Related papers: Building explainable graph neural network by spars…

Evaluating the blood-brain barrier (BBB) permeability of drug molecules is a critical step in brain drug development. Traditional methods for the evaluation require complicated in vitro or in vivo testing. Alternatively, in silico…

As proteins with similar structures often have similar functions, analysis of protein structures can help predict protein functions and is thus important. We consider the problem of protein structure classification, which computationally…

Subgraph GNNs are provably expressive neural architectures that learn graph representations from sets of subgraphs. Unfortunately, their applicability is hampered by the computational complexity associated with performing message passing on…

Recent research on graph neural networks (GNNs) has explored mechanisms for capturing local uncertainty and exploiting graph hierarchies to mitigate data sparsity and leverage structural properties. However, the synergistic integration of…

Recent advances in graph convolutional networks have significantly improved the performance of chemical predictions, raising a new research question: "how do we explain the predictions of graph convolutional networks?" A possible approach…

In this study, we present the Graph Sub-Graph Network (GSN), a novel hybrid image classification model merging the strengths of Convolutional Neural Networks (CNNs) for feature extraction and Graph Neural Networks (GNNs) for structural…

In drug discovery, knowledge of the graph structure of chemical compounds is essential. Many thousands of scientific articles in chemistry and pharmaceutical sciences have investigated chemical compounds, but in cases the details of the…

Convolution Neural Networks on Graphs are important generalization and extension of classical CNNs. While previous works generally assumed that the graph structures of samples are regular with unified dimensions, in many applications, they…

Graph Neural Networks (GNNs) are important across different domains, such as social network analysis and recommendation systems, due to their ability to model complex relational data. This paper introduces subgraph queries as a new task for…

The advent of Graph Neural Networks (GNNs) has revolutionized the field of machine learning, offering a novel paradigm for learning on graph-structured data. Unlike traditional neural networks, GNNs are capable of capturing complex…

Graph neural networks (GNN) have been shown to provide substantial performance improvements for atomistic material representation and modeling compared with descriptor-based machine learning models. While most existing GNN models for…

Graph neural networks (GNNs) are a class of deep models that operate on data with arbitrary topology represented as graphs. We introduce an efficient memory layer for GNNs that can jointly learn node representations and coarsen the graph.…

Recently, graph Convolutional Neural Networks (graph CNNs) have been widely used for graph data representation and semi-supervised learning tasks. However, existing graph CNNs generally use a fixed graph which may be not optimal for…

Proteins play a vital role in biological processes and are indispensable for living organisms. Accurate representation of proteins is crucial, especially in drug development. Recently, there has been a notable increase in interest in…

Graph neural networks (GNNs) have attracted much attention due to their ability to leverage the intrinsic geometries of the underlying data. Although many different types of GNN models have been developed, with many benchmarking procedures…

Hypergraph offers a framework to depict the multilateral relationships in real-world complex data. Predicting higher-order relationships, i.e hyperedge, becomes a fundamental problem for the full understanding of complicated interactions.…

How to produce expressive molecular representations is a fundamental challenge in AI-driven drug discovery. Graph neural network (GNN) has emerged as a powerful technique for modeling molecular data. However, previous supervised approaches…

Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…

The prediction of physicochemical properties from molecular structures is a crucial task for artificial intelligence aided molecular design. A growing number of Graph Neural Networks (GNNs) have been proposed to address this challenge.…

Graph Neural Networks (GNNs) are widely used for graph representation learning in many application domains. The expressiveness of vanilla GNNs is upper-bounded by 1-dimensional Weisfeiler-Leman (1-WL) test as they operate on rooted subtrees…