Graph Anomaly Detection (GAD) plays a vital role in various data mining applications such as e-commerce fraud prevention and malicious user detection. Recently, Graph Neural Network (GNN) based approach has demonstrated great effectiveness in GAD by first encoding graph data into low-dimensional representations and then identifying anomalies under the guidance of supervised or unsupervised signals. However, existing GNN-based approaches implicitly follow the homophily principle (i.e., the "like attracts like" phenomenon) and fail to learn discriminative embedding for anomalies that connect vast normal nodes. Moreover, such approaches identify anomalies in a unified global perspective but overlook diversified abnormal patterns conditioned on local graph context, leading to suboptimal performance. To overcome the aforementioned limitations, in this paper, we propose a Multi-hypersphere Heterophilic Graph Learning (MHetGL) framework for unsupervised GAD. Specifically, we first devise a Heterophilic Graph Encoding (HGE) module to learn distinguishable representations for potential anomalies by purifying and augmenting their neighborhood in a fully unsupervised manner. Then, we propose a Multi-Hypersphere Learning (MHL) module to enhance the detection capability for context-dependent anomalies by jointly incorporating critical patterns from both global and local perspectives. Extensive experiments on ten real-world datasets show that MHetGL outperforms 14 baselines. Our code is publicly available at https://github.com/KennyNH/MHetGL.
Simulating the complex interactions between soft tissues and rigid anatomy is critical for applications in surgical training, planning, and robotic-assisted interventions. Traditional Finite Element Method (FEM)-based simulations, while accurate, are computationally expensive and impractical for real-time scenarios. Learning-based approaches have shown promise in accelerating predictions but have fallen short in modeling soft-rigid interactions effectively. We introduce MIXPINN, a physics-informed Graph Neural Network (GNN) framework for mixed-material simulations, explicitly capturing soft-rigid interactions using graph-based augmentations. Our approach integrates Virtual Nodes (VNs) and Virtual Edges (VEs) to enhance rigid body constraint satisfaction while preserving computational efficiency. By leveraging a graph-based representation of biomechanical structures, MIXPINN learns high-fidelity deformations from FEM-generated data and achieves real-time inference with sub-millimeter accuracy. We validate our method in a realistic clinical scenario, demonstrating superior performance compared to baseline GNN models and traditional FEM methods. Our results show that MIXPINN reduces computational cost by an order of magnitude while maintaining high physical accuracy, making it a viable solution for real-time surgical simulation and robotic-assisted procedures.
Identifying transcription factor binding sites (TFBS) is crucial for understanding gene regulation, as these sites enable transcription factors (TFs) to bind to DNA and modulate gene expression. Despite advances in high-throughput sequencing, accurately identifying TFBS remains challenging due to the vast genomic data and complex binding patterns. GCBLANE, a graph-enhanced convolutional bidirectional Long Short-Term Memory (LSTM) attention network, is introduced to address this issue. It integrates convolutional, multi-head attention, and recurrent layers with a graph neural network to detect key features for TFBS prediction. On 690 ENCODE ChIP-Seq datasets, GCBLANE achieved an average AUC of 0.943, and on 165 ENCODE datasets, it reached an AUC of 0.9495, outperforming advanced models that utilize multimodal approaches, including DNA shape information. This result underscores GCBLANE's effectiveness compared to other methods. By combining graph-based learning with sequence analysis, GCBLANE significantly advances TFBS prediction.
Accurate staging of Diabetic Retinopathy (DR) is essential for guiding timely interventions and preventing vision loss. However, current staging models are hardly interpretable, and most public datasets contain no clinical reasoning or interpretation beyond image-level labels. In this paper, we present a novel method that integrates graph representation learning with vision-language models (VLMs) to deliver explainable DR diagnosis. Our approach leverages optical coherence tomography angiography (OCTA) images by constructing biologically informed graphs that encode key retinal vascular features such as vessel morphology and spatial connectivity. A graph neural network (GNN) then performs DR staging while integrated gradients highlight critical nodes and edges and their individual features that drive the classification decisions. We collect this graph-based knowledge which attributes the model's prediction to physiological structures and their characteristics. We then transform it into textual descriptions for VLMs. We perform instruction-tuning with these textual descriptions and the corresponding image to train a student VLM. This final agent can classify the disease and explain its decision in a human interpretable way solely based on a single image input. Experimental evaluations on both proprietary and public datasets demonstrate that our method not only improves classification accuracy but also offers more clinically interpretable results. An expert study further demonstrates that our method provides more accurate diagnostic explanations and paves the way for precise localization of pathologies in OCTA images.
Predicting the emergence of multiple chronic conditions (MCC) is crucial for early intervention and personalized healthcare, as MCC significantly impacts patient outcomes and healthcare costs. Graph neural networks (GNNs) are effective methods for modeling complex graph data, such as those found in MCC. However, a significant challenge with GNNs is their reliance on an existing graph structure, which is not readily available for MCC. To address this challenge, we propose a novel generative framework for GNNs that constructs a representative underlying graph structure by utilizing the distribution of the data to enhance predictive analytics for MCC. Our framework employs a graph variational autoencoder (GVAE) to capture the complex relationships in patient data. This allows for a comprehensive understanding of individual health trajectories and facilitates the creation of diverse patient stochastic similarity graphs while preserving the original feature set. These variations of patient stochastic similarity graphs, generated from the GVAE decoder, are then processed by a GNN using a novel Laplacian regularization technique to refine the graph structure over time and improves the prediction accuracy of MCC. A contextual Bandit is designed to evaluate the stochastically generated graphs and identify the best-performing graph for the GNN model iteratively until model convergence. We validate the performance of the proposed contextual Bandit algorithm against $\varepsilon$-Greedy and multi-armed Bandit algorithms on a large cohort (n = 1,592) of patients with MCC. These advancements highlight the potential of the proposed approach to transform predictive healthcare analytics, enabling a more personalized and proactive approach to MCC management.
Abstract— Recently, many data mining models based on heterogeneous graph (HG) have emerged. Among these, HG embedding is an important and indispensable process. However, the existing HG embedding models usually use graph neural network to learn embeddings separately on different meta-paths, ignoring the fact that different meta-paths contain not only their unique semantics but also related semantics. This may result in semantic overlap or irrelevance, which needs to be a feasible and effective tradeoff for high-quality HG embedding, yet studies thereof have rarely been reported. In this article, we propose semantic tradeoff HG embedding (STHGE) by first introducing the Hilbert–Schmidt independence criterion (HSIC) as restriction. The main idea of STHGE is to regard semantic tradeoff as independence tradeoff (or correlation) between different meta-path spaces. Specifically, we first transform the original features of nodes into different meta-path feature spaces with HSIC restriction between them. Then, we use graph attention network to learn the embeddings of nodes on different meta-paths with HSIC restrictions. Finally, we concatenate the embeddings on different meta-paths to perform prediction. Experimental results on three heterogeneous datasets not only demonstrate the effectiveness of STHGE but also demonstrate that STHGE can achieve a new semantic tradeoff between different meta-paths. Furthermore, we demonstrate the robustness of STHGE.
Synthetic lethality (SL) is a promising gene interaction for cancer therapy. Recent SL prediction methods integrate knowledge graphs (KGs) into graph neural networks (GNNs) and employ attention mechanisms to extract local subgraphs as explanations for target gene pairs. However, attention mechanisms often lack fidelity, typically generate a single explanation per gene pair, and fail to ensure trustworthy high-order structures in their explanations. To overcome these limitations, we propose Diverse Graph Information Bottleneck for Synthetic Lethality (DGIB4SL), a KG-based GNN that generates multiple faithful explanations for the same gene pair and effectively encodes high-order structures. Specifically, we introduce a novel DGIB objective, integrating a Determinant Point Process (DPP) constraint into the standard IB objective, and employ 13 motif-based adjacency matrices to capture high-order structures in gene representations. Experimental results show that DGIB4SL outperforms state-of-the-art baselines and provides multiple explanations for SL prediction, revealing diverse biological mechanisms underlying SL inference.
In massive multi-input multi-output (MIMO) systems, the main bottlenecks of location- and orientation-assisted beam alignment using deep neural networks (DNNs) are large training overhead and significant performance degradation. This paper proposes a graph neural network (GNN)-based beam selection approach that reduces the training overhead and improves the alignment accuracy, by capitalizing on the strong expressive ability and few trainable parameters of GNN. The channels of beams are correlated according to the beam direction. Therefore, we establish a graph according to the angular correlation between beams and use GNN to capture the channel correlation between adjacent beams, which helps accelerate the learning process and enhance the beam alignment performance. Compared to existing DNN-based algorithms, the proposed method requires only 20\% of the dataset size to achieve equivalent accuracy and improves the Top-1 accuracy by 10\% when using the same dataset.
As the quantities of data recorded by embedded edge sensors grow, so too does the need for intelligent local processing. Such data often comes in the form of time-series signals, based on which real-time predictions can be made locally using an AI model. However, a hardware-software approach capable of making low-latency predictions with low power consumption is required. In this paper, we present a hardware implementation of an event-graph neural network for time-series classification. We leverage an artificial cochlea model to convert the input time-series signals into a sparse event-data format that allows the event-graph to drastically reduce the number of calculations relative to other AI methods. We implemented the design on a SoC FPGA and applied it to the real-time processing of the Spiking Heidelberg Digits (SHD) dataset to benchmark our approach against competitive solutions. Our method achieves a floating-point accuracy of 92.7% on the SHD dataset for the base model, which is only 2.4% and 2% less than the state-of-the-art models with over 10% and 67% fewer model parameters, respectively. It also outperforms FPGA-based spiking neural network implementations by 19.3% and 4.5%, achieving 92.3% accuracy for the quantised model while using fewer computational resources and reducing latency.
This paper presents a method for load balancing and dynamic pricing in electric vehicle (EV) charging networks, utilizing reinforcement learning (RL) to enhance network performance. The proposed framework integrates a pre-trained graph neural network to predict demand elasticity and inform pricing decisions. The spatio-temporal EV charging demand prediction (EVCDP) dataset from Shenzhen is utilized to capture the geographic and temporal characteristics of the charging stations. The RL model dynamically adjusts prices at individual stations based on occupancy, maximum station capacity, and demand forecasts, ensuring an equitable network load distribution while preventing station overloads. By leveraging spatially-aware demand predictions and a carefully designed reward function, the framework achieves efficient load balancing and adaptive pricing strategies that respond to localized demand and global network dynamics, ensuring improved network stability and user satisfaction. The efficacy of the approach is validated through simulations on the dataset, showing significant improvements in load balancing and reduced overload as the RL agent iteratively interacts with the environment and learns to dynamically adjust pricing strategies based on real-time demand patterns and station constraints. The findings highlight the potential of adaptive pricing and load-balancing strategies to address the complexities of EV infrastructure, paving the way for scalable and user-centric solutions.
Physical manipulation of garments is often crucial when performing fabric-related tasks, such as hanging garments. However, due to the deformable nature of fabrics, these operations remain a significant challenge for robots in household, healthcare, and industrial environments. In this paper, we propose GraphGarment, a novel approach that models garment dynamics based on robot control inputs and applies the learned dynamics model to facilitate garment manipulation tasks such as hanging. Specifically, we use graphs to represent the interactions between the robot end-effector and the garment. GraphGarment uses a graph neural network (GNN) to learn a dynamics model that can predict the next garment state given the current state and input action in simulation. To address the substantial sim-to-real gap, we propose a residual model that compensates for garment state prediction errors, thereby improving real-world performance. The garment dynamics model is then applied to a model-based action sampling strategy, where it is utilized to manipulate the garment to a reference pre-hanging configuration for garment-hanging tasks. We conducted four experiments using six types of garments to validate our approach in both simulation and real-world settings. In simulation experiments, GraphGarment achieves better garment state prediction performance, with a prediction error 0.46 cm lower than the best baseline. Our approach also demonstrates improved performance in the garment-hanging simulation experiment with enhancements of 12%, 24%, and 10%, respectively. Moreover, real-world robot experiments confirm the robustness of sim-to-real transfer, with an error increase of 0.17 cm compared to simulation results. Supplementary material is available at:https://sites.google.com/view/graphgarment.
Graph neural networks (GNNs) have delivered remarkable results in various fields. However, the rapid increase in the scale of graph data has introduced significant performance bottlenecks for GNN inference. Both computational complexity and memory usage have risen dramatically, with memory becoming a critical limitation. Although graph sampling-based subgraph learning methods can help mitigate computational and memory demands, they come with drawbacks such as information loss and high redundant computation among subgraphs. This paper introduces an innovative processing paradgim for distributed graph learning that abstracts GNNs with a new set of programming interfaces and leverages Just-In-Time (JIT) compilation technology to its full potential. This paradigm enables GNNs to highly exploit the computational resources of distributed clusters by eliminating the drawbacks of subgraph learning methods, leading to a more efficient inference process. Our experimental results demonstrate that on industry-scale graphs of up to \textbf{500 million nodes and 22.4 billion edges}, our method can produce a performance boost of up to \textbf{27.4 times}.
Continual Graph Learning (CGL), which aims to accommodate new tasks over evolving graph data without forgetting prior knowledge, is garnering significant research interest. Mainstream solutions adopt the memory replay-based idea, ie, caching representative data from earlier tasks for retraining the graph model. However, this strategy struggles with scalability issues for constantly evolving graphs and raises concerns regarding data privacy. Inspired by recent advancements in the prompt-based learning paradigm, this paper introduces a novel prompt-driven continual graph learning (PROMPTCGL) framework, which learns a separate prompt for each incoming task and maintains the underlying graph neural network model fixed. In this way, PROMPTCGL naturally avoids catastrophic forgetting of knowledge from previous tasks. More specifically, we propose hierarchical prompting to instruct the model from both feature- and topology-level to fully address the variability of task graphs in dynamic continual learning. Additionally, we develop a personalized prompt generator to generate tailored prompts for each graph node while minimizing the number of prompts needed, leading to constant memory consumption regardless of the graph scale. Extensive experiments on four benchmarks show that PROMPTCGL achieves superior performance against existing CGL approaches while significantly reducing memory consumption. Our code is available at https://github.com/QiWang98/PromptCGL.
We propose a novel Graph Neural Network-based method for segmentation based on data fusion of multimodal Scanning Electron Microscope (SEM) images. In most cases, Backscattered Electron (BSE) images obtained using SEM do not contain sufficient information for mineral segmentation. Therefore, imaging is often complemented with point-wise Energy-Dispersive X-ray Spectroscopy (EDS) spectral measurements that provide highly accurate information about the chemical composition but that are time-consuming to acquire. This motivates the use of sparse spectral data in conjunction with BSE images for mineral segmentation. The unstructured nature of the spectral data makes most traditional image fusion techniques unsuitable for BSE-EDS fusion. We propose using graph neural networks to fuse the two modalities and segment the mineral phases simultaneously. Our results demonstrate that providing EDS data for as few as 1% of BSE pixels produces accurate segmentation, enabling rapid analysis of mineral samples. The proposed data fusion pipeline is versatile and can be adapted to other domains that involve image data and point-wise measurements.
Link prediction is a crucial task in many downstream applications of graph machine learning. To this end, Graph Neural Network (GNN) is a widely used technique for link prediction, mainly in transductive settings, where the goal is to predict missing links between existing nodes. However, many real-life applications require an inductive setting that accommodates for new nodes, coming into an existing graph. Thus, recently inductive link prediction has attracted considerable attention, and a multi-layer perceptron (MLP) is the popular choice of most studies to learn node representations. However, these approaches have limited expressivity and do not fully capture the graph's structural signal. Therefore, in this work we propose LEAP, an inductive link prediction method based on LEArnable toPology augmentation. Unlike previous methods, LEAP models the inductive bias from both the structure and node features, and hence is more expressive. To the best of our knowledge, this is the first attempt to provide structural contexts for new nodes via learnable augmentation in inductive settings. Extensive experiments on seven real-world homogeneous and heterogeneous graphs demonstrates that LEAP significantly surpasses SOTA methods. The improvements are up to 22\% and 17\% in terms of AUC and average precision, respectively. The code and datasets are available on GitHub (https://github.com/AhmedESamy/LEAP/)
Loop closures are essential for correcting odometry drift and creating consistent maps, especially in the context of large-scale navigation. Current methods using dense point clouds for accurate place recognition do not scale well due to computationally expensive scan-to-scan comparisons. Alternative object-centric approaches are more efficient but often struggle with sensitivity to viewpoint variation. In this work, we introduce REGRACE, a novel approach that addresses these challenges of scalability and perspective difference in re-localization by using LiDAR-based submaps. We introduce rotation-invariant features for each labeled object and enhance them with neighborhood context through a graph neural network. To identify potential revisits, we employ a scalable bag-of-words approach, pooling one learned global feature per submap. Additionally, we define a revisit with geometrical consistency cues rather than embedding distance, allowing us to recognize far-away loop closures. Our evaluations demonstrate that REGRACE achieves similar results compared to state-of-the-art place recognition and registration baselines while being twice as fast.
Graph unlearning aims to remove a subset of graph entities (i.e. nodes and edges) from a graph neural network (GNN) trained on the graph. Unlike machine unlearning for models trained on Euclidean-structured data, effectively unlearning a model trained on non-Euclidean-structured data, such as graphs, is challenging because graph entities exhibit mutual dependencies. Existing works utilize graph partitioning, influence function, or additional layers to achieve graph unlearning. However, none of them can achieve high scalability and effectiveness without additional constraints. In this paper, we achieve more effective graph unlearning by utilizing the embedding space. The primary training objective of a GNN is to generate proper embeddings for each node that encapsulates both structural information and node feature representations. Thus, directly optimizing the embedding space can effectively remove the target nodes' information from the model. Based on this intuition, we propose node-level contrastive unlearning (Node-CUL). It removes the influence of the target nodes (unlearning nodes) by contrasting the embeddings of remaining nodes and neighbors of unlearning nodes. Through iterative updates, the embeddings of unlearning nodes gradually become similar to those of unseen nodes, effectively removing the learned information without directly incorporating unseen data. In addition, we introduce a neighborhood reconstruction method that optimizes the embeddings of the neighbors in order to remove influence of unlearning nodes to maintain the utility of the GNN model. Experiments on various graph data and models show that our Node-CUL achieves the best unlearn efficacy and enhanced model utility with requiring comparable computing resources with existing frameworks.
Multi-agent coordination is crucial for reliable multi-robot navigation in shared spaces such as automated warehouses. In regions of dense robot traffic, local coordination methods may fail to find a deadlock-free solution. In these scenarios, it is appropriate to let a central unit generate a global schedule that decides the passing order of robots. However, the runtime of such centralized coordination methods increases significantly with the problem scale. In this paper, we propose to leverage Graph Neural Network Variational Autoencoders (GNN-VAE) to solve the multi-agent coordination problem at scale faster than through centralized optimization. We formulate the coordination problem as a graph problem and collect ground truth data using a Mixed-Integer Linear Program (MILP) solver. During training, our learning framework encodes good quality solutions of the graph problem into a latent space. At inference time, solution samples are decoded from the sampled latent variables, and the lowest-cost sample is selected for coordination. Finally, the feasible proposal with the highest performance index is selected for the deployment. By construction, our GNN-VAE framework returns solutions that always respect the constraints of the considered coordination problem. Numerical results show that our approach trained on small-scale problems can achieve high-quality solutions even for large-scale problems with 250 robots, being much faster than other baselines. Project page: https://mengyuest.github.io/gnn-vae-coord
Traffic classification is vital for cybersecurity, yet encrypted traffic poses significant challenges. We present PacketCLIP, a multi-modal framework combining packet data with natural language semantics through contrastive pretraining and hierarchical Graph Neural Network (GNN) reasoning. PacketCLIP integrates semantic reasoning with efficient classification, enabling robust detection of anomalies in encrypted network flows. By aligning textual descriptions with packet behaviors, it offers enhanced interpretability, scalability, and practical applicability across diverse security scenarios. PacketCLIP achieves a 95% mean AUC, outperforms baselines by 11.6%, and reduces model size by 92%, making it ideal for real-time anomaly detection. By bridging advanced machine learning techniques and practical cybersecurity needs, PacketCLIP provides a foundation for scalable, efficient, and interpretable solutions to tackle encrypted traffic classification and network intrusion detection challenges in resource-constrained environments.
Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: $3.6\%$ increase in drug response prediction correlation, $9.6\%$ improvement in single-cell drug classification AUC, and $1.1\%$ average gain in gene perturbation prediction accuracy.