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The identification of active binding drugs for target proteins (termed as drug-target interaction prediction) is the key challenge in virtual screening, which plays an essential role in drug discovery. Although recent deep learning-based…

We propose an end-to-end model to predict drug-drug interactions (DDIs) by employing graph-augmented convolutional networks. And this is implemented by combining graph CNN with an attentive pooling network to extract structural relations…

Accurate prediction of drug-target interactions (DTI) is critical for drug discovery. Existing methods often rely on single-modal representations (e.g., sequences or graphs) or combine only two modalities, overlooking 3D structural…

Molecular representation learning has shown great success in advancing AI-based drug discovery. The core of many recent works is based on the fact that the 3D geometric structure of molecules provides essential information about their…

Illuminating the interconnections between drugs and genes is an important topic in drug development and precision medicine. Currently, computational predictions of drug-gene interactions mainly focus on the binding interactions without…

Since multidrug combination is widely applied, the accurate prediction of drug-drug interaction (DDI) is becoming more and more critical. In our method, we use graph to represent drug-drug interaction: nodes represent drug; edges represent…

Motivation: Exploring drug-protein interactions (DPIs) work as a pivotal step in drug discovery. The fast expansion of available biological data enables computational methods effectively assist in experimental methods. Among them, deep…

Accurate prediction of drug-drug interactions (DDI) is crucial for medication safety and effective drug development. However, existing methods often struggle to capture structural information across different scales, from local functional…

In this paper we study the practicality and usefulness of incorporating distributed representations of graphs into models within the context of drug pair scoring. We argue that the real world growth and update cycles of drug pair scoring…

We present an end-to-end, interpretable, deep-learning architecture to learn a graph kernel that predicts the outcome of chronic disease drug prescription. This is achieved through a deep metric learning collaborative with a Support Vector…

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

A common starting point for drug design is to find small chemical groups or "fragments" that form interactions with distinct subregions in a protein binding pocket. The subsequent challenge is to assemble these fragments into a molecule…

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph…

Predicting drug-drug interactions (DDI) is the problem of predicting side effects (unwanted outcomes) of a pair of drugs using drug information and known side effects of many pairs. This problem can be formulated as predicting labels (i.e.…

Accurate drug target affinity prediction can improve drug candidate selection, accelerate the drug discovery process, and reduce drug production costs. Previous work focused on traditional fingerprints or used features extracted based on…

Predicting the interaction between a compound and a target is crucial for rapid drug repurposing. Deep learning has been successfully applied in drug-target affinity (DTA) problem. However, previous deep learning-based methods ignore…

Predicting user influence in social networks is a critical problem, and hypergraphs, as a prevalent higher-order modeling approach, provide new perspectives for this task. However, the absence of explicit cascade or infection probability…

Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding methods are evaluated on social and information networks…

Identifying pills given their captured images under various conditions and backgrounds has been becoming more and more essential. Several efforts have been devoted to utilizing the deep learning-based approach to tackle the pill recognition…

Laboratory testing and medication prescription are two of the most important routines in daily clinical practice. Developing an artificial intelligence system that can automatically make lab test imputations and medication recommendations…