Related papers: A Lightweight Neural Model for Biomedical Entity L…

Extracting clinically relevant information from unstructured medical narratives such as admission notes, discharge summaries, and emergency case histories remains a challenge in clinical natural language processing (NLP). Medical Entity…

Prevalent solution for BioNER involves using representation learning techniques coupled with sequence labeling. However, such methods are inherently task-specific, demonstrate poor generalizability, and often require dedicated model for…

Named Entity Recognition (NER) in the rare disease domain poses unique challenges due to limited labeled data, semantic ambiguity between entity types, and long-tail distributions. In this study, we evaluate the capabilities of GPT-4o for…

Medical Entity Recognition (MedER) is an essential NLP task for extracting meaningful entities from the medical corpus. Nowadays, MedER-based research outcomes can remarkably contribute to the development of automated systems in the medical…

Biomedical named entity recognition (NER) and entity linking (EL) strongly depend on annotated corpora, but the utility of these resources for benchmarking is often assumed rather than characterized. We present a corpus-centric framework…

The increasing depth of parametric domain knowledge in large language models (LLMs) is fueling their rapid deployment in real-world applications. Understanding model vulnerabilities in high-stakes and knowledge-intensive tasks is essential…

Entity linking aims to establish a link between entity mentions in a document and the corresponding entities in knowledge graphs (KGs). Previous work has shown the effectiveness of global coherence for entity linking. However, most of the…

Recent advances in natural language processing (NLP) have been driven bypretrained language models like BERT, RoBERTa, T5, and GPT. Thesemodels excel at understanding complex texts, but biomedical literature, withits domain-specific…

Biomedical entity linking and event extraction are two crucial tasks to support text understanding and retrieval in the biomedical domain. These two tasks intrinsically benefit each other: entity linking disambiguates the biomedical…

Named entity recognition (NER) is a widely applicable natural language processing task and building block of question answering, topic modeling, information retrieval, etc. In the medical domain, NER plays a crucial role by extracting…

We study clinical Named Entity Recognition (NER) on the CADEC corpus and compare three families of approaches: (i) BERT-style encoders (BERT Base, BioClinicalBERT, RoBERTa-large), (ii) GPT-4o used with few-shot in-context learning (ICL)…

Forms are a widespread type of template-based document used in a great variety of fields including, among others, administration, medicine, finance, or insurance. The automatic extraction of the information included in these documents is…

For languages with no annotated resources, unsupervised transfer of natural language processing models such as named-entity recognition (NER) from resource-rich languages would be an appealing capability. However, differences in words and…

Named entity recognition is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the…

Named Entity Recognition (NER) or the extraction of concepts from clinical text is the task of identifying entities in text and slotting them into categories such as problems, treatments, tests, clinical departments, occurrences (such as…

Despite recent progress, Biomedical Entity Linking (BEL) with large language models (LLMs) remains computationally inefficient and challenging to deploy in practical settings. In this work, we demonstrate that instruction-tuning of…

Named entity recognition (NER) and entity linking (EL) are two fundamentally related tasks, since in order to perform EL, first the mentions to entities have to be detected. However, most entity linking approaches disregard the mention…

Entity matching is the task of linking records from different sources that refer to the same real-world entity. Past work has primarily treated entity linking as a standard supervised learning problem. However, supervised entity matching…

In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical entities (e.g. diseases and drugs) from the ever-growing…

Entity Linking (EL) has traditionally relied on large annotated datasets and extensive model fine-tuning. While recent few-shot methods leverage large language models (LLMs) through prompting to reduce training requirements, they often…