial Resistance Genes?

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

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