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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…
Overall, the two main contributions of this work include the application of sentence simplification to association extraction as described above, and the use of distributional semantics for concept extraction. The proposed work on concept…
Distant Supervised Relation Extraction (DSRE) is usually formulated as a problem of classifying a bag of sentences that contain two query entities, into the predefined relation classes. Most existing methods consider those relation classes…
We present a novel system that automatically extracts and generates informative and descriptive sentences from the biomedical corpus and facilitates the efficient search for relational knowledge. Unlike previous search engines or…
We present an approach to minimally supervised relation extraction that combines the benefits of learned representations and structured learning, and accurately predicts sentence-level relation mentions given only proposition-level…
We propose a novel neural method to extract drug-drug interactions (DDIs) from texts using external drug molecular structure information. We encode textual drug pairs with convolutional neural networks and their molecular pairs with graph…
With the increasing legalization of medical and recreational use of cannabis, more research is needed to understand the association between depression and consumer behavior related to cannabis consumption. Big social media data has…
Causal relation extraction of biomedical entities is one of the most complex tasks in biomedical text mining, which involves two kinds of information: entity relations and entity functions. One feasible approach is to take relation…
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…
Convolutional Neural Networks (CNNs) have revolutionized the understanding of visual content. This is mainly due to their ability to break down an image into smaller pieces, extract multi-scale localized features and compose them to…
The Clinical E-Science Framework (CLEF) project was used to extract important information from medical texts by building a system for the purpose of clinical research, evidence-based healthcare and genotype-meets-phenotype informatics. The…
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…
Document-level relation extraction aims to extract relations among entities within a document. Compared with its sentence-level counterpart, Document-level relation extraction requires inference over multiple sentences to extract complex…
Most work in relation extraction forms a prediction by looking at a short span of text within a single sentence containing a single entity pair mention. This approach often does not consider interactions across mentions, requires redundant…
Off-the-shelf biomedical embeddings obtained from the recently released various pre-trained language models (such as BERT, XLNET) have demonstrated state-of-the-art results (in terms of accuracy) for the various natural language…
The extraction of biomedical data has significant academic and practical value in contemporary biomedical sciences. In recent years, drug repositioning, a cost-effective strategy for drug development by discovering new indications for…
Joint entity-relation extraction is a critical task in transforming unstructured or semi-structured text into triplets, facilitating the construction of large-scale knowledge graphs, and supporting various downstream applications. Despite…
Drug-drug interaction (DDI) prediction is critical for treatment safety. While large language models (LLMs) show promise in pharmaceutical tasks, their effectiveness in DDI prediction remains challenging. Inspired by the well-established…
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…
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…