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Automatic conversion of free-text radiology reports into structured data using Natural Language Processing (NLP) techniques is crucial for analyzing diseases on a large scale. While effective for tasks in widely spoken languages like…

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…

Hypergraphs are characterized by complex topological structure, representing higher-order interactions among multiple entities through hyperedges. Lately, hypergraph-based deep learning methods to learn informative data representations for…

Knowledge graph embedding techniques are widely used for knowledge graph refinement tasks such as graph completion and triple classification. These techniques aim at embedding the entities and relations of a Knowledge Graph (KG) in a low…

In recent years, summarizers that incorporate domain knowledge into the process of text summarization have outperformed generic methods, especially for summarization of biomedical texts. However, construction and maintenance of domain…

This paper introduces an approach for building a Named Entity Recognition (NER) model built upon a Bidirectional Encoder Representations from Transformers (BERT) architecture, specifically utilizing the SlovakBERT model. This NER model…

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…

Biomedical entity linking is the task of linking entity mentions in a biomedical document to referent entities in a knowledge base. Recently, many BERT-based models have been introduced for the task. While these models have achieved…

The Bidirectional Encoder Representations from Transformers (BERT) model has achieved the state-of-the-art performance for many natural language processing (NLP) tasks. Yet, limited research has been contributed to studying its…

Small and imbalanced datasets commonly seen in healthcare represent a challenge when training classifiers based on deep learning models. So motivated, we propose a novel framework based on BioBERT (Bidirectional Encoder Representations from…

Objective: To develop a corpus annotated for diet-microbiome associations from the biomedical literature and train natural language processing (NLP) models to identify these associations, thereby improving the understanding of their role in…

Supervised named entity recognition (NER) in the biomedical domain depends on large sets of annotated texts with the given named entities. The creation of such datasets can be time-consuming and expensive, while extraction of new entities…

Abstracts derived from biomedical literature possess distinct domain-specific characteristics, including specialised writing styles and biomedical terminologies, which necessitate a deep understanding of the related literature. As a result,…

The knowledge extraction task is to extract triple relations (head entity-relation-tail entity) from unstructured text data. The existing knowledge extraction methods are divided into "pipeline" method and joint extraction method. The…

Bioinformatics workflows are essential for complex biological data analyses and are often described in scientific articles with source code in public repositories. Extracting detailed workflow information from articles can improve…

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…

Curation of biomedical knowledge bases (KBs) relies on extracting accurate multi-entity relational facts from the literature - a process that remains largely manual and expert-driven. An essential step in this workflow is retrieving…

Protein-protein interactions (PPIs) are critical to normal cellular function and are related to many disease pathways. However, only 4% of PPIs are annotated with PTMs in biological knowledge databases such as IntAct, mainly performed…

Background: Identifying relationships between clinical events and temporal expressions is a key challenge in meaningfully analyzing clinical text for use in advanced AI applications. While previous studies exist, the state-of-the-art…

Fact triples are a common form of structured knowledge used within the biomedical domain. As the amount of unstructured scientific texts continues to grow, manual annotation of these texts for the task of relation extraction becomes…