Related papers: OEMA: Ontology-Enhanced Multi-Agent Collaboration …

Tools to explore scientific literature are essential for scientists, especially in biomedicine, where about a million new papers are published every year. Many such tools provide users the ability to search for specific entities (e.g.…

Background and Objective: Biomedical Named Entity Recognition (BioNER) is a foundational task in medical informatics, crucial for downstream applications like drug discovery and clinical trial matching. However, adapting general-domain…

Using language models (LMs) pre-trained in a self-supervised setting on large corpora and then fine-tuning for a downstream task has helped to deal with the problem of limited label data for supervised learning tasks such as Named Entity…

Despite the huge and continuous advances in computational linguistics, the lack of annotated data for Named Entity Recognition (NER) is still a challenging issue, especially in low-resource languages and when domain knowledge is required…

Objective: This work aimed to demonstrate the effectiveness of a hybrid approach based on Sentence BERT model and retrofitting algorithm to compute relatedness between any two biomedical concepts. Materials and Methods: We generated concept…

This study proposes a medical entity extraction method based on Transformer to enhance the information extraction capability of medical literature. Considering the professionalism and complexity of medical texts, we compare the performance…

Recent multilingual named entity recognition (NER) work has shown that large language models (LLMs) can provide effective synthetic supervision, yet such datasets have mostly appeared as by-products of broader experiments rather than as…

This paper presents ReverseNER, a method aimed at overcoming the limitation of large language models (LLMs) in zero-shot named entity recognition (NER) tasks, arising from their reliance on pre-provided demonstrations. ReverseNER tackles…

We present NER Retriever, a zero-shot retrieval framework for ad-hoc Named Entity Retrieval, a variant of Named Entity Recognition (NER), where the types of interest are not provided in advance, and a user-defined type description is used…

Electronic Patient Record (EPR) systems contain valuable clinical information, but much of it is trapped in unstructured text, limiting its use for research and decision-making. Large language models can extract such information but require…

Identification of key variables such as medications, diseases, relations from health records and clinical notes has a wide range of applications in the clinical domain. n2c2 2022 provided shared tasks on challenges in natural language…

Motivation: Biomedical named-entity normalization involves connecting biomedical entities with distinct database identifiers in order to facilitate data integration across various fields of biology. Existing systems for biomedical named…

Large language models (LLMs) have shown remarkable capabilities in Natural Language Processing (NLP), especially in domains where labeled data is scarce or expensive, such as clinical domain. However, to unlock the clinical knowledge hidden…

FDA Medical Device recalls are critical and time-sensitive events, requiring swift identification of impacted devices to inform the public of a recall event and ensure patient safety. The OpenFDA device recall dataset contains valuable…

Accurate symptom-to-disease classification and clinically grounded treatment recommendations remain challenging, particularly in heterogeneous patient settings with high diagnostic risk. Existing large language model (LLM)-based systems…

Clinical studies often require understanding elements of a patient's narrative that exist only in free text clinical notes. To transform notes into structured data for downstream use, these elements are commonly extracted and normalized to…

Named entity recognition (NER) suffers from the scarcity of annotated training data, especially for low-resource languages without labeled data. Cross-lingual NER has been proposed to alleviate this issue by transferring knowledge from…

This work presents our participation in the EvalLLM 2025 challenge on biomedical Named Entity Recognition (NER) and health event extraction in French (few-shot setting). For NER, we propose three approaches combining large language models…

In biomedical and neurodegenerative disorders, accurate and early disease identification remains challenging due to the scarcity of labeled data and the complexity of imaging patterns. To address these challenges, we introduce ARMA-C3, a…

Biomedical question-answering (QA) has gained increased attention for its capability to provide users with high-quality information from a vast scientific literature. Although an increasing number of biomedical QA datasets has been recently…