Related papers: BioBERT Based SNP-traits Associations Extraction f…

In this paper, we present our system for the BioNNE English track, which aims to extract 8 types of biomedical nested named entities from biomedical text. We use a large language model (Mixtral 8x7B instruct) and ScispaCy NER model to…

Recently, the automatic prediction of personality traits has received increasing attention and has emerged as a hot topic within the field of affective computing. In this work, we present a novel deep learning-based approach for automated…

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…

This paper conducts a comprehensive investigation into applying large language models, particularly on BioBERT, in healthcare. It begins with thoroughly examining previous natural language processing (NLP) approaches in healthcare, shedding…

Extracting precise geographical information from textual contents is crucial in a plethora of applications. For example, during hazardous events, a robust and unbiased toponym extraction framework can provide an avenue to tie the location…

Knowledge of a disease includes information of various aspects of the disease, such as signs and symptoms, diagnosis and treatment. This disease knowledge is critical for many health-related and biomedical tasks, including consumer health…

The newly emerged transformer technology has a tremendous impact on NLP research. In the general English domain, transformer-based models have achieved state-of-the-art performances on various NLP benchmarks. In the clinical domain,…

Automated annotation of clinical text with standardized medical concepts is critical for enabling structured data extraction and decision support. SNOMED CT provides a rich ontology for labeling clinical entities, but manual annotation is…

Despite the widespread success of self-supervised learning via masked language models (MLM), accurately capturing fine-grained semantic relationships in the biomedical domain remains a challenge. This is of paramount importance for…

Motivation: Protein-protein interactions (PPI) are critical to the function of proteins in both normal and diseased cells, and many critical protein functions are mediated by interactions.Knowledge of the nature of these interactions is…

Neural networks have long strived to emulate the learning capabilities of the human brain. While deep neural networks (DNNs) draw inspiration from the brain in neuron design, their training methods diverge from biological foundations.…

As the number of open and shared scientific datasets on the Internet increases under the open science movement, efficiently retrieving these datasets is a crucial task in information retrieval (IR) research. In recent years, the development…

Introduction: This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". Background: The proliferation of archetypes as a means to represent information of…

Objective: To discover candidate drugs to repurpose for COVID-19 using literature-derived knowledge and knowledge graph completion methods. Methods: We propose a novel, integrative, and neural network-based literature-based discovery (LBD)…

Relation extraction is an efficient way of mining the extraordinary wealth of human knowledge on the Web. Existing methods rely on domain-specific training data or produce noisy outputs. We focus here on extracting targeted relations from…

Objective: This work aimed to demonstrate the effectiveness of a hybrid approach based on Sentence BERT model and retrofitting algorithm to compute relatedness between any two biomedical concepts. Materials and Methods: We generated concept…

Biomedical question answering (QA) is a challenging task due to the scarcity of data and the requirement of domain expertise. Pre-trained language models have been used to address these issues. Recently, learning relationships between…

With the rapid growth of the scientific literature, manually selecting appropriate citations for a paper is becoming increasingly challenging and time-consuming. While several approaches for automated citation recommendation have been…

In this paper, we report our method for the Information Extraction task in 2019 Language and Intelligence Challenge. We incorporate BERT into the multi-head selection framework for joint entity-relation extraction. This model extends…

Document structure extraction has been a widely researched area for decades. Recent work in this direction has been deep learning-based, mostly focusing on extracting structure using fully convolution NN through semantic segmentation. In…