Related papers: Harnessing Large Language Models for Biomedical Na…

The terminology used in Biomedicine shows lexical peculiarities that have required the elaboration of terminological resources and information retrieval systems with specific functionalities. The main characteristics are the high rates of…

The massive scale and growth of textual biomedical data have made its indexing and classification increasingly important. However, existing research on this topic mainly utilized convolutional and recurrent neural networks, which generally…

Large Language Models (LLMs) have demonstrated significant potential in transforming clinical applications. In this study, we investigate the efficacy of four techniques in adapting LLMs for clinical use-cases: continuous pretraining,…

Large language models (LLMs) have shown potential in biomedical applications, leading to efforts to fine-tune them on domain-specific data. However, the effectiveness of this approach remains unclear. This study evaluates the performance of…

Dataset curation has become a basis for strong large language model (LLM) performance. While various rule-based filtering heuristics exist for English and multilingual datasets, model-based filtering techniques have primarily focused on…

Large Language Models (LLMs) have shown impressive abilities in data annotation, opening the way for new approaches to solve classic NLP problems. In this paper, we show how to use LLMs to create NuNER, a compact language representation…

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…

Pre-trained language models (PLMs) have proven to be effective for document re-ranking task. However, they lack the ability to fully interpret the semantics of biomedical and health-care queries and often rely on simplistic patterns for…

We present a refined approach to biomedical question-answering (QA) services by integrating large language models (LLMs) with Multi-BERT configurations. By enhancing the ability to process and prioritize vast amounts of complex biomedical…

This work presents biomedical and clinical language models for Spanish by experimenting with different pretraining choices, such as masking at word and subword level, varying the vocabulary size and testing with domain data, looking for…

Developing high-performing systems for detecting biomedical named entities has major implications. State-of-the-art deep-learning based solutions for entity recognition often require large annotated datasets, which is not available in the…

The introduction of Large Language Models (LLMs), and the vast volume of publicly available medical data, amplified the application of NLP to the medical domain. However, LLMs are pretrained on data that are not explicitly relevant to the…

Objective: Most existing fine-tuned biomedical large language models (LLMs) focus on enhancing performance in monolingual biomedical question answering and conversation tasks. To investigate the effectiveness of the fine-tuned LLMs on…

Efficient text classification is essential for handling the increasing volume of academic publications. This study explores the use of pre-trained language models (PLMs), including BERT, SciBERT, BioBERT, and BlueBERT, fine-tuned on the Web…

In this study, we investigate the potential of Large Language Models to complement biomedical knowledge graphs in the training of semantic models for the biomedical and clinical domains. Drawing on the wealth of the UMLS knowledge graph and…

We present BioLunar, developed using the Lunar framework, as a tool for supporting biological analyses, with a particular emphasis on molecular-level evidence enrichment for biomarker discovery in oncology. The platform integrates Large…

Domain adaptation is an effective solution to data scarcity in low-resource scenarios. However, when applied to token-level tasks such as bioNER, domain adaptation methods often suffer from the challenging linguistic characteristics that…

As demonstrated by the proprietary Large Language Models (LLMs) such as GPT and Claude series, LLMs have the potential to achieve remarkable proficiency across a wide range of domains, including law, medicine, finance, science, code, etc.,…

There has been an influx of biomedical domain-specific language models, showing language models pre-trained on biomedical text perform better on biomedical domain benchmarks than those trained on general domain text corpora such as…

This study evaluated the effect of BioBERT in medical text processing for the task of medical named entity recognition. Through comparative experiments with models such as BERT, ClinicalBERT, SciBERT, and BlueBERT, the results showed that…