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Graph neural networks (GNNs) have demonstrated a significant boost in prediction performance on graph data. At the same time, the predictions made by these models are often hard to interpret. In that regard, many efforts have been made to…

Machine Learning · Computer Science 2023-05-24 Yiqiao Li , Jianlong Zhou , Sunny Verma , Fang Chen

Multi-graph learning is crucial for extracting meaningful signals from collections of heterogeneous graphs. However, effectively integrating information across graphs with differing topologies, scales, and semantics, often in the absence of…

Machine Learning · Computer Science 2026-02-02 Zahra Moslemi , Ziyi Liang , Norbert Fortin , Babak Shahbaba

The growing adoption of Graph Neural Networks (GNNs) in high-stakes domains like healthcare and finance demands reliable explanations of their decision-making processes. While inherently interpretable GNN architectures like Graph…

Machine Learning · Computer Science 2025-05-27 Rishabh Bhattacharya , Hari Shankar , Vaishnavi Shivkumar , Ponnurangam Kumaraguru

Graph Neural Networks (GNNs) have become a powerful tool for modeling and analyzing data with graph structures. The wide adoption in numerous applications underscores the value of these models. However, the complexity of these methods often…

Artificial Intelligence · Computer Science 2025-12-10 Tien Cuong Bui

Data-driven surrogate modeling has surged in capability in recent years with the emergence of graph neural networks (GNNs), which can operate directly on mesh-based representations of data. The goal of this work is to introduce an…

Machine Learning · Computer Science 2024-10-25 Shivam Barwey , Hojin Kim , Romit Maulik

Graph Neural Networks (GNNs) have emerged as the predominant approach for learning over graph-structured data. However, most GNNs operate as black-box models and require post-hoc explanations, which may not suffice in high-stakes scenarios…

Machine Learning · Computer Science 2025-10-14 Maya Bechler-Speicher , Amir Globerson , Ran Gilad-Bachrach

Subgraph-enhanced graph neural networks (SGNN) can increase the expressive power of the standard message-passing framework. This model family represents each graph as a collection of subgraphs, generally extracted by random sampling or with…

Machine Learning · Computer Science 2023-04-17 Indro Spinelli , Michele Guerra , Filippo Maria Bianchi , Simone Scardapane

Graphs neural networks (GNNs) learn node features by aggregating and combining neighbor information, which have achieved promising performance on many graph tasks. However, GNNs are mostly treated as black-boxes and lack human intelligible…

Machine Learning · Computer Science 2020-06-05 Hao Yuan , Jiliang Tang , Xia Hu , Shuiwang Ji

Graph neural networks (GNNs) have emerged as a powerful model to capture critical graph patterns. Instead of treating them as black boxes in an end-to-end fashion, attempts are arising to explain the model behavior. Existing works mainly…

Machine Learning · Computer Science 2024-02-22 Yi Nian , Yurui Chang , Wei Jin , Lu Lin

Graph Neural Networks (GNNs) have become a standard approach for learning from graph-structured data. However, their reliance on parametric classifiers (most often linear softmax layers) limits interpretability and sometimes hinders…

Machine Learning · Computer Science 2026-02-03 Zeljko Bolevic , Milos Brajovic , Isidora Stankovic , Ljubisa Stankovic

With the growing use of deep learning methods, particularly graph neural networks, which encode intricate interconnectedness information, for a variety of real tasks, there is a necessity for explainability in such settings. In this paper,…

Machine Learning · Computer Science 2022-11-04 Harsh Patel , Shivam Sahni

Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect…

Machine Learning · Computer Science 2020-11-10 Emily Alsentzer , Samuel G. Finlayson , Michelle M. Li , Marinka Zitnik

Graph Neural Networks (GNNs) are versatile, powerful machine learning methods that enable graph structure and feature representation learning, and have applications across many domains. For applications critically requiring interpretation,…

Machine Learning · Computer Science 2020-07-02 Chris Lin , Gerald J. Sun , Krishna C. Bulusu , Jonathan R. Dry , Marylens Hernandez

Graph neural networks (GNNs) are highly effective on a variety of graph-related tasks; however, they lack interpretability and transparency. Current explainability approaches are typically local and treat GNNs as black-boxes. They do not…

Machine Learning · Computer Science 2023-03-10 Han Xuanyuan , Pietro Barbiero , Dobrik Georgiev , Lucie Charlotte Magister , Pietro Lió

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…

Machine Learning · Computer Science 2025-09-22 Xiao Yue , Guangzhi Qu , Lige Gan

Advances in machine learning have led to graph neural network-based methods for drug discovery, yielding promising results in molecular design, chemical synthesis planning, and molecular property prediction. However, current graph neural…

Quantitative Methods · Quantitative Biology 2021-07-13 Jiahua Rao , Shuangjia Zheng , Yuedong Yang

Graph Neural Networks (GNNs) are a popular class of machine learning models. Inspired by the learning to explain (L2X) paradigm, we propose L2XGNN, a framework for explainable GNNs which provides faithful explanations by design. L2XGNN…

Machine Learning · Computer Science 2024-06-17 Giuseppe Serra , Mathias Niepert

Data in tabular format is frequently occurring in real-world applications. Graph Neural Networks (GNNs) have recently been extended to effectively handle such data, allowing feature interactions to be captured through representation…

Machine Learning · Computer Science 2024-08-14 Amr Alkhatib , Sofiane Ennadir , Henrik Boström , Michalis Vazirgiannis

Interpretable Graph Neural Networks (GNNs) aim to reveal the underlying reasoning behind model predictions, attributing their decisions to specific subgraphs that are informative. However, existing subgraph-based interpretable methods…

Machine Learning · Computer Science 2025-05-02 Jie Yang , Yuwen Wang , Kaixuan Chen , Tongya Zheng , Yihe Zhou , Zhenbang Xiao , Ji Cao , Mingli Song , Shunyu Liu

Interpretable graph learning is in need as many scientific applications depend on learning models to collect insights from graph-structured data. Previous works mostly focused on using post-hoc approaches to interpret pre-trained models…

Machine Learning · Computer Science 2022-06-20 Siqi Miao , Miaoyuan Liu , Pan Li
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