Related papers: Predicting Drug-Drug Interactions Using Knowledge …

Drug-target interaction (DTI) prediction plays a crucial role in drug discovery, and deep learning approaches have achieved state-of-the-art performance in this field. We introduce an ensemble of deep learning models (EnsembleDLM) for DTI…

Medical knowledge bases (KBs), distilled from biomedical literature and regulatory actions, are expected to provide high-quality information to facilitate clinical decision making. Entity disambiguation (also referred to as entity linking)…

Knowledge graphs (KGs) serve as fundamental structures for organizing interconnected data across diverse domains. However, most KGs remain incomplete, limiting their effectiveness in downstream applications. Knowledge graph completion (KGC)…

Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on molecular graphs, GNNs offer an intuitive and expressive…

Accurately predicting drug-drug interactions (DDIs) is crucial for pharmaceutical research and clinical safety. Recent deep learning models often suffer from high computational costs and limited generalization across datasets. In this…

A fundamental task for knowledge graphs (KGs) is knowledge graph completion (KGC). It aims to predict unseen edges by learning representations for all the entities and relations in a KG. A common concern when learning representations on…

We present a method for finding hierarchy-aware embeddings of knowledge graphs (KGs) using graph neural networks (GNNs) enriched with a semantic loss derived from underlying ontologies. This method yields embeddings that better reflect…

In this paper, we review recent developments and the role of Graph Neural Networks (GNNs) in computational drug discovery, including molecule generation, molecular property prediction, and drug-drug interaction prediction. By summarizing…

Drug repurposing is often framed as a candidate identification task, but existing approaches provide limited guidance for distinguishing biologically plausible candidates from historically well-connected ones. Here we introduce DrugKLM, a…

OBJECTIVE: Leverage existing biomedical NLP tools and DS domain terminology to produce a novel and comprehensive knowledge graph containing dietary supplement (DS) information for discovering interactions between DS and drugs, or…

Graph Neural Networks (GNNs) have gained traction in the complex domain of drug discovery because of their ability to process graph-structured data such as drug molecule models. This approach has resulted in a myriad of methods and models…

Knowledge Graph (KG) is a graph based data structure to represent facts of the world where nodes represent real world entities or abstract concept and edges represent relation between the entities. Graph as representation for knowledge has…

Accurate prediction of drug target interactions is critical for accelerating drug discovery and elucidating complex biological mechanisms. In this work, we frame drug target prediction as a link prediction task on heterogeneous biomedical…

The discovery of drug-target interactions (DTIs) is a pivotal process in pharmaceutical development. Computational approaches are a promising and efficient alternative to tedious and costly wet-lab experiments for predicting novel DTIs from…

The vast collection of machine learning records available on the web presents a significant opportunity for meta-learning, where past experiments are leveraged to improve performance. Two crucial meta-learning tasks are pipeline performance…

Knowledge Graphs (KGs) have emerged as invaluable resources for enriching recommendation systems by providing a wealth of factual information and capturing semantic relationships among items. Leveraging KGs can significantly enhance…

Knowledge graph embedding (KGE) is a technique that enhances knowledge graphs by addressing incompleteness and improving knowledge retrieval. A limitation of the existing KGE models is their underutilization of ontologies, specifically the…

In this paper, we present a novel diagnostic framework that integrates Knowledge Graphs (KGs) and Large Language Models (LLMs) to support system diagnostics in high-reliability systems such as nuclear power plants. Traditional diagnostic…

This paper studies graph-based recommendation, where an interaction graph is constructed from historical records and is lever-aged to alleviate data sparsity and cold start problems. We reveal an early summarization problem in existing…

Drug-drug interaction(DDI) prediction is an important task in the medical health machine learning community. This study presents a new method, multi-view graph contrastive representation learning for drug-drug interaction prediction,…