Graph Neural Networks (GNNs) are essential for processing graph-structured data and have wide applications in critical domains. The increasing use of GNNs in high-stakes scenarios requires robust explainability to ensure trust and transparency in decision-making. A common approach to explaining GNNs is to identify subgraphs, a.k.a. explanations, that significantly influence model predictions. However, this task is challenging due to the distribution shifts from the original training graphs to the explanation subgraphs, a factor that is largely overlooked in the existing research. These shifts arise because GNNs are trained on original graphs, while explanation subgraphs often differ in properties such as the number of nodes or structural patterns. As a result, GNNs may struggle to generalize to explanation subgraphs with a different distribution from its training data. In this paper, we systematically investigate the Out-Of-Distribution (OOD) problem through theoretical analysis and empirical studies. To address this challenge, we first develop a theoretical framework that formalizes the notion of explanation subgraphs through sufficiency and minimality criteria, ensuring both prediction preservation and structural compactness. Our analysis reveals a fundamental distributional disparity between explanation subgraphs and original graphs, leading to a novel concept of proxy graphs proposed in this work. Proxy graphs maintain the essential explanatory information while conforming to the original data distribution through a combination of parametric and non-parametric optimization approaches. Empirical evaluations on diverse datasets show that our method improves the quality and reliability of GNN explanations, advancing the field of GNN explainability.

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 applications that require reliable and transparent insights. While existing methods have primarily focused on explaining molecular substructures in 2D GNNs, the transition to 3D GNNs introduces unique challenges, such as handling the implicit dense edge structures created by a cutoff radius. To tackle this, we introduce a novel explanation method specifically designed for 3D GNNs, which localizes the explanation to the immediate neighborhood of each node within the 3D space. Each node is assigned an radius of influence, defining the localized region within which message passing captures spatial and structural interactions crucial for the model's predictions. This method leverages the spatial and geometric characteristics inherent in 3D graphs. By constraining the subgraph to a localized radius of influence, the approach not only enhances interpretability but also aligns with the physical and structural dependencies typical of 3D graph applications, such as molecular learning.

Large Language Models (LLMs) have become integral to human decision-making processes. However, their outputs are not always reliable, often requiring users to assess the accuracy of the information provided manually. This issue is exacerbated by hallucinated responses, which are frequently presented with convincing but incorrect explanations, leading to trust concerns among users. To address this challenge, we propose GE-Chat, a knowledge Graph-enhanced retrieval-augmented generation framework designed to deliver Evidence-based responses. Specifically, when users upload a document, GE-Chat constructs a knowledge graph to support a retrieval-augmented agent, enriching the agent's responses with external knowledge beyond its training data. We further incorporate Chain-of-Thought (CoT) reasoning, n-hop subgraph searching, and entailment-based sentence generation to ensure accurate evidence retrieval. Experimental results demonstrate that our approach improves the ability of existing models to identify precise evidence in free-form contexts, offering a reliable mechanism for verifying LLM-generated conclusions and enhancing trustworthiness.

Explaining Graph Neural Networks (GNNs) has garnered significant attention due to the need for interpretability, enabling users to understand the behavior of these black-box models better and extract valuable insights from their predictions.While numerous post-hoc instance-level explanation methods have been proposed to interpret GNN predictions, the reliability of these explanations remains uncertain, particularly in out-of-distribution or unknown test datasets.In this paper, we address this challenge by introducing an explainer framework with the confidence scoring module (ConfExplainer), grounded in theoretical principle, which is a generalized graph information bottleneck with confidence constraint (GIB-CC), that quantifies the reliability of generated explanations.Experimental results demonstrate the superiority of our approach, highlighting the effectiveness of the confidence score in enhancing the trustworthiness and robustness of GNN explanations.

Graph Neural Networks (GNNs) have become a building block in graph data processing, with wide applications in critical domains. The growing needs to deploy GNNs in high-stakes applications necessitate explainability for users in the decision-making processes. A popular paradigm for the explainability of GNNs is to identify explainable subgraphs by comparing their labels with the ones of original graphs. This task is challenging due to the substantial distributional shift from the original graphs in the training set to the set of explainable subgraphs, which prevents accurate prediction of labels with the subgraphs. To address it, in this paper, we propose a novel method that generates proxy graphs for explainable subgraphs that are in the distribution of training data. We introduce a parametric method that employs graph generators to produce proxy graphs. A new training objective based on information theory is designed to ensure that proxy graphs not only adhere to the distribution of training data but also preserve explanatory factors. Such generated proxy graphs can be reliably used to approximate the predictions of the labels of explainable subgraphs. Empirical evaluations across various datasets demonstrate our method achieves more accurate explanations for GNNs.

Graph regression is a fundamental task that has gained significant attention in various graph learning tasks. However, the inference process is often not easily interpretable. Current explanation techniques are limited to understanding Graph Neural Network (GNN) behaviors in classification tasks, leaving an explanation gap for graph regression models. In this work, we propose a novel explanation method to interpret the graph regression models (XAIG-R). Our method addresses the distribution shifting problem and continuously ordered decision boundary issues that hinder existing methods away from being applied in regression tasks. We introduce a novel objective based on the graph information bottleneck theory (GIB) and a new mix-up framework, which can support various GNNs and explainers in a model-agnostic manner. Additionally, we present a self-supervised learning strategy to tackle the continuously ordered labels in regression tasks. We evaluate our proposed method on three benchmark datasets and a real-life dataset introduced by us, and extensive experiments demonstrate its effectiveness in interpreting GNN models in regression tasks.

Graph Neural Networks (GNNs) have received increasing attention due to their ability to learn from graph-structured data. However, their predictions are often not interpretable. Post-hoc instance-level explanation methods have been proposed to understand GNN predictions. These methods seek to discover substructures that explain the prediction behavior of a trained GNN. In this paper, we shed light on the existence of the distribution shifting issue in existing methods, which affects explanation quality, particularly in applications on real-life datasets with tight decision boundaries. To address this issue, we introduce a generalized Graph Information Bottleneck (GIB) form that includes a label-independent graph variable, which is equivalent to the vanilla GIB. Driven by the generalized GIB, we propose a graph mixup method, MixupExplainer, with a theoretical guarantee to resolve the distribution shifting issue. We conduct extensive experiments on both synthetic and real-world datasets to validate the effectiveness of our proposed mixup approach over existing approaches. We also provide a detailed analysis of how our proposed approach alleviates the distribution shifting issue.

To avoid the exposure of original source code, the variable names deployed in the wild are often replaced by short, meaningless names, thus making the code difficult to understand and be analyzed. We introduce DeMinify, a Deep-Learning (DL)-based approach that formulates such recovery problem as the prediction of missing features in a Graph Convolutional Network–Missing Features. The graph represents both the relations among the variables and the relations among their types, in which the names or types of some nodes are missing. Moreover, DeMinify leverages dual-task learning to propagate the mutual impact between the learning of the variable names and that of their types. We conducted experiments to evaluate DeMinify in both name recovery and type prediction on a Python dataset with 180k methods and a JavaScript (JS) dataset with 322k files. For variable name prediction, in 76.7% and 81.6% of the cases in Python and JS code respectively, DeMinify can predict correctly the variables' names with a single suggested name. DeMinify relatively improves 15.3%–40.7% and 7.7%–49.7% in top-1 accuracy over the state-of-the-art variable name recovery approaches for Python and JS code, respectively. It also relatively improves 14.5%–51.9% in top-1 accuracy over the existing type prediction approaches. Our experimental results showed that learning of data types helps improve variable name recovery and vice versa.

Software Vulnerabilities (SVs) are security flaws that are exploitable in cyber-attacks. Delay in the detection and assessment of SVs might cause serious consequences due to the unknown impacts on the attacked systems. The state-of-the-art approaches have been proposed to work directly on the committed code changes for early detection. However, none of them could provide both commit-level vulnerability detection and assessment at once. Moreover, the assessment approaches still suffer low accuracy due to limited representations for code changes and surrounding contexts.