相关论文: Biomedical Nested NER with Large Language Model an…

Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base. It plays a vital role in information extraction pipelines for the life sciences literature. We review recent work in the field and find that, as…

Biomedical Named Entity Recognition (BioNER), task6 in BioASQ (A challenge in large-scale biomedical semantic indexing and question answering), is crucial for extracting information from scientific literature but faces hurdles such as…

In biomedical literature, it is common for entity boundaries to not align with word boundaries. Therefore, effective identification of entity spans requires approaches capable of considering tokens that are smaller than words. We introduce…

Clinical text is rich in information, with mentions of treatment, medication and anatomy among many other clinical terms. Multiple terms can refer to the same core concepts which can be referred as a clinical entity. Ontologies like the…

Biomedical named entity recognition (NER) is a critial task that aims to identify structured information in clinical text, which is often replete with complex, technical terms and a high degree of variability. Accurate and reliable NER can…

Pre-trained language models induce dense entity representations that offer strong performance on entity-centric NLP tasks, but such representations are not immediately interpretable. This can be a barrier to model uptake in important…

Large Language Models (LLMs) demonstrate remarkable versatility in various NLP tasks but encounter distinct challenges in biomedical due to the complexities of language and data scarcity. This paper investigates LLMs application in the…

Despite their strong linguistic capabilities, Large Language Models (LLMs) are computationally demanding and require substantial resources for fine-tuning, which is unadapted to privacy and budget constraints of many healthcare settings. To…

We present a weakly-supervised data augmentation approach to improve Named Entity Recognition (NER) in a challenging domain: extracting biomedical entities (e.g., proteins) from the scientific literature. First, we train a neural NER (NNER)…

Automatically locating named entities in natural language text - named entity recognition - is an important task in the biomedical domain. Many named entity mentions are ambiguous between several bioconcept types, however, causing text…

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…

There are a few challenges related to the task of biomedical named entity recognition, which are: the existing methods consider a fewer number of biomedical entities (e.g., disease, symptom, proteins, genes); and these methods do not…

In this report, we describe our participant named-entity recognition system at VLSP 2018 evaluation campaign. We formalized the task as a sequence labeling problem using BIO encoding scheme. We applied a feature-based model which combines…

Motivation: The proliferation of Biomedical research articles has made the task of information retrieval more important than ever. Scientists and Researchers are having difficulty in finding articles that contain information relevant to…

In this paper, we present our approach to extracting structured information from unstructured Electronic Health Records (EHR) [2] which can be used to, for example, study adverse drug reactions in patients due to chemicals in their…

Motivation: Named Entity Recognition (NER) is a key task to support biomedical research. In Biomedical Named Entity Recognition (BioNER), obtaining high-quality expert annotated data is laborious and expensive, leading to the development of…

Pretrained language models have shown success in many natural language processing tasks. Many works explore incorporating knowledge into language models. In the biomedical domain, experts have taken decades of effort on building large-scale…

Biomedical named entities often play important roles in many biomedical text mining tools. However, due to the incompleteness of provided synonyms and numerous variations in their surface forms, normalization of biomedical entities is very…

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…

This paper shines a light on the potential of definition-based semantic models for detecting idiomatic and semi-idiomatic multiword expressions (MWEs) in clinical terminology. Our study focuses on biomedical entities defined in the UMLS…