Related papers: Biomedical Information Extraction for Disease Gene…
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…
Biomedical Information Extraction is an exciting field at the crossroads of Natural Language Processing, Biology and Medicine. It encompasses a variety of different tasks that require application of state-of-the-art NLP techniques, such as…
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…
Biomedical event extraction is an information extraction task to obtain events from biomedical text, whose targets include the type, the trigger, and the respective arguments involved in an event. Traditional biomedical event extraction…
Objectives: Despite the recent adoption of large language models (LLMs) for biomedical information extraction, challenges in prompt engineering and algorithms persist, with no dedicated software available. To address this, we developed…
Biomedical information extraction (BioIE) is important to many applications, including clinical decision support, integrative biology, and pharmacovigilance, and therefore it has been an active research. Unlike existing reviews covering a…
Automatic extraction of information from publications is key to making scientific knowledge machine readable at a large scale. The extracted information can, for example, facilitate academic search, decision making, and knowledge graph…
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,…
Compared to the general news domain, information extraction (IE) from biomedical text requires much broader domain knowledge. However, many previous IE methods do not utilize any external knowledge during inference. Due to the exponential…
The biomedical literature provides a rich source of knowledge such as protein-protein interactions (PPIs), drug-drug interactions (DDIs) and chemical-protein interactions (CPIs). Biomedical relation extraction aims to automatically extract…
Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on…
Automatically extracting Protein-Protein Interactions (PPI) from biomedical literature provides additional support for precision medicine efforts. This paper proposes a novel memory network-based model (MNM) for PPI extraction, which…
Information Extraction (IE) from text refers to the task of extracting structured knowledge from unstructured text. The task typically consists of a series of sub-tasks such as Named Entity Recognition and Relation Extraction. Sourcing…
Biomedical information is growing rapidly in the recent years and retrieving useful data through information extraction system is getting more attention. In the current research, we focus on different aspects of relation extraction…
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…
The surging amount of biomedical literature & digital clinical records presents a growing need for text mining techniques that can not only identify but also semantically relate entities in unstructured data. In this paper we propose a text…
Question Answer (QA) systems for biomedical experiments facilitate cross-disciplinary communication, and serve as a foundation for downstream tasks, e.g., laboratory automation. High Information Density (HID) and Multi-Step Reasoning (MSR)…
Extracting fine-grained experimental findings from literature can provide dramatic utility for scientific applications. Prior work has developed annotation schemas and datasets for limited aspects of this problem, failing to capture the…
Information Extraction (IE) from scientific texts can be used to guide readers to the central information in scientific documents. But narrow IE systems extract only a fraction of the information captured, and Open IE systems do not perform…
Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. Meanwhile, knowledge bases (KBs) contain huge amounts of structured information of protein…