Related papers: Weisfeiler-Lehman Embedding for Molecular Graph Ne…

Message passing graph neural networks (GNNs) are known to have their expressiveness upper-bounded by 1-dimensional Weisfeiler-Leman (1-WL) algorithm. To achieve more powerful GNNs, existing attempts either require ad hoc features, or…

Stars' chemical signatures provide invaluable insights into stellar cluster formation. This study utilized the Weisfeiler-Lehman (WL) Graph Kernel to examine a 15-dimensional elemental abundance space. Through simulating chemical…

Graph Neural Networks (GNNs) have emerged as prominent models for representation learning on graph structured data. GNNs follow an approach of message passing analogous to 1-dimensional Weisfeiler Lehman (1-WL) test for graph isomorphism…

Accurate RNA secondary structure prediction is vital for understanding cellular regulation and disease mechanisms. Deep learning (DL) methods have surpassed traditional algorithms by predicting complex features like pseudoknots and…

Today we have a good theoretical understanding of the representational power of Graph Neural Networks (GNNs). For example, their limitations have been characterized in relation to a hierarchy of Weisfeiler-Lehman (WL) isomorphism tests.…

Nowadays the development of new functional materials/chemical compounds using machine learning (ML) techniques is a hot topic and includes several crucial steps, one of which is the choice of chemical structure representation. Classical…

Applying machine learning to molecules is challenging because of their natural representation as graphs rather than vectors.Several architectures have been recently proposed for deep learning from molecular graphs, but they suffer from…

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…

In recent years, there has been a significant amount of research focused on expanding the expressivity of Graph Neural Networks (GNNs) beyond the Weisfeiler-Lehman (1-WL) framework. While many of these studies have yielded advancements in…

Accurate prediction of molecular properties is essential in drug discovery and related fields. However, existing graph neural networks (GNNs) often struggle to simultaneously capture both local and global molecular structures. In this work,…

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.…

Learning representations of sets of nodes in a graph is crucial for applications ranging from node-role discovery to link prediction and molecule classification. Graph Neural Networks (GNNs) have achieved great success in graph…

Graph Neural Networks (GNN) are inherently limited in their expressive power. Recent seminal works (Xu et al., 2019; Morris et al., 2019b) introduced the Weisfeiler-Lehman (WL) hierarchy as a measure of expressive power. Although this…

Research into deep learning models for molecular property prediction has primarily focused on the development of better Graph Neural Network (GNN) architectures. Though new GNN variants continue to improve performance, their modifications…

Graph Neural Networks (GNNs) are effective tools for graph representation learning. Most GNNs rely on a recursive neighborhood aggregation scheme, named message passing, thereby their theoretical expressive power is limited to the…

Learning to optimize is a rapidly growing area that aims to solve optimization problems or improve existing optimization algorithms using machine learning (ML). In particular, the graph neural network (GNN) is considered a suitable ML model…

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…

Graph Neural Networks (GNNs) are limited in their expressive power, struggle with long-range interactions and lack a principled way to model higher-order structures. These problems can be attributed to the strong coupling between the…

Graph neural networks are designed to learn functions on graphs. Typically, the relevant target functions are invariant with respect to actions by permutations. Therefore the design of some graph neural network architectures has been…

Graph Nerual Networks (GNNs) are effective models in graph embedding. It extracts shallow features and neighborhood information by aggregating neighbor information to learn the embedding representation of different nodes. However, the local…