Related papers: Benchmarking for Biomedical Natural Language Proce…
Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains; however, these models encounter issues such as generating inaccurate information or hallucinations.…
Motivation: State-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network…
With the explosive growth of biomedical literature, designing automatic tools to extract information from the literature has great significance in biomedical research. Recently, transformer-based BERT models adapted to the biomedical domain…
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…
Language model (LM) pretraining can learn various knowledge from text corpora, helping downstream tasks. However, existing methods such as BERT model a single document, and do not capture dependencies or knowledge that span across…
Recent innovations in architecture, pre-training, and fine-tuning have led to the remarkable in-context learning and reasoning abilities of large auto-regressive language models such as LLaMA and DeepSeek. In contrast, encoders like BERT…
Large language models (LLMs) have demonstrated dominating performance in many NLP tasks, especially on generative tasks. However, they often fall short in some information extraction tasks, particularly those requiring domain-specific…
The success of bidirectional encoders using masked language models, such as BERT, on numerous natural language processing tasks has prompted researchers to attempt to incorporate these pre-trained models into neural machine translation…
In recent years, major advancements in natural language processing (NLP) have been driven by the emergence of large language models (LLMs), which have significantly revolutionized research and development within the field. Building upon…
Bipolar disorder is a chronic mental illness frequently underdiagnosed due to subtle early symptoms and social stigma. This paper explores the advanced natural language processing (NLP) models for recognizing signs of bipolar disorder based…
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)…
Biomedical entity linking aims to map biomedical mentions, such as diseases and drugs, to standard entities in a given knowledge base. The specific challenge in this context is that the same biomedical entity can have a wide range of names,…
Biomedical literature is a rapidly expanding field of science and technology. Classification of biomedical texts is an essential part of biomedicine research, especially in the field of biology. This work proposes the fine-tuned DistilBERT,…
As Transformers have become state-of-the-art models for natural language processing (NLP) tasks, the need to understand and explain their predictions is increasingly apparent. Especially in unsupervised applications, such as information…
Time is an important aspect of documents and is used in a range of NLP and IR tasks. In this work, we investigate methods for incorporating temporal information during pre-training to further improve the performance on time-related tasks.…
Automated knowledge curation for biomedical ontologies is key to ensure that they remain comprehensive, high-quality and up-to-date. In the era of foundational language models, this study compares and analyzes three NLP paradigms for…
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…
This paper presents a framework for Named Entity Recognition (NER) leveraging the Bidirectional Encoder Representations from Transformers (BERT) model in natural language processing (NLP). NER is a fundamental task in NLP with broad…
Since the introduction of the original BERT (i.e., BASE BERT), researchers have developed various customized BERT models with improved performance for specific domains and tasks by exploiting the benefits of transfer learning. Due to the…
Small and imbalanced datasets commonly seen in healthcare represent a challenge when training classifiers based on deep learning models. So motivated, we propose a novel framework based on BioBERT (Bidirectional Encoder Representations from…