Related papers: Quantitative Evaluation of Explainable Graph Neura…

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) have shown great ability in modeling graph-structured data for various domains. However, GNNs are known as black-box models that lack interpretability. Without understanding their inner working, we cannot fully…

Currently, attention mechanisms have garnered increasing attention in Graph Neural Networks (GNNs), such as Graph Attention Networks (GATs) and Graph Transformers (GTs). It is not only due to the commendable boost in performance they offer…

As one of the most popular machine learning models today, graph neural networks (GNNs) have attracted intense interest recently, and so does their explainability. Users are increasingly interested in a better understanding of GNN models and…

The surge in black-box AI models has prompted the need to explain the internal mechanism and justify their reliability, especially in high-stakes applications, such as healthcare and autonomous driving. Due to the lack of a rigorous…

Graph Machine Learning (GML) has numerous applications, such as node/graph classification and link prediction, in real-world domains. Providing human-understandable explanations for GML models is a challenging yet fundamental task to foster…

With the rapid deployment of graph neural networks (GNNs) based techniques into a wide range of applications such as link prediction, node classification, and graph classification the explainability of GNNs has become an indispensable…

Designing new molecules with a set of predefined properties is a core problem in modern drug discovery and development. There is a growing need for de-novo design methods that would address this problem. We present MolecularRNN, the graph…

Explainable Graph Neural Networks (GNNs) have been developed and applied to drug-protein binding prediction to identify the key chemical structures in a drug that have active interactions with the target proteins. However, the key…

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,…

The crux of molecular property prediction is to generate meaningful representations of the molecules. One promising route is to exploit the molecular graph structure through Graph Neural Networks (GNNs). It is well known that both atoms and…

Graph Neural Networks (GNNs) are deep learning models that take graph data as inputs, and they are applied to various tasks such as traffic prediction and molecular property prediction. However, owing to the complexity of the GNNs, it has…

Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs.GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating…

Recently, subgraphs-enhanced Graph Neural Networks (SGNNs) have been introduced to enhance the expressive power of Graph Neural Networks (GNNs), which was proved to be not higher than the 1-dimensional Weisfeiler-Leman isomorphism test. The…

Dementia is a progressive neurodegenerative disorder with multiple etiologies, including Alzheimer's disease, Parkinson's disease, frontotemporal dementia, and vascular dementia. Its clinical and biological heterogeneity makes diagnosis and…

Graph Neural Networks (GNNs) are neural models that leverage the dependency structure in graphical data via message passing among the graph nodes. GNNs have emerged as pivotal architectures in analyzing graph-structured data, and their…

As Graph Neural Networks (GNNs) are increasingly being employed in critical real-world applications, several methods have been proposed in recent literature to explain the predictions of these models. However, there has been little to no…

Learning and reasoning about 3D molecular structures with varying size is an emerging and important challenge in machine learning and especially in drug discovery. Equivariant Graph Neural Networks (GNNs) can simultaneously leverage the…

Graph Neural Networks (GNNs) excel in graph-based learning tasks, but their complex, non-linear operations often render them as opaque "black boxes". This opacity hinders user trust, complicates debugging, bias detection, and adoption in…

Graph Neural Networks (GNNs) have achieved remarkable success in various applications, but their performance can be sensitive to specific data properties of the graph datasets they operate on. Current literature on understanding the…