Related papers: Enhancing Biomedical Relation Extraction with Dire…

Biomedical entity linking (BioEL) has achieved remarkable progress with the help of pre-trained language models. However, existing BioEL methods usually struggle to handle rare and difficult entities due to long-tailed distribution. To…

Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base. It plays a vital role in information extraction pipelines for the life sciences literature. We review recent work in the field and find that, as…

Relation extraction is essential for extracting and understanding biographical information in the context of digital humanities and related subjects. There is a growing interest in the community to build datasets capable of training machine…

Extracting biomedical relations from large corpora of scientific documents is a challenging natural language processing task. Existing approaches usually focus on identifying a relation either in a single sentence (mention-level) or across…

Scientific information extraction (SciIE) is critical for converting unstructured knowledge from scholarly articles into structured data (entities and relations). Several datasets have been proposed for training and validating SciIE models.…

Progress in biomedical Named Entity Recognition (NER) and Entity Linking (EL) is currently hindered by a fragmented data landscape, a lack of resources for building explainable models, and the limitations of semantically-blind evaluation…

While coreference resolution is traditionally used as a component in individual document understanding, in this work we take a more global view and explore what can we learn about a domain from the set of all document-level coreference…

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.…

Biomedical entity linking is the task of identifying mentions of biomedical concepts in text documents and mapping them to canonical entities in a target thesaurus. Recent advancements in entity linking using BERT-based models follow a…

Biomedical Named Entity Recognition (NER) is a fundamental task of Biomedical Natural Language Processing for extracting relevant information from biomedical texts, such as clinical records, scientific publications, and electronic health…

In Biomedical Natural Language Processing (BioNLP) tasks, such as Relation Extraction, Named Entity Recognition, and Text Classification, the scarcity of high-quality data remains a significant challenge. This limitation poisons large…

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,…

Because protein-protein interactions (PPIs) are crucial to understand living systems, harvesting these data is essential to probe disease development and discern gene/protein functions and biological processes. Some curated datasets contain…

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) 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…

We advance the state of the art in biomolecular interaction extraction with three contributions: (i) We show that deep, Abstract Meaning Representations (AMR) significantly improve the accuracy of a biomolecular interaction extraction…

Biomedical event extraction is critical in understanding biomolecular interactions described in scientific corpus. One of the main challenges is to identify nested structured events that are associated with non-indicative trigger words. We…

Extracting biographical information from online documents is a popular research topic among the information extraction (IE) community. Various natural language processing (NLP) techniques such as text classification, text summarisation and…

Document-level relation extraction (DocRE) is an active area of research in natural language processing (NLP) concerned with identifying and extracting relationships between entities beyond sentence boundaries. Compared to the more…

Motivation: State-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network…