Related papers: A deep graph model for the signed interaction pred…

Drug combination therapy is a powerful solution for the treatment of complex disease such as cancers due to its capability of therapeutic efficacy and reducing side effects. Nevertheless, it is very difficult to screen all drug combinations…

Community detection, aiming to group the graph nodes into clusters with dense inner-connection, is a fundamental graph mining task. Recently, it has been studied on the heterogeneous graph, which contains multiple types of nodes and edges,…

This paper presents a novel graph-based deep learning model for tasks involving relations between two nodes (edge-centric tasks), where the focus lies on predicting relationships and interactions between pairs of nodes rather than node…

Graph Convolution Network (GCN) has attracted significant attention and become the most popular method for learning graph representations. In recent years, many efforts have been focused on integrating GCN into the recommender tasks and…

Deep generative models for graphs have exhibited promising performance in ever-increasing domains such as design of molecules (i.e, graph of atoms) and structure prediction of proteins (i.e., graph of amino acids). Existing work typically…

Network embedding has attracted an increasing attention over the past few years. As an effective approach to solve graph mining problems, network embedding aims to learn a low-dimensional feature vector representation for each node of a…

Identifying influential nodes in complex networks is of great importance, and has many applications in practice. For example, finding influential nodes in e-commerce network can provide merchants with customers with strong purchase intent;…

Accurate predictions on tabular data rely on capturing complex, dataset-specific feature interactions. Attention-based methods and graph neural networks, referred to as graph-based tabular deep learning (GTDL), aim to improve predictions by…

The era of "data deluge" has sparked renewed interest in graph-based learning methods and their widespread applications ranging from sociology and biology to transportation and communications. In this context of graph-aware methods, the…

Towards developing effective and efficient brain-computer interface (BCI) systems, precise decoding of brain activity measured by electroencephalogram (EEG), is highly demanded. Traditional works classify EEG signals without considering the…

Graph Convolutional Networks (GCNs) have recently been shown to be quite successful in modeling graph-structured data. However, the primary focus has been on handling simple undirected graphs. Multi-relational graphs are a more general and…

Skeleton-based human action recognition has attracted much attention with the prevalence of accessible depth sensors. Recently, graph convolutional networks (GCNs) have been widely used for this task due to their powerful capability to…

Due to the fact much of today's data can be represented as graphs, there has been a demand for generalizing neural network models for graph data. One recent direction that has shown fruitful results, and therefore growing interest, is the…

Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational…

In the treatment of complex diseases, treatment regimens using a single drug often yield limited efficacy and can lead to drug resistance. In contrast, combination drug therapies can significantly improve therapeutic outcomes through…

Introduction Accurate prediction of protein-protein interactions (PPIs) is crucial for understanding cellular functions and advancing drug development. Existing in-silico methods use direct sequence embeddings from Protein Language Models…

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…

Accurate modelling and quantification of predictive uncertainty is crucial in deep learning since it allows a model to make safer decisions when the data is ambiguous and facilitates the users' understanding of the model's confidence in its…

Motivation: Molecular interaction networks summarize complex biological processes as graphs, whose structure is informative of biological function at multiple scales. Simultaneously, omics technologies measure the variation or activity of…

Molecular interaction networks are powerful resources for the discovery. They are increasingly used with machine learning methods to predict biologically meaningful interactions. While deep learning on graphs has dramatically advanced the…