Isar Nejadgholi, Kathleen C. Fraser, Berry De Bruijn, Muqun Li, Astha LaPlante, Khaldoun Zine El Abidine
| Challenge: | Entity recognition is a critical first step to a number of clinical NLP applications, such as entity linking and relation extraction. |
| Approach: | They propose to use general and domain-specific information to combine general and specific information to create a new entity recognition method. |
| Outcome: | The proposed method produces a state-of-the-art result on a newly released dataset, MedMentions. |
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Biomedical Interpretable Entity Representations (2021.findings-acl)
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| Challenge: | Existing work on general interpretable representation learning does not transfer to biomedicine . pre-trained models induce dense entity representations but are not immediately interpretable. |
| Approach: | They propose a method that exploits BIER's final sparse and intermediate dense representations to facilitate model and entity type debugging. |
| Outcome: | The proposed model performs well on biomedical tasks including disambiguation and label classification. |
Embedding Strategies for Specialized Domains: Application to Clinical Entity Recognition (P19-2)
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| Challenge: | Off-the-shelf word embeddings tend to perform poorly on texts from specialized domains such as clinical reports. |
| Approach: | They combine off-the-shelf contextual embeddings with static word2vec embedders trained on a small in-domain corpus built from task data to reach and sometimes outperform representations learned from a large corpus in the medical domain. |
| Outcome: | The proposed embedding strategies outperform representations learned from a large corpus in the medical domain. |
NERetrieve: Dataset for Next Generation Named Entity Recognition and Retrieval (2023.findings-emnlp)
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| Challenge: | Named Entity Recognition (NER) is a widely adopted NLP task . authors present three variants of NER task, with dataset to support them . |
| Approach: | They propose three variants of the NER task, together with a dataset to support them . they propose a move towards more fine-grained entities and zero-shot recognition . |
| Outcome: | The proposed model matches or surpasses existing models in NER tasks . the proposed model is based on a large, silver-annotated corpus of 4 million paragraphs . |
UmlsBERT: Clinical Domain Knowledge Augmentation of Contextual Embeddings Using the Unified Medical Language System Metathesaurus (2021.naacl-main)
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| Challenge: | Contextual word embedding models do not take into account structured expert domain knowledge from a knowledge base. |
| Approach: | They propose a contextual embedding model that integrates domain knowledge during the pre-training process via a novel knowledge augmentation strategy. |
| Outcome: | The proposed model outperforms existing domain-specific models on common named-entity recognition (NER) and clinical natural language inference tasks. |
Self-Alignment Pretraining for Biomedical Entity Representations (2021.naacl-main)
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| Challenge: | Existing approaches to self-supervised learning of biomedical entities are limited in the biomedic domain. |
| Approach: | They propose a pretraining scheme that self-aligns the representation space of biomedical entities. |
| Outcome: | The proposed framework achieves state-of-the-art on six MEL benchmarking datasets. |
Where do LLMs currently stand on biomedical NER in both clean and noisy settings ? (2026.findings-eacl)
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| Challenge: | despite advances in medicine, many diseases remain without effective treatments . clinical meta-analysis is essential for drug discovery and clinical research . |
| Approach: | They investigate the performance of large language models (LLMs) on biomedical NER tasks . findings suggest LLMs exhibit a notable degree of robustness to noise . |
| Outcome: | The proposed models are closing the performance gap with BERT-based models and demonstrate particular strengths in low-data settings. |
OpenBioNER: Lightweight Open-Domain Biomedical Named Entity Recognition Through Entity Type Description (2025.findings-naacl)
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Alessio Cocchieri, Giacomo Frisoni, Marcos Martínez Galindo, Gianluca Moro, Giuseppe Tagliavini, Francesco Candoli
| Challenge: | Biomedical Named Entity Recognition (BioNER) is a computationally expensive and limited tool . specialized 7B NER LLMs and GPT-4o can't match textual spans with entity types . |
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Entity Decomposition with Filtering: A Zero-Shot Clinical Named Entity Recognition Framework (2025.naacl-long)
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| Challenge: | Recent studies have demonstrated that large language models (LLMs) can perform in named entity recognition tasks. |
| Approach: | They propose a framework for clinical named entity recognition that decomposes the entity recognition task into several retrievals of sub-types and then filters them. |
| Outcome: | The proposed framework improves on the clinical named entity recognition task. |
A Framework for Flexible Extraction of Clinical Event Contextual Properties from Electronic Health Records (2025.acl-industry)
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| Challenge: | EHRs contain vast amounts of valuable clinical data, stored as unstructured text. |
| Approach: | They propose a method that uses existing NER+L methods to classify medical entities at scale using a named entity recognition and linking task. |
| Outcome: | The proposed model outperforms Bi-LSTM in minority class tasks with up to 28% of the time and 32% faster training time. |
Deep Neural Models for Medical Concept Normalization in User-Generated Texts (P19-2)
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| Challenge: | a medical concept normalization problem is a challenge since social media texts are ambiguous and noisy . a recent study shows that neural architectures leverage the semantic meaning of the entity mention . |
| Approach: | They propose to map a health-related entity mention to a controlled vocabulary . they use powerful neural networks and contextualized word representation models . |
| Outcome: | The proposed model outperforms existing state-of-the-art models in mapping medical concepts to medical terms . the proposed model is based on recurrent neural networks and contextualized word representation models . |