Related papers: GraphPINE: Graph Importance Propagation for Interp…

Large-scale "pre-train and prompt learning" paradigms have demonstrated remarkable adaptability, enabling broad applications across diverse domains such as question answering, image recognition, and multimodal retrieval. This approach fully…

Graph neural networks (GNNs) have emerged as a powerful tool for modeling graph-structured data. However, existing GNNs often struggle with heterophilic graphs, where connected nodes tend to have dissimilar features or labels. While…

Modeling and generating graphs is fundamental for studying networks in biology, engineering, and social sciences. However, modeling complex distributions over graphs and then efficiently sampling from these distributions is challenging due…

We introduce Attention Graphs, a new tool for mechanistic interpretability of Graph Neural Networks (GNNs) and Graph Transformers based on the mathematical equivalence between message passing in GNNs and the self-attention mechanism in…

Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on molecular graphs, GNNs offer an intuitive and expressive…

Explainability is crucial for the application of black-box Graph Neural Networks (GNNs) in critical fields such as healthcare, finance, cybersecurity, and more. Various feature attribution methods, especially the perturbation-based methods,…

The success of Graph Neural Networks (GNNs) has led to a need for understanding their decision-making process and providing explanations for their predictions, which has given rise to explainable AI (XAI) that offers transparent…

Heterogeneous graph neural networks (HGNs) are prominent approaches to node classification tasks on heterogeneous graphs. Despite the superior performance, insights about the predictions made from HGNs are obscure to humans. Existing…

3D Geometric Graph Neural Networks (GNNs) have emerged as transformative tools for modeling molecular data. Despite their predictive power, these models often suffer from limited interpretability, raising concerns for scientific…

Graph neural networks (GNNs), which propagate the node features through the edges and learn how to transform the aggregated features under label supervision, have achieved great success in supervised feature extraction for both node-level…

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…

Graph Neural Networks (GNNs) have achieved tremendous success in a variety of real-world applications by relying on the fixed graph data as input. However, the initial input graph might not be optimal in terms of specific downstream tasks,…

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…

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…

Accurate prediction of drug-target interaction (DTI) is essential for in silico drug design. For the purpose, we propose a novel approach for predicting DTI using a GNN that directly incorporates the 3D structure of a protein-ligand…

The integration of deep learning approaches in biomedical research has been transformative, enabling breakthroughs in various applications. Despite these strides, its application in protein inference is impeded by the scarcity of…

We explore different strategies to integrate prior domain knowledge into the design of a deep neural network (DNN). We focus on graph neural networks (GNN), with a use case of estimating the potential energy of chemical systems (molecules…

Graphs are a central representation in biomedical research, capturing molecular interaction networks, gene regulatory circuits, cell--cell communication maps, and knowledge graphs. Despite their importance, currently there is not a broadly…

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…

Graphs are a fundamental abstraction for modeling relational data. However, graphs are discrete and combinatorial in nature, and learning representations suitable for machine learning tasks poses statistical and computational challenges. In…