Related papers: Graph Diffusion Network for Drug-Gene Prediction

Heterogeneous graphs (HGs) are common in real-world scenarios and often exhibit heterophily. However, most existing studies focus on either heterogeneity or heterophily in isolation, overlooking the prevalence of heterophilic HGs in…

For translational impact, both accurate drug response prediction and biological plausibility of predictive features are needed. We present drGT, a heterogeneous graph deep learning model over drugs, genes, and cell lines that couples…

Predicating macroscopic influences of drugs on human body, like efficacy and toxicity, is a central problem of small-molecule based drug discovery. Molecules can be represented as an undirected graph, and we can utilize graph convolution…

Graph neural networks (GNNs) continue to achieve state-of-the-art performance on many graph learning tasks, but rely on the assumption that a given graph is a sufficient approximation of the true neighborhood structure. When a system…

Graph Neural Networks (GNNs) have been widely applied to different tasks such as bioinformatics, drug design, and social networks. However, recent studies have shown that GNNs are vulnerable to adversarial attacks which aim to mislead the…

Graph Neural Networks (GNNs) have achieved significant success in various learning tasks on graph-structured data. Nevertheless, most GNNs struggle to generalize to heterophilic neighborhoods. Additionally, many GNNs ignore the directional…

Diffusion models, as a novel generative paradigm, have achieved remarkable success in various image generation tasks such as image inpainting, image-to-text translation, and video generation. Graph generation is a crucial computational task…

Graph Neural Networks (GNNs) aim to extend deep learning techniques to graph data and have achieved significant progress in graph analysis tasks (e.g., node classification) in recent years. However, similar to other deep neural networks…

Graph neural networks~(GNNs) apply deep learning techniques to graph-structured data and have achieved promising performance in graph representation learning. However, existing GNNs rely heavily on enough labels or well-designed negative…

Graph convolutional neural networks have recently shown great potential for the task of zero-shot learning. These models are highly sample efficient as related concepts in the graph structure share statistical strength allowing…

Graph classification is an important area in both modern research and industry. Multiple applications, especially in chemistry and novel drug discovery, encourage rapid development of machine learning models in this area. To keep up with…

Heterophilic Graph Neural Networks (HGNNs) have shown promising results for semi-supervised learning tasks on graphs. Notably, most real-world heterophilic graphs are composed of a mixture of nodes with different neighbor patterns,…

Synergistic drug combinations provide huge potentials to enhance therapeutic efficacy and to reduce adverse reactions. However, effective and synergistic drug combination prediction remains an open question because of the unknown causal…

Graph Neural Networks (GNNs) have demonstrated significant success in learning from graph-structured data across various domains. Despite their great successful, one critical challenge is often overlooked by existing works, i.e., the…

Graph Neural Networks (GNNs) have been emerging as a promising method for relational representation including recommender systems. However, various challenging issues of social graphs hinder the practical usage of GNNs for social…

Graph Neural Networks (GNNs) have demonstrated remarkable efficacy in tackling a wide array of graph-related tasks across diverse domains. However, a significant challenge lies in their propensity to generate biased predictions,…

This paper presents HGEN that pioneers ensemble learning for heterogeneous graphs. We argue that the heterogeneity in node types, nodal features, and local neighborhood topology poses significant challenges for ensemble learning,…

Graphs are essential representations of many real-world data such as social networks. Recent years have witnessed the increasing efforts made to extend the neural network models to graph-structured data. These methods, which are usually…

Recent years have witnessed the significant success of applying graph neural networks (GNNs) in learning effective node representations for classification. However, current GNNs are mostly built under the balanced data-splitting, which is…

Motivation: Predicting Drug-Target Interaction (DTI) is a well-studied topic in bioinformatics due to its relevance in the fields of proteomics and pharmaceutical research. Although many machine learning methods have been successfully…