LGNN: a novel linear graph neural network algorithm.

A central question in neuroscience is how self-organizing dynamic interactions in the brain emerge on their relatively static structural backbone. Due to the complexity of spatial and temporal dependencies between different brain areas, fully comprehending the interplay between structure and function is still challenging and an area of intense research. In this paper we present a graph neural network (GNN) framework, to describe functional interactions based on the structural anatomical layout. A GNN allows us to process graph-structured spatio-temporal signals, providing a possibility to combine structural information derived from diffusion tensor imaging (DTI) with temporal neural activity profiles, like that observed in functional magnetic resonance imaging (fMRI). Moreover, dynamic interactions between different brain regions discovered by this data-driven approach can provide a multi-modal measure of causal connectivity strength. We assess the proposed model’s accuracy by evaluating its capabilities to replicate empirically observed neural activation profiles, and compare the performance to those of a vector auto regression (VAR), like that typically used in Granger causality. We show that GNNs are able to capture long-term dependencies in data and also computationally scale up to the analysis of large-scale networks. Finally we confirm that features learned by a GNN can generalize across MRI scanner types and acquisition protocols, by demonstrating that the performance on small datasets can be improved by pre-training the GNN on data from an earlier study. We conclude that the proposed multi-modal GNN framework can provide a novel perspective on the structure-function relationship in the brain. Accordingly this approach appears to be promising for the characterization of the information flow in brain networks.

Learning node representations against perturbations

Trainable-parameter-free structural-diversity message passing for graph neural networks.

The human gut microbiome is a complex ecosystem whose disruption is implicated in a wide spectrum of diseases, yet translating microbiome research into actionable therapeutics is hindered by a critical trade-off: existing models either prioritize predictive accuracy at the expense of interpretability or sacrifice performance for mechanistic insight, limiting their ability to pinpoint specific disease-driving microbial interactions and taxa. To address this, we introduce graph neural network for interpretable microbiome (GIM), a graph neural network framework that integrates minimally processed taxonomic metadata as sparse node embeddings within an unweighted complete graph, enabling direct modeling of high-order microbial interactions through message passing. GIM achieves state-of-the-art classification performance on microbiome-disease prediction tasks (e.g. healthy vs. allergic states), while generating finegrained, experimentally validated attributions at the level of taxonomic ranks, driver microbes, and putative microbe-to-microbe interactions. By bridging the gap between predictive accuracy and biological interpretability, GIM overcomes a key limitation in current approaches, offering a unified framework to both predict dysbiosis-associated disease states and identify actionable microbial targets for therapeutic intervention. This dual capability represents a critical advance toward precision microbiome engineering and scalable hypothesis generation in translational microbiome research.

A spatial–temporal graph neural network framework for automated software bug triaging

Given a network, it is well recognized that attributed network embedding represents each node of the network in a low-dimensional space, and, thus, brings considerable benefits for numerous graph mining tasks. In practice, a diverse set of graph tasks can be processed efficiently via the compact representation that preserves content and structure information. The majority of attributed network embedding approaches, especially, the graph neural network (GNN) algorithms, are substantially costly in either time or space due to the expensive learning process, while the randomized hashing technique, locality-sensitive hashing (LSH), which does not need learning, can speedup the embedding process at the expense of losing some accuracy. In this article, we propose the MPSketch model, which bridges the performance gap between the GNN framework and the LSH framework by adopting the LSH technique to pass messages and capture high-order proximity in a larger aggregated information pool from the neighborhood. The extensive experimental results confirm that in node classification and link prediction, the proposed MPSketch algorithm enjoys performance comparable to the state-of-the-art learning-based algorithms and outperforms the existing LSH algorithms, while running faster than the GNN algorithms by 3-4 orders of magnitude. More precisely, MPSketch runs 2121, 1167, and 1155 times faster than GraphSAGE, GraphZoom, and FATNet on average, respectively.

In node classification, traditional graph neural networks (GNNs) typically assume implicit homophily, indicating that intraclass nodes are likely connected. However, real-world graphs frequently exhibit heterophily, in which interclass nodes are also commonly connected. To address this challenge, recent methods have adopted approaches such as expanding local neighborhoods and employing adaptive message aggregation to enhance the GNN performance on heterophily graphs. Nevertheless, these methods are restricted by the homophily assumption and fail to effectively capture long-range dependencies (e.g., widely separated intraclass nodes) and insufficiently leverage the graph topology. This study investigates the performance differences of GNN when it is applied to both homophily and heterophily graphs and finds that the distinguishability of neighborhood label distributions (NLDs) exhibits a significant correlation with the accuracy of node classification. To assess the impact of NLD on node classification, this study proposes a novel homophily metric based on node distinguishability. Subsequently, this study introduces a new GNN model named NLD-based GNN (NLDGNN) for node classification. First, NLDGNN initializes node representations by integrating node features with node NLDs. To address long-range dependencies in heterophily graphs, NLDGNN utilizes the global label relationship matrix with low-rank characteristics for global message passing. By combining the attention scores derived from the initial node representations, NLDGNN constructs the global label relationship matrix for enhanced message passing, thereby improving the expressiveness of node representations. Experimental results indicate that NLDGNN outperforms existing GNN models on both real-world homophily and heterophily graphs. The code of this study is available at https://github.com/wanli6/NLDGNN.

Accurate differentiation of parkinsonian syndromes remains challenging due to overlapping clinical manifestations and subtle neuroimaging variations. This study introduces an explainable graph neural network (GNN) framework integrating a Regional Radiomics Similarity Network (R2SN) and Transformer-based attention mechanisms to address this diagnostic dilemma. Our study prospectively enrolled 1,495 participants, including 220 healthy controls and 1,275 patients diagnosed with idiopathic Parkinson's disease (IPD), multiple system atrophy (MSA), or progressive supranuclear palsy (PSP), all undergoing standardized 18F-fluorodeoxyglucose positron emission tomography imaging. Metabolic networks were constructed by encoding edge weights derived from radiomic feature similarity matrices, enabling simultaneous quantification of microscopic metabolic heterogeneity and macroscale network reorganization. The proposed framework achieved superior classification performance with F1-scores of 92.5% (MSA), 96.3% (IPD), and 86.7% (PSP), significantly outperforming comparators by 5.5-8.3%. Multiscale interpretability analysis revealed: (1) Regional hypometabolism in pathognomonic nodes (putamen in IPD, midbrain tegmentum in PSP); (2) Disease-specific connectivity disruptions (midbrain-prefrontal disconnection in PSP, cerebellar-pontine decoupling in MSA). The substructure attention mechanism reduced computational complexity by 41% while enhancing diagnostic specificity (PSP precision +5.2%). The proposed R2SN-based explainable GNN framework for parkinsonian syndrome differentiation establishes a new paradigm for precision subtyping of neurodegenerative disorders, with methodological extensibility to other network-driven neurological conditions.

Network representation learning is receiving increasing attention from scholars. Among them, methods based on graph neural networks have become particularly popular. However, most existing methods currently only focus on networks with a single type of relations. In the real world, networks contain a wealth of diverse information, with multiple types of relationships between nodes. In this paper, we propose a graph neural network-based multiplex network representation learning model (GNMRL). We model nodes within each layer of the multiplex network by aggregating neighbor information. Additionally, since nodes are influenced by different network layers, we integrate node interaction information across network layers. We conducted systematic experiments on four datasets, and the results show that GNMRL outperforms other comparison methods in both link prediction and node classification tasks.

Graph Neural Networks (GNNs) are the most common approach for learning complex relational data represented using graph data structures. Although GNNs are effective at learning representations of both nodes and graphs for a given task, the learning process is computationally expensive and as such, time and energy-inefficient. This paper investigates this challenge within the context of recent work on untrained graph representations that only train the solver model. We present Graph Vector Function Architecture (GVFA), a novel alternative to learning graph representations in GNNs that is based on hyperdimensional computing (HDC) principles. GVFA is a general zero-shot approach for graph and node representations without learning. As such, our representations are not task-specific and the computational costs of constructing them is substantially lower compared to learning-based GNN. Empirically, we demonstrate the expressiveness and generalization properties of different GVFA configurations. Our experimental results demonstrate that GVFA outperforms several classic GNNs on their benchmark datasets in terms of classification accuracy for both graph and node classification tasks, while also yielding a substantial reduction in training time.

We investigate works under the propagation-based fake news detection domain, which recently seeks to improve performance through the use of Graph Neural Networks (GNNs). Generally, existing works argue that using GNNs can give results superior to what was obtained using classic graph-based methods. We agree with this argument given that GNNs are capable of gaining superior performance by leveraging node features. But we argue that existing works haven't identified the fact that the expressivity of GNNs is limited and bounded by node features. Existing works do not acknowledge that, by utilizing GNNs, they implicitly assume node features are strongly correlated to node labels. There are evidence that node features that have been employed do not necessarily correlate to node label. Instead of having a profound theoretical motivation, they have empirically observed that focusing on nodes features with strong feature-label correlation can increase predictive capability. This is a sub-optimal approach to view this problem, in fact, we argue that finding node features based on correlation is not practical or effective. Our first contribution is shifting readers from a node-level view i.e correlating node features with labels, to a graph-level view. In the graph-level view, we exploit the relationship between graph isomorphism and GNNs' expressivity which can be utilized to well understand and interpret the relation between node features and GNNs' expressivity. We conduct a wide range of experiments on basis of both node-level view and graph-level view and found graph-level view is more interpretable and strongly matches with results. Further, we gained insights on node features that wouldn't be obtainable by a node-level view. In order to have a fair and comprehensive analysis of node features, we built a unified dataset that includes a wide range of node features. Our results indicate, as we improve model accuracy on basis of the graph level view, models' generalizability decreases. We provide our hypothesis for this performance trade-off on the basis of the graph-level view. Our results and insights call for a much broader discussion on whether any sort of filtering method is effective. So, we conclude our work by providing readers with possible solutions that can be helpful to find harmony between node features and GNNs' expressivity.

KNN-GNN: A powerful graph neural network enhanced by aggregating K-nearest neighbors in common subspace

MIGP: Metapath Integrated Graph Prompt Neural Network

Graph neural networks (GNNs) have been widely used to learn node representations from graph data in an unsupervised way for downstream tasks. However, when applied to detect anomalies (e.g., outliers, unexpected density), they deliver unsatisfactory performance as existing loss functions fail. For example, any loss based on random walk (RW) algorithms would no longer work because the assumption that anomalous nodes were close with each other could not hold. Moreover, the nature of class imbalance in anomaly detection tasks brings great challenges to reduce the prediction error. In this work, we propose a novel loss function to train GNNs for anomaly-detectable node representations. It evaluates node similarity using global grouping patterns discovered from graph mining algorithms. It can automatically adjust margins for minority classes based on data distribution. Theoretically, we prove that the prediction error is bounded given the proposed loss function. We empirically investigate the GNN effectiveness of different loss variants based on different algorithms. Experiments on two real-world datasets show that they perform significantly better than RW-based loss for graph anomaly detection.

Traffic flow forecasting is essential for managing congestion, improving safety, and optimizing various transportation systems. However, it remains a prevailing challenge due to the stochastic nature of urban traffic and environmental factors. Better predictions require models capable of accommodating the traffic variability influenced by multiple dynamic and complex interdependent factors. In this work, we propose a Graph Neural Network (GNN) framework to address the stochasticity by leveraging adaptive adjacency matrices using log-normal distributions and Coefficient of Variation (CV) values to reflect real-world travel time variability. Additionally, weather factors such as temperature, wind speed, and precipitation adjust edge weights and enable GNN to capture evolving spatio-temporal dependencies across traffic stations. This enhancement over the static adjacency matrix allows the model to adapt effectively to traffic stochasticity and changing environmental conditions. Furthermore, we utilize the Adaptive Conformal Prediction (ACP) framework to provide reliable uncertainty quantification, achieving target coverage while maintaining acceptable prediction intervals. Experimental results demonstrate that the proposed model, in comparison with baseline methods, showed better prediction accuracy and uncertainty bounds. We, then, validate this method by constructing traffic scenarios in SUMO and applying Monte-Carlo simulation to derive a travel time distribution for a Vehicle Under Test (VUT) to reflect real-world variability. The simulated mean travel time of the VUT falls within the intervals defined by INRIX historical data, verifying the model’s robustness.