With recent advancements in non-invasive techniques for measuring brain activity, such as magnetic resonance imaging (MRI), the study of structural and functional brain networks through graph signal processing (GSP) has gained notable prominence. GSP stands as a key tool in unraveling the interplay between the brain's function and structure, enabling the analysis of graphs defined by the connections between regions of interest -- referred to as connectomes in this context. Our work represents a further step in this direction by exploring supervised contrastive learning methods within the realm of graph representation learning. The main objective of this approach is to generate subject-level (i.e., graph-level) vector representations that bring together subjects sharing the same label while separating those with different labels. These connectome embeddings are derived from a graph neural network Encoder-Decoder architecture, which jointly considers structural and functional connectivity. By leveraging data augmentation techniques, the proposed framework achieves state-of-the-art performance in a gender classification task using Human Connectome Project data. More broadly, our connectome-centric methodological advances support the promising prospect of using GSP to discover more about brain function, with potential impact to understanding heterogeneity in the neurodegeneration for precision medicine and diagnosis.
Functional MRI (fMRI) and single-cell transcriptomics are pivotal in Alzheimer's disease (AD) research, each providing unique insights into neural function and molecular mechanisms. However, integrating these complementary modalities remains largely unexplored. Here, we introduce scBIT, a novel method for enhancing AD prediction by combining fMRI with single-nucleus RNA (snRNA). scBIT leverages snRNA as an auxiliary modality, significantly improving fMRI-based prediction models and providing comprehensive interpretability. It employs a sampling strategy to segment snRNA data into cell-type-specific gene networks and utilizes a self-explainable graph neural network to extract critical subgraphs. Additionally, we use demographic and genetic similarities to pair snRNA and fMRI data across individuals, enabling robust cross-modal learning. Extensive experiments validate scBIT's effectiveness in revealing intricate brain region-gene associations and enhancing diagnostic prediction accuracy. By advancing brain imaging transcriptomics to the single-cell level, scBIT sheds new light on biomarker discovery in AD research. Experimental results show that incorporating snRNA data into the scBIT model significantly boosts accuracy, improving binary classification by 3.39% and five-class classification by 26.59%. The codes were implemented in Python and have been released on GitHub (https://github.com/77YQ77/scBIT) and Zenodo (https://zenodo.org/records/11599030) with detailed instructions.
The exploration of cellular heterogeneity within the tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) is essential for understanding cancer progression and response to therapy. Current scRNA-seq approaches, however, lack spatial context and rely on incomplete datasets of ligand-receptor interactions (LRIs), limiting accurate cell type annotation and cell-cell communication (CCC) inference. This study addresses these challenges using a novel graph neural network (GNN) model that enhances cell type prediction and cell interaction analysis. Our study utilized a dataset consisting of 49,020 cells from 19 patients across three cancer types: Leukemia, Breast Invasive Carcinoma, and Colorectal Cancer. The proposed scGSL model demonstrated robust performance, achieving an average accuracy of 84.83%, precision of 86.23%, recall of 81.51%, and an F1 score of 80.92% across all datasets. These metrics represent a significant enhancement over existing methods, which typically exhibit lower performance metrics. Additionally, by reviewing existing literature on gene interactions within the TME, the scGSL model proves to robustly identify biologically meaningful gene interactions in an unsupervised manner, validated by significant expression differences in key gene pairs across various cancers. The source code and data used in this paper can be found in https://github.com/LiYuechao1998/scGSL.
Reinforcement Learning (RL) methods used for solving real-world optimization problems often involve dynamic state-action spaces, larger scale, and sparse rewards, leading to significant challenges in convergence, scalability, and efficient exploration of the solution space. This study introduces GNN-DT, a novel Decision Transformer (DT) architecture that integrates Graph Neural Network (GNN) embedders with a novel residual connection between input and output tokens crucial for handling dynamic environments. By learning from previously collected trajectories, GNN-DT tackles the sparse rewards limitations of online RL algorithms and delivers high-quality solutions in real-time. We evaluate GNN-DT on the complex electric vehicle (EV) charging optimization problem and prove that its performance is superior and requires significantly fewer training trajectories, thus improving sample efficiency compared to existing DT and offline RL baselines. Furthermore, GNN-DT exhibits robust generalization to unseen environments and larger action spaces, addressing a critical gap in prior offline and online RL approaches.
In high-energy physics, the increasing luminosity and detector granularity at the Large Hadron Collider are driving the need for more efficient data processing solutions. Machine Learning has emerged as a promising tool for reconstructing charged particle tracks, due to its potentially linear computational scaling with detector hits. The recent implementation of a graph neural network-based track reconstruction pipeline in the first level trigger of the LHCb experiment on GPUs serves as a platform for comparative studies between computational architectures in the context of high-energy physics. This paper presents a novel comparison of the throughput of ML model inference between FPGAs and GPUs, focusing on the first step of the track reconstruction pipeline$\unicode{x2013}$an implementation of a multilayer perceptron. Using HLS4ML for FPGA deployment, we benchmark its performance against the GPU implementation and demonstrate the potential of FPGAs for high-throughput, low-latency inference without the need for an expertise in FPGA development and while consuming significantly less power.
Retrieval-augmented generation (RAG) has proven effective in integrating knowledge into large language models (LLMs). However, conventional RAGs struggle to capture complex relationships between pieces of knowledge, limiting their performance in intricate reasoning that requires integrating knowledge from multiple sources. Recently, graph-enhanced retrieval augmented generation (GraphRAG) builds graph structure to explicitly model these relationships, enabling more effective and efficient retrievers. Nevertheless, its performance is still hindered by the noise and incompleteness within the graph structure. To address this, we introduce GFM-RAG, a novel graph foundation model (GFM) for retrieval augmented generation. GFM-RAG is powered by an innovative graph neural network that reasons over graph structure to capture complex query-knowledge relationships. The GFM with 8M parameters undergoes a two-stage training process on large-scale datasets, comprising 60 knowledge graphs with over 14M triples and 700k documents. This results in impressive performance and generalizability for GFM-RAG, making it the first graph foundation model applicable to unseen datasets for retrieval without any fine-tuning required. Extensive experiments on three multi-hop QA datasets and seven domain-specific RAG datasets demonstrate that GFM-RAG achieves state-of-the-art performance while maintaining efficiency and alignment with neural scaling laws, highlighting its potential for further improvement.
Learning the solution operators of PDEs on arbitrary domains is challenging due to the diversity of possible domain shapes, in addition to the often intricate underlying physics. We propose an end-to-end graph neural network (GNN) based neural operator to learn PDE solution operators from data on point clouds in arbitrary domains. Our multi-scale model maps data between input/output point clouds by passing it through a downsampled regional mesh. Many novel elements are also incorporated to ensure resolution invariance and temporal continuity. Our model, termed RIGNO, is tested on a challenging suite of benchmarks, composed of various time-dependent and steady PDEs defined on a diverse set of domains. We demonstrate that RIGNO is significantly more accurate than neural operator baselines and robustly generalizes to unseen spatial resolutions and time instances.
In diffraction-based crystal structure analysis, thermal ellipsoids, quantified via Anisotropic Displacement Parameters (ADPs), are critical yet challenging to determine. ADPs capture atomic vibrations, reflecting thermal and structural properties, but traditional computation is often expensive. This paper introduces CartNet, a novel graph neural network (GNN) for efficiently predicting crystal properties by encoding atomic geometry into Cartesian coordinates alongside the crystal temperature. CartNet integrates a neighbour equalization technique to emphasize covalent and contact interactions, and a Cholesky-based head to ensure valid ADP predictions. We also propose a rotational SO(3) data augmentation strategy during training to handle unseen orientations. An ADP dataset with over 200,000 experimental crystal structures from the Cambridge Structural Database (CSD) was curated to validate the approach. CartNet significantly reduces computational costs and outperforms existing methods in ADP prediction by 10.87%, while delivering a 34.77% improvement over theoretical approaches. We further evaluated CartNet on other datasets covering formation energy, band gap, total energy, energy above the convex hull, bulk moduli, and shear moduli, achieving 7.71% better results on the Jarvis Dataset and 13.16% on the Materials Project Dataset. These gains establish CartNet as a state-of-the-art solution for diverse crystal property predictions. Project website and online demo: https://www.ee.ub.edu/cartnet
The distributionally robust optimization (DRO)-based graph neural network methods improve recommendation systems' out-of-distribution (OOD) generalization by optimizing the model's worst-case performance. However, these studies fail to consider the impact of noisy samples in the training data, which results in diminished generalization capabilities and lower accuracy. Through experimental and theoretical analysis, this paper reveals that current DRO-based graph recommendation methods assign greater weight to noise distribution, leading to model parameter learning being dominated by it. When the model overly focuses on fitting noise samples in the training data, it may learn irrelevant or meaningless features that cannot be generalized to OOD data. To address this challenge, we design a Distributionally Robust Graph model for OOD recommendation (DRGO). Specifically, our method first employs a simple and effective diffusion paradigm to alleviate the noisy effect in the latent space. Additionally, an entropy regularization term is introduced in the DRO objective function to avoid extreme sample weights in the worst-case distribution. Finally, we provide a theoretical proof of the generalization error bound of DRGO as well as a theoretical analysis of how our approach mitigates noisy sample effects, which helps to better understand the proposed framework from a theoretical perspective. We conduct extensive experiments on four datasets to evaluate the effectiveness of our framework against three typical distribution shifts, and the results demonstrate its superiority in both independently and identically distributed distributions (IID) and OOD.
As cyber threats grow increasingly sophisticated, reinforcement learning (RL) is emerging as a promising technique to create intelligent and adaptive cyber defense systems. However, most existing autonomous defensive agents have overlooked the inherent graph structure of computer networks subject to cyber attacks, potentially missing critical information and constraining their adaptability. To overcome these limitations, we developed a custom version of the Cyber Operations Research Gym (CybORG) environment, encoding network state as a directed graph with realistic low-level features. We employ a Graph Attention Network (GAT) architecture to process node, edge, and global features, and adapt its output to be compatible with policy gradient methods in RL. Our GAT-based approach offers key advantages over flattened alternatives: policies that demonstrate resilience to certain types of unexpected dynamic network topology changes, reasonable generalisation to networks of varying sizes within the same structural distribution, and interpretable defensive actions grounded in tangible network properties. We demonstrate that GAT defensive policies can be trained using our low-level directed graph observations, even when unexpected connections arise during simulation. Evaluations across networks of different sizes, but consistent subnetwork structure, show our policies achieve comparable performance to policies trained specifically for each network configuration. Our study contributes to the development of robust cyber defence systems that can better adapt to real-world network security challenges.
Heterogeneous information networks (HINs) can be used to model various real-world systems. As HINs consist of multiple types of nodes, edges, and node features, it is nontrivial to directly apply graph neural network (GNN) techniques in heterogeneous cases. There are two remaining major challenges. First, homogeneous message passing in a recursive manner neglects the distinct types of nodes and edges in different hops, leading to unnecessary information mixing. This often results in the incorporation of ``noise'' from uncorrelated intermediate neighbors, thereby degrading performance. Second, feature learning should be handled differently for different types, which is challenging especially when the type sizes are large. To bridge this gap, we develop a novel framework - AutoGNR, to directly utilize and automatically extract effective heterogeneous information. Instead of recursive homogeneous message passing, we introduce a non-recursive message passing mechanism for GNN to mitigate noise from uncorrelated node types in HINs. Furthermore, under the non-recursive framework, we manage to efficiently perform neural architecture search for an optimal GNN structure in a differentiable way, which can automatically define the heterogeneous paths for aggregation. Our tailored search space encompasses more effective candidates while maintaining a tractable size. Experiments show that AutoGNR consistently outperforms state-of-the-art methods on both normal and large scale real-world HIN datasets.
Although the pure component vapor pressure is one of the most important properties for designing chemical processes, no broadly applicable, sufficiently accurate, and open-source prediction method has been available. To overcome this, we have developed GRAPPA - a hybrid graph neural network for predicting vapor pressures of pure components. GRAPPA enables the prediction of the vapor pressure curve of basically any organic molecule, requiring only the molecular structure as input. The new model consists of three parts: A graph attention network for the message passing step, a pooling function that captures long-range interactions, and a prediction head that yields the component-specific parameters of the Antoine equation, from which the vapor pressure can readily and consistently be calculated for any temperature. We have trained and evaluated GRAPPA on experimental vapor pressure data of almost 25,000 pure components. We found excellent prediction accuracy for unseen components, outperforming state-of-the-art group contribution methods and other machine learning approaches in applicability and accuracy. The trained model and its code are fully disclosed, and GRAPPA is directly applicable via the interactive website ml-prop.mv.rptu.de.
Determining whether a candidate crystalline material is thermodynamically stable depends on identifying its true ground-state structure, a central challenge in computational materials science. We introduce CrystalGRW, a diffusion-based generative model on Riemannian manifolds that proposes novel crystal configurations and can predict stable phases validated by density functional theory. The crystal properties, such as fractional coordinates, atomic types, and lattice matrices, are represented on suitable Riemannian manifolds, ensuring that new predictions generated through the diffusion process preserve the periodicity of crystal structures. We incorporate an equivariant graph neural network to also account for rotational and translational symmetries during the generation process. CrystalGRW demonstrates the ability to generate realistic crystal structures that are close to their ground states with accuracy comparable to existing models, while also enabling conditional control, such as specifying a desired crystallographic point group. These features help accelerate materials discovery and inverse design by offering stable, symmetry-consistent crystal candidates for experimental validation.
Graph Neural Networks (GNNs) are popular deep learning models designed to process graph-structured data through recursive neighborhood aggregations in the message passing process. When applied to semi-supervised node classification, the message-passing enables GNNs to understand short-range spatial interactions, but also causes them to suffer from over-smoothing and over-squashing. These challenges hinder model expressiveness and prevent the use of deeper models to capture long-range node interactions (LRIs) within the graph. Popular solutions for LRIs detection are either too expensive to process large graphs due to high time complexity or fail to generalize across diverse graph structures. To address these limitations, we propose a mechanism called \emph{information flow control}, which leverages a novel connectivity measure, called \emph{information flow score}, to address over-smoothing and over-squashing with linear computational overhead, supported by theoretical evidence. Finally, to prove the efficacy of our methodology we design DeltaGNN, the first scalable and generalizable approach for detecting long-range and short-range interactions. We benchmark our model across 10 real-world datasets, including graphs with varying sizes, topologies, densities, and homophilic ratios, showing superior performance with limited computational complexity. The implementation of the proposed methods are publicly available at https://github.com/basiralab/DeltaGNN.
Global placement, a critical step in designing the physical layout of computer chips, is essential to optimize chip performance. Prior global placement methods optimize each circuit design individually from scratch. Their neglect of transferable knowledge limits solution efficiency and chip performance as circuit complexity drastically increases. This study presents TransPlace, a global placement framework that learns to place millions of mixed-size cells in continuous space. TransPlace introduces i) Netlist Graph to efficiently model netlist topology, ii) Cell-flow and relative position encoding to learn SE(2)-invariant representation, iii) a tailored graph neural network architecture for informed parameterization of placement knowledge, and iv) a two-stage strategy for coarse-to-fine placement. Compared to state-of-the-art placement methods, TransPlace-trained on a few high-quality placements-can place unseen circuits with 1.2x speedup while reducing congestion by 30%, timing by 9%, and wirelength by 5%.
In recent years, traffic flow prediction has played a crucial role in the management of intelligent transportation systems. However, traditional forecasting methods often model non-Euclidean low-dimensional traffic data as a simple graph with single-type nodes and edges, failing to capture similar trends among nodes of the same type. To address this limitation, this paper proposes MHGNet, a novel framework for modeling spatiotemporal multi-heterogeneous graphs. Within this framework, the STD Module decouples single-pattern traffic data into multi-pattern traffic data through feature mappings of timestamp embedding matrices and node embedding matrices. Subsequently, the Node Clusterer leverages the Euclidean distance between nodes and different types of limit points to perform clustering with O(N) time complexity. The nodes within each cluster undergo residual subgraph convolution within the spatiotemporal fusion subgraphs generated by the DSTGG Module, followed by processing in the SIE Module for node repositioning and redistribution of weights. To validate the effectiveness of MHGNet, this paper conducts extensive ablation studies and quantitative evaluations on four widely used benchmarks, demonstrating its superior performance.
Graph neural networks (GNNs) have demonstrated superior performance in collaborative recommendation through their ability to conduct high-order representation smoothing, effectively capturing structural information within users' interaction patterns. However, existing GNN paradigms face significant challenges in scalability and robustness when handling large-scale, noisy, and real-world datasets. To address these challenges, we present LightGNN, a lightweight and distillation-based GNN pruning framework designed to substantially reduce model complexity while preserving essential collaboration modeling capabilities. Our LightGNN framework introduces a computationally efficient pruning module that adaptively identifies and removes redundant edges and embedding entries for model compression. The framework is guided by a resource-friendly hierarchical knowledge distillation objective, whose intermediate layer augments the observed graph to maintain performance, particularly in high-rate compression scenarios. Extensive experiments on public datasets demonstrate LightGNN's effectiveness, significantly improving both computational efficiency and recommendation accuracy. Notably, LightGNN achieves an 80% reduction in edge count and 90% reduction in embedding entries while maintaining performance comparable to more complex state-of-the-art baselines. The implementation of our LightGNN framework is available at the github repository: https://github.com/HKUDS/LightGNN.
Real-world graph data environments intrinsically exist noise (e.g., link and structure errors) that inevitably disturb the effectiveness of graph representation and downstream learning tasks. For homogeneous graphs, the latest works use original node features to synthesize a similarity graph that can correct the structure of the noised graph. This idea is based on the homogeneity assumption, which states that similar nodes in the homogeneous graph tend to have direct links in the original graph. However, similar nodes in heterogeneous graphs usually do not have direct links, which can not be used to correct the original noise graph. This causes a significant challenge in noised heterogeneous graph learning. To this end, this paper proposes a novel synthesized similarity-based graph neural network compatible with noised heterogeneous graph learning. First, we calculate the original feature similarities of all nodes to synthesize a similarity-based high-order graph. Second, we propose a similarity-aware encoder to embed original and synthesized graphs with shared parameters. Then, instead of graph-to-graph supervising, we synchronously supervise the original and synthesized graph embeddings to predict the same labels. Meanwhile, a target-based graph extracted from the synthesized graph contrasts the structure of the metapath-based graph extracted from the original graph to learn the mutual information. Extensive experiments in numerous real-world datasets show the proposed method achieves state-of-the-art records in the noised heterogeneous graph learning tasks. In highlights, +5$\sim$6\% improvements are observed in several noised datasets compared with previous SOTA methods. The code and datasets are available at https://github.com/kg-cc/NoiseHGNN.
Feature-based image matching has extensive applications in computer vision. Keypoints detected in images can be naturally represented as graph structures, and Graph Neural Networks (GNNs) have been shown to outperform traditional deep learning techniques. Consequently, the paradigm of image matching via GNNs has gained significant prominence in recent academic research. In this paper, we first introduce an innovative adaptive graph construction method that utilizes a filtering mechanism based on distance and dynamic threshold similarity. This method dynamically adjusts the criteria for incorporating new vertices based on the characteristics of existing vertices, allowing for the construction of more precise and robust graph structures while avoiding redundancy. We further combine the vertex processing capabilities of GNNs with the global awareness capabilities of Transformers to enhance the model's representation of spatial and feature information within graph structures. This hybrid model provides a deeper understanding of the interrelationships between vertices and their contributions to the matching process. Additionally, we employ the Sinkhorn algorithm to iteratively solve for optimal matching results. Finally, we validate our system using extensive image datasets and conduct comprehensive comparative experiments. Experimental results demonstrate that our system achieves an average improvement of 3.8x-40.3x in overall matching performance. Additionally, the number of vertices and edges significantly impacts training efficiency and memory usage; therefore, we employ multi-GPU technology to accelerate the training process. Our code is available at https://github.com/songxf1024/GIMS.
Credit card fraud incurs a considerable cost for both cardholders and issuing banks. Contemporary methods apply machine learning-based classifiers to detect fraudulent behavior from labeled transaction records. But labeled data are usually a small proportion of billions of real transactions due to expensive labeling costs, which implies that they do not well exploit many natural features from unlabeled data. Therefore, we propose a semi-supervised graph neural network for fraud detection. Specifically, we leverage transaction records to construct a temporal transaction graph, which is composed of temporal transactions (nodes) and interactions (edges) among them. Then we pass messages among the nodes through a Gated Temporal Attention Network (GTAN) to learn the transaction representation. We further model the fraud patterns through risk propagation among transactions. The extensive experiments are conducted on a real-world transaction dataset and two publicly available fraud detection datasets. The result shows that our proposed method, namely GTAN, outperforms other state-of-the-art baselines on three fraud detection datasets. Semi-supervised experiments demonstrate the excellent fraud detection performance of our model with only a tiny proportion of labeled data.