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Accurate prediction of drug response in precision medicine requires models that capture how specific chemical substructures interact with cellular pathway states. However, most existing deep learning approaches treat chemical and…

We investigate molecular mechanisms of resistant or sensitive response of cancer drug combination therapies in an inductive and interpretable manner. Though deep learning algorithms are widely used in the drug synergy prediction problem, it…

Accurate prediction of drug-target interaction (DTI) is essential for in silico drug design. For the purpose, we propose a novel approach for predicting DTI using a GNN that directly incorporates the 3D structure of a protein-ligand…

Drug synergy prediction is a critical task in the development of effective combination therapies for complex diseases, including cancer. Although existing methods have shown promising results, they often operate as black-box predictors that…

Visual relationship detection can bridge the gap between computer vision and natural language for scene understanding of images. Different from pure object recognition tasks, the relation triplets of subject-predicate-object lie on an…

In clinical treatment, identifying potential adverse reactions of drugs can help assist doctors in making medication decisions. In response to the problems in previous studies that features are high-dimensional and sparse, independent…

Drug-Target Interaction (DTI) prediction is vital for drug discovery, yet challenges persist in achieving model interpretability and optimizing performance. We propose a novel transformer-based model, FragXsiteDTI, that aims to address…

Latent representations of drugs and their targets produced by contemporary graph autoencoder models have proved useful in predicting many types of node-pair interactions on large networks, including drug-drug, drug-target, and target-target…

Concomitant administration of drugs can cause drug-drug interactions (DDIs). Some drug combinations are beneficial, but other ones may cause negative effects which are previously unrecorded. Previous works on DDI prediction usually rely on…

Drug combinations are essential in cancer therapy, leveraging synergistic drug-drug interactions (DDI) to enhance efficacy and combat resistance. However, the vast combinatorial space makes experimental screening impractical, and existing…

We developed DyGETViz, a novel framework for effectively visualizing dynamic graphs (DGs) that are ubiquitous across diverse real-world systems. This framework leverages recent advancements in discrete-time dynamic graph (DTDG) models to…

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…

Drug similarity has been studied to support downstream clinical tasks such as inferring novel properties of drugs (e.g. side effects, indications, interactions) from known properties. The growing availability of new types of drug features…

Industrial carbon emissions are a major driver of climate change, yet modeling these emissions is challenging due to multicollinearity among factors and complex interdependencies across sectors and time. We propose a novel graph-based deep…

Drug-drug interactions (DDI) can cause severe adverse drug reactions and pose a major challenge to medication therapy. Recently, informatics-based approaches are emerging for DDI studies. In this paper, we aim to identify key…

In silico prediction of drug-target interactions (DTI) is significant for drug discovery because it can largely reduce timelines and costs in the drug development process. Specifically, deep learning-based DTI approaches have been shown…

Drug-drug interaction event (DDIE) prediction is crucial for preventing adverse reactions and ensuring optimal therapeutic outcomes. However, existing methods often face challenges with imbalanced datasets, complex interaction mechanisms,…

The integration of Artificial Intelligence (AI) into the field of drug discovery has been a growing area of interdisciplinary scientific research. However, conventional AI models are heavily limited in handling complex biomedical structures…

Drug-drug interaction prediction is a crucial issue in molecular biology. Traditional methods of observing drug-drug interactions through medical experiments require significant resources and labor. This paper presents a medical knowledge…

Uncovering the underlying causal mechanisms of complex real-world systems remains a significant challenge, as these systems often entail high data collection costs and involve unknown interventions. We introduce MetaCaDI, the first…