Related papers: BioRED: A Rich Biomedical Relation Extraction Data…
Objective: Medical relations are the core components of medical knowledge graphs that are needed for healthcare artificial intelligence. However, the requirement of expert annotation by conventional algorithm development processes creates a…
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…
Information Extraction (IE), encompassing Named Entity Recognition (NER), Named Entity Linking (NEL), and Relation Extraction (RE), is critical for transforming the rapidly growing volume of scientific publications into structured,…
Successful biomedical relation extraction can provide evidence to researchers and clinicians about possible unknown associations between biomedical entities, advancing the current knowledge we have about those entities and their inherent…
Expert curation is essential to capture knowledge of enzyme functions from the scientific literature in FAIR open knowledgebases but cannot keep pace with the rate of new discoveries and new publications. In this work we present EnzChemRED,…
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…
The advancement of biomedical named entity recognition (BNER) and biomedical relation extraction (BRE) researches promotes the development of text mining in biological domains. As a cornerstone of BRE, robust BNER system is required to…
The DocRED dataset is one of the most popular and widely used benchmarks for document-level relation extraction (RE). It adopts a recommend-revise annotation scheme so as to have a large-scale annotated dataset. However, we find that the…
Relation Extraction (RE) aims to label relations between groups of marked entities in raw text. Most current RE models learn context-aware representations of the target entities that are then used to establish relation between them. This…
Relation Extraction (RE) has attracted increasing attention, but current RE evaluation is limited to in-domain evaluation setups. Little is known on how well a RE system fares in challenging, but realistic out-of-distribution evaluation…
The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature,…
Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations…
Causal relation extraction (CRE) is central to biomedical text mining, but current resources often conflate causal relations with broader associations, restrict annotation to sentence-level examples, or focus mainly on explicit causal cues.…
We introduce ChemDisGene, a new dataset for training and evaluating multi-class multi-label document-level biomedical relation extraction models. Our dataset contains 80k biomedical research abstracts labeled with mentions of chemicals,…
We introduce a biomedical information extraction (IE) pipeline that extracts biological relationships from text and demonstrate that its components, such as named entity recognition (NER) and relation extraction (RE), outperform…
Contextual Relation Extraction (CRE) is mainly used for constructing a knowledge graph with a help of ontology. It performs various tasks such as semantic search, query answering, and textual entailment. Relation extraction identifies the…
Relation Extraction (RE) is the task of extracting semantic relationships between entities in a sentence and aligning them to relations defined in a vocabulary, which is generally in the form of a Knowledge Graph (KG) or an ontology.…
Relation extraction (RE) consists in identifying and structuring automatically relations of interest from texts. Recently, BERT improved the top performances for several NLP tasks, including RE. However, the best way to use BERT, within a…
With the advent of artificial intelligence (AI), many researchers are attempting to extract structured information from document-level biomedical literature by fine-tuning large language models (LLMs). However, they face significant…
In this paper, we present FoodChem, a new Relation Extraction (RE) model for identifying chemicals present in the composition of food entities, based on textual information provided in biomedical peer-reviewed scientific literature. The RE…