Related papers: MAGE: Model-Level Graph Neural Networks Explanatio…

Frequent and structurally related subgraphs, also known as network motifs, are valuable features of many graph datasets. However, the high computational complexity of identifying motif sets in arbitrary datasets (motif mining) has limited…

Integrating multi-omics data, such as DNA methylation, mRNA expression, and microRNA (miRNA) expression, offers a comprehensive view of the biological mechanisms underlying disease. However, the high dimensionality of multi-omics data, the…

Graph Neural Networks (GNNs) are increasingly adopted across domains such as molecular biology and social network analysis, yet their black-box nature hinders interpretability and trust. This is especially problematic in high-stakes…

In this work, we propose a methodology for investigating the use of semantic attention to enhance the explainability of Graph Neural Network (GNN)-based models. Graph Deep Learning (GDL) has emerged as a promising field for tasks like scene…

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…

Challenges persist in providing interpretable explanations for neural network reasoning in explainable AI (xAI). Existing methods like Integrated Gradients produce noisy maps, and LIME, while intuitive, may deviate from the model's…

Graph neural networks (GNNs) have demonstrated promising performance across various chemistry-related tasks. However, conventional graphs only model the pairwise connectivity in molecules, failing to adequately represent higher-order…

Human brains lie at the core of complex neurobiological systems, where the neurons, circuits, and subsystems interact in enigmatic ways. Understanding the structural and functional mechanisms of the brain has long been an intriguing pursuit…

Graph Masked Autoencoders (GMAEs) have emerged as a notable self-supervised learning approach for graph-structured data. Existing GMAE models primarily focus on reconstructing node-level information, categorizing them as single-scale GMAEs.…

As post hoc explanations are increasingly used to understand the behavior of graph neural networks (GNNs), it becomes crucial to evaluate the quality and reliability of GNN explanations. However, assessing the quality of GNN explanations is…

Networks are a powerful tool to model complex systems, and the definition of many Graph Neural Networks (GNN), Deep Learning algorithms that can handle networks, has opened a new way to approach many real-world problems that would be hardly…

Due to the nature of deep learning approaches, it is inherently difficult to understand which aspects of a molecular graph drive the predictions of the network. As a mitigation strategy, we constrain certain weights in a multi-task graph…

Graph Neural Networks achieve remarkable results on problems with structured data but come as black-box predictors. Transferring existing explanation techniques, such as occlusion, fails as even removing a single node or edge can lead to…

Graph Neural Networks (GNNs) have been widely deployed in various real-world applications. However, most GNNs are black-box models that lack explanations. One strategy to explain GNNs is through counterfactual explanation, which aims to…

Providing interpretability of deep-learning models to non-experts, while fundamental for a responsible real-world usage, is challenging. Attribution maps from xAI techniques, such as Integrated Gradients, are a typical example of a…

Foundation models have achieved remarkable success across many domains, relying on pretraining over vast amounts of data. Graph-structured data often lacks the same scale as unstructured data, making the development of graph foundation…

Uncovering rationales behind predictions of graph neural networks (GNNs) has received increasing attention over recent years. Instance-level GNN explanation aims to discover critical input elements, like nodes or edges, that the target GNN…

Link prediction is one of the central problems in graph mining. However, recent studies highlight the importance of higher-order network analysis, where complex structures called motifs are the first-class citizens. We first show that…

The graph neural network (GNN) has been a powerful deep-learning tool in chemistry domain, due to its close connection with molecular graphs. Most GNN models collect and update atom and molecule features from the fed atom (and, in some…

Graph neural networks (GNN) are very popular methods in machine learning and have been applied very successfully to the prediction of the properties of molecules and materials. First-order GNNs are well known to be incomplete, i.e., there…