Related papers: Self-Alignment Pretraining for Biomedical Entity R…

In recent years, with the growing amount of biomedical documents, coupled with advancement in natural language processing algorithms, the research on biomedical named entity recognition (BioNER) has increased exponentially. However, BioNER…

Background: Transformer-based language models have shown strong performance on many Natural LanguageProcessing (NLP) tasks. Masked Language Models (MLMs) attract sustained interest because they can be adaptedto different languages and…

Biomedical entity linking, a main component in automatic information extraction from health-related texts, plays a pivotal role in connecting textual entities (such as diseases, drugs and body parts mentioned by patients) to their…

Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained…

Recently, the performance of Pre-trained Language Models (PLMs) has been significantly improved by injecting knowledge facts to enhance their abilities of language understanding. For medical domains, the background knowledge sources are…

With hundreds of multilingual embedding models available, practitioners lack clear guidance on which provide genuine cross-lingual semantic alignment versus task performance through language-specific patterns. Task-driven benchmarks (MTEB)…

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…

Developing high-performance entity normalization algorithms that can alleviate the term variation problem is of great interest to the biomedical community. Although deep learning-based methods have been successfully applied to biomedical…

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,…

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…

Background and Objective: Biomedical Named Entity Recognition (BioNER) is a foundational task in medical informatics, crucial for downstream applications like drug discovery and clinical trial matching. However, adapting general-domain…

Electronic health records (EHR) contain narrative notes that provide extensive details on the medical condition and management of patients. Natural language processing (NLP) of clinical notes can use observed frequencies of clinical terms…

We explore the suitability of unsupervised representation learning methods on biomedical text -- BioBERT, SciBERT, and BioSentVec -- for biomedical question answering. To further improve unsupervised representations for biomedical QA, we…

Named entity recognition (NER) stands as a fundamental and pivotal task within the realm of Natural Language Processing. Particularly within the domain of Biomedical Method NER, this task presents notable challenges, stemming from the…

The exponential growth of online textual content across diverse domains has necessitated advanced methods for automated text classification. Large Language Models (LLMs) based on transformer architectures have shown significant success in…

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…

In recent years, pre-trained language models (PLMs) achieve the best performance on a wide range of natural language processing (NLP) tasks. While the first models were trained on general domain data, specialized ones have emerged to more…

Images in the medical domain are fundamentally different from the general domain images. Consequently, it is infeasible to directly employ general domain Visual Question Answering (VQA) models for the medical domain. Additionally, medical…

This study proposes a medical entity extraction method based on Transformer to enhance the information extraction capability of medical literature. Considering the professionalism and complexity of medical texts, we compare the performance…

Entity linking is the task of linking mentions of named entities in natural language text, to entities in a curated knowledge-base. This is of significant importance in the biomedical domain, where it could be used to semantically annotate…