Related papers: BALI: Enhancing Biomedical Language Representation…

Large Language Models (LLMs) have significantly advanced medical question-answering by leveraging extensive clinical data and medical literature. However, the rapid evolution of medical knowledge and the labor-intensive process of manually…

Large language models (LLMs) offer new opportunities for constructing knowledge graphs (KGs) from unstructured clinical narratives. However, existing approaches often rely on structured inputs and lack robust validation of factual accuracy…

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…

Off-the-shelf biomedical embeddings obtained from the recently released various pre-trained language models (such as BERT, XLNET) have demonstrated state-of-the-art results (in terms of accuracy) for the various natural language…

Graph Neural Networks (GNNs) have been widely used in diverse brain network analysis tasks based on preprocessed functional magnetic resonance imaging (fMRI) data. However, their performances are constrained due to high feature sparsity and…

The way we analyse clinical texts has undergone major changes over the last years. The introduction of language models such as BERT led to adaptations for the (bio)medical domain like PubMedBERT and ClinicalBERT. These models rely on large…

Enriching existing medical terminology knowledge bases (KBs) is an important and never-ending work for clinical research because new terminology alias may be continually added and standard terminologies may be newly renamed. In this paper,…

Retrieval augmented generation (RAG) has shown great power in improving Large Language Models (LLMs). However, most existing RAG-based LLMs are dedicated to retrieving single modality information, mainly text; while for many real-world…

Knowledge-enhanced language models (KELMs) have emerged as promising tools to bridge the gap between large-scale language models and domain-specific knowledge. KELMs can achieve higher factual accuracy and mitigate hallucinations by…

Engineering LLMs to accelerate life sciences research requires a robust alignment with biomedical knowledge. We observe that biomedical text exhibits a fundamentally different uncertainty structure from general text: dense low-confidence…

Background : Knowledge is evolving over time, often as a result of new discoveries or changes in the adopted methods of reasoning. Also, new facts or evidence may become available, leading to new understandings of complex phenomena. This is…

This work presents a Biomedical Literature Question Answering (Q&A) system based on a Retrieval-Augmented Generation (RAG) architecture, designed to improve access to accurate, evidence-based medical information. Addressing the shortcomings…

Entity linking (EL) aligns textual mentions with their corresponding entities in a knowledge base, facilitating various applications such as semantic search and question answering. Recent advances in multimodal entity linking (MEL) have…

In Natural Language Processing (NLP), Machine Reading Comprehension (MRC) is the task of answering a question based on a given context. To handle questions in the medical domain, modern language models such as BioBERT, SciBERT and even…

Large language models (LLMs) show promise for diagnostic reasoning but often lack reliable, knowledge grounded inference. Knowledge graphs (KGs), such as the Unified Medical Language System (UMLS), offer structured biomedical knowledge that…

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…

In this paper, we propose Knowledge Base augmented Language Model (KBLaM), a new method for augmenting Large Language Models (LLMs) with external knowledge. KBLaM works with a knowledge base (KB) constructed from a corpus of documents,…

Large language models (LLMs) have demonstrated significant potential in clinical decision support. Yet LLMs still suffer from hallucinations and lack fine-grained contextual medical knowledge, limiting their high-stake healthcare…

Medical deep learning models depend heavily on domain-specific knowledge to perform well on knowledge-intensive clinical tasks. Prior work has primarily leveraged unimodal knowledge graphs, such as the Unified Medical Language System…

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…