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Graph neural networks (GNNs) are among the most powerful tools in deep learning. They routinely solve complex problems on unstructured networks, such as node classification, graph classification, or link prediction, with high accuracy.…

Graph representation learning (GRL) models have succeeded in many scenarios. Real-world graphs have imbalanced distribution, such as node labels and degrees, which leaves a critical challenge to GRL. Imbalanced inputs can lead to imbalanced…

Graph Neural Networks (GNNs) are a framework for graph representation learning, where a model learns to generate low dimensional node embeddings that encapsulate structural and feature-related information. GNNs are usually trained in an…

Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequences have demonstrated significant success in sequence-based…

Machine learning methods have a long history of applications in high energy physics (HEP). Recently, there is a growing interest in exploiting these methods to reconstruct particle signatures from raw detector data. In order to benefit 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…

Graph Neural Networks (GNN) have shown a strong potential to be integrated into commercial products for network control and management. Early works using GNN have demonstrated an unprecedented capability to learn from different network…

Link prediction with knowledge graphs has been thoroughly studied in graph machine learning, leading to a rich landscape of graph neural network architectures with successful applications. Nonetheless, it remains challenging to transfer the…

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…

Graphs are a powerful tool for representing and analyzing unstructured, non-Euclidean data ubiquitous in the healthcare domain. Two prominent examples are molecule property prediction and brain connectome analysis. Importantly, recent works…

Recent years have witnessed the success of heterogeneous graph neural networks (HGNNs) in modeling heterogeneous information networks (HINs). In this paper, we focus on the benchmark task of HGNNs, i.e., node classification, and empirically…

Predicting interactions between structured entities lies at the core of numerous tasks such as drug regimen and new material design. In recent years, graph neural networks have become attractive. They represent structured entities as graphs…

Graph Neural Networks (GNNs) bring the power of deep representation learning to graph and relational data and achieve state-of-the-art performance in many applications. GNNs compute node representations by taking into account the topology…

Comprehending the interplay between spatial and temporal characteristics of neural dynamics can contribute to our understanding of information processing in the human brain. Graph neural networks (GNNs) provide a new possibility to…

Graph convolutional networks (GCNs) can effectively capture the features of related nodes and improve the performance of the model. More attention is paid to employing GCN in Skeleton-Based action recognition. But existing methods based on…

Subgraph classification is an emerging field in graph representation learning where the task is to classify a group of nodes (i.e., a subgraph) within a graph. Subgraph classification has applications such as predicting the cellular…

Higher-order features bring significant accuracy gains in semantic dependency parsing. However, modeling higher-order features with exact inference is NP-hard. Graph neural networks (GNNs) have been demonstrated to be an effective tool for…

Graph neural networks (GNNs) excel at predictive tasks on graph-structured data but often lack the ability to incorporate symbolic domain knowledge and perform general reasoning. Relational Bayesian Networks (RBNs), in contrast, enable…

Graph Neural Networks (GNNs) have gained traction in the complex domain of drug discovery because of their ability to process graph-structured data such as drug molecule models. This approach has resulted in a myriad of methods and models…

One significant challenge of exploiting Graph neural networks (GNNs) in real-life scenarios is that they are always treated as black boxes, therefore leading to the requirement of interpretability. To address this, model-level…