Related papers: Enhancing Biomedical Relation Extraction with Dire…

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…

Constructing large-scaled medical knowledge graphs can significantly boost healthcare applications for medical surveillance, bring much attention from recent research. An essential step in constructing large-scale MKG is extracting…

Entity and relation extraction is the necessary step in structuring medical text. However, the feature extraction ability of the bidirectional long short term memory network in the existing model does not achieve the best effect. At the…

Information Extraction is a well-researched area of Natural Language Processing with applications in web search and question answering concerned with identifying entities and relationships between them as expressed in a given context,…

Named entity recognition (NER) is the very first step in the linguistic processing of any new domain. It is currently a common process in BioNLP on English clinical text. However, it is still in its infancy in other major languages, as it…

The biological literature is rich with sentences that describe causal relations. Methods that automatically extract such sentences can help biologists to synthesize the literature and even discover latent relations that had not been…

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…

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…

Accurate recognition of biomedical named entities is critical for medical information extraction and knowledge discovery. However, existing methods often struggle with nested entities, entity boundary ambiguity, and cross-lingual…

State-of-the-art deep learning entity linking methods rely on extensive human-labelled data, which is costly to acquire. Current datasets are limited in size, leading to inadequate coverage of biomedical concepts and diminished performance…

Document-level Relation Extraction (DocRE) is the task of extracting all semantic relationships from a document. While studies have been conducted on English DocRE, limited attention has been given to DocRE in non-English languages. This…

Relation extraction (RE) involves identifying the relations between entities from underlying content. RE serves as the foundation for many natural language processing (NLP) and information retrieval applications, such as knowledge graph…

Document-level relation extraction faces two overlooked challenges: long-tail problem and multi-label problem. Previous work focuses mainly on obtaining better contextual representations for entity pairs, hardly address the above…

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…

We introduce Biomed-Enriched, a biomedical text dataset constructed from PubMed via a two-stage annotation process. In the first stage, a large language model annotates 400K paragraphs from PubMed scientific articles, assigning scores for…

The overwhelming amount of biomedical scientific texts calls for the development of effective language models able to tackle a wide range of biomedical natural language processing (NLP) tasks. The most recent dominant approaches are…

Here we present the training and evaluation of NanoNER, a Named Entity Recognition (NER) model for Nanobiology. NER consists in the identification of specific entities in spans of unstructured texts and is often a primary task in Natural…

Recent advances in natural language processing (NLP) have been driven bypretrained language models like BERT, RoBERTa, T5, and GPT. Thesemodels excel at understanding complex texts, but biomedical literature, withits domain-specific…

The ever-growing volume of biomedical publications creates a critical need for efficient knowledge discovery. In this context, we introduce an open-source end-to-end framework designed to construct knowledge around specific diseases…

End-to-end relation extraction (E2ERE) is an important task in information extraction, more so for biomedicine as scientific literature continues to grow exponentially. E2ERE typically involves identifying entities (or named entity…