The increase in high-dimensional multiomics data demands advanced integration models to capture the complexity of human diseases. Graph-based deep learning integration models, despite their promise, struggle with small patient cohorts and high-dimensional features, often applying independent feature selection without modeling relationships among omics. Furthermore, conventional graph-based omics models focus on homogeneous graphs, lacking multiple types of nodes and edges to capture diverse structures. We introduce a Heterogeneous Graph ATtention network for omics integration (HeteroGATomics) to improve cancer diagnosis. HeteroGATomics performs multimodal feature selection through a multi-agent system, creating dedicated networks of feature and patient similarity for each omics modality. These networks are then combined into one heterogeneous graph for learning holistic omics-specific representations and integrating predictions across modalities. Experiments on three cancer multiomics datasets show that HeteroGATomics outperforms baseline methods across most evaluation metrics in cancer diagnosis. External validation on an independent breast cancer cohort further demonstrates its generalizability, where HeteroGATomics outperforms graph-based multiomics integration methods across evaluation metrics. Moreover, HeteroGATomics enhances interpretability by identifying important biomarkers contributing to the diagnosis outcomes.
The collection and release of street-level recordings as Open Data play a vital role in advancing autonomous driving systems and AI research. However, these datasets pose significant privacy risks, particularly for pedestrians, due to the presence of Personally Identifiable Information (PII) that extends beyond biometric traits such as faces. In this paper, we present cRID, a novel cross-modal framework combining Large Vision-Language Models, Graph Attention Networks, and representation learning to detect textual describable clues of PII and enhance person re-identification (Re-ID). Our approach focuses on identifying and leveraging interpretable features, enabling the detection of semantically meaningful PII beyond low-level appearance cues. We conduct a systematic evaluation of PII presence in person image datasets. Our experiments show improved performance in practical cross-dataset Re-ID scenarios, notably from Market-1501 to CUHK03-np (detected), highlighting the framework's practical utility. Code is available at https://github.com/RAufschlaeger/cRID.
As one of the most detrimental code smells, code clones significantly increase software maintenance costs and heighten vulnerability risks, making their detection a critical challenge in software engineering. Abstract Syntax Trees (ASTs) dominate deep learning-based code clone detection due to their precise syntactic structure representation, but they inherently lack semantic depth. Recent studies address this by enriching AST-based representations with semantic graphs, such as Control Flow Graphs (CFGs) and Data Flow Graphs (DFGs). However, the effectiveness of various enriched AST-based representations and their compatibility with different graph-based machine learning techniques remains an open question, warranting further investigation to unlock their full potential in addressing the complexities of code clone detection. In this paper, we present a comprehensive empirical study to rigorously evaluate the effectiveness of AST-based hybrid graph representations in Graph Neural Network (GNN)-based code clone detection. We systematically compare various hybrid representations ((CFG, DFG, Flow-Augmented ASTs (FA-AST)) across multiple GNN architectures. Our experiments reveal that hybrid representations impact GNNs differently: while AST+CFG+DFG consistently enhances accuracy for convolution- and attention-based models (Graph Convolutional Networks (GCN), Graph Attention Networks (GAT)), FA-AST frequently introduces structural complexity that harms performance. Notably, GMN outperforms others even with standard AST representations, highlighting its superior cross-code similarity detection and reducing the need for enriched structures.
Traffic data imputation is fundamentally important to support various applications in intelligent transportation systems such as traffic flow prediction. However, existing time-to-space sequential methods often fail to effectively extract features in block-wise missing data scenarios. Meanwhile, the static graph structure for spatial feature propagation significantly constrains the models flexibility in handling the distribution shift issue for the nonstationary traffic data. To address these issues, this paper proposes a SpatioTemporal Attention Mixture of experts network named STAMImputer for traffic data imputation. Specifically, we introduce a Mixture of Experts (MoE) framework to capture latent spatio-temporal features and their influence weights, effectively imputing block missing. A novel Low-rank guided Sampling Graph ATtention (LrSGAT) mechanism is designed to dynamically balance the local and global correlations across road networks. The sampled attention vectors are utilized to generate dynamic graphs that capture real-time spatial correlations. Extensive experiments are conducted on four traffic datasets for evaluation. The result shows STAMImputer achieves significantly performance improvement compared with existing SOTA approaches. Our codes are available at https://github.com/RingBDStack/STAMImupter.
Action coordination in human structure is indispensable for the spatial constraints of 2D joints to recover 3D pose. Usually, action coordination is represented as a long-range dependence among body parts. However, there are two main challenges in modeling long-range dependencies. First, joints should not only be constrained by other individual joints but also be modulated by the body parts. Second, existing methods make networks deeper to learn dependencies between non-linked parts. They introduce uncorrelated noise and increase the model size. In this paper, we utilize a pyramid structure to better learn potential long-range dependencies. It can capture the correlation across joints and groups, which complements the context of the human sub-structure. In an effective cross-scale way, it captures the pyramid-structured long-range dependence. Specifically, we propose a novel Pyramid Graph Attention (PGA) module to capture long-range cross-scale dependencies. It concatenates information from various scales into a compact sequence, and then computes the correlation between scales in parallel. Combining PGA with graph convolution modules, we develop a Pyramid Graph Transformer (PGFormer) for 3D human pose estimation, which is a lightweight multi-scale transformer architecture. It encapsulates human sub-structures into self-attention by pooling. Extensive experiments show that our approach achieves lower error and smaller model size than state-of-the-art methods on Human3.6M and MPI-INF-3DHP datasets. The code is available at https://github.com/MingjieWe/PGFormer.
Research on Graph Structure Learning (GSL) provides key insights for graph-based clustering, yet current methods like Graph Neural Networks (GNNs), Graph Attention Networks (GATs), and contrastive learning often rely heavily on the original graph structure. Their performance deteriorates when the original graph's adjacency matrix is too sparse or contains noisy edges unrelated to clustering. Moreover, these methods depend on learning node embeddings and using traditional techniques like k-means to form clusters, which may not fully capture the underlying graph structure between nodes. To address these limitations, this paper introduces DeSE, a novel unsupervised graph clustering framework incorporating Deep Structural Entropy. It enhances the original graph with quantified structural information and deep neural networks to form clusters. Specifically, we first propose a method for calculating structural entropy with soft assignment, which quantifies structure in a differentiable form. Next, we design a Structural Learning layer (SLL) to generate an attributed graph from the original feature data, serving as a target to enhance and optimize the original structural graph, thereby mitigating the issue of sparse connections between graph nodes. Finally, our clustering assignment method (ASS), based on GNNs, learns node embeddings and a soft assignment matrix to cluster on the enhanced graph. The ASS layer can be stacked to meet downstream task requirements, minimizing structural entropy for stable clustering and maximizing node consistency with edge-based cross-entropy loss. Extensive comparative experiments are conducted on four benchmark datasets against eight representative unsupervised graph clustering baselines, demonstrating the superiority of the DeSE in both effectiveness and interpretability.
Cost-aware Dynamic Workflow Scheduling (CADWS) is a key challenge in cloud computing, focusing on devising an effective scheduling policy to efficiently schedule dynamically arriving workflow tasks, represented as Directed Acyclic Graphs (DAG), to suitable virtual machines (VMs). Deep reinforcement learning (DRL) has been widely employed for automated scheduling policy design. However, the performance of DRL is heavily influenced by the design of the problem-tailored policy network and is highly sensitive to hyperparameters and the design of reward feedback. Considering the above-mentioned issues, this study proposes a novel DRL method combining Graph Attention Networks-based policy network and Evolution Strategy, referred to as GATES. The contributions of GATES are summarized as follows: (1) GATES can capture the impact of current task scheduling on subsequent tasks by learning the topological relationships between tasks in a DAG. (2) GATES can assess the importance of each VM to the ready task, enabling it to adapt to dynamically changing VM resources. (3) Utilizing Evolution Strategy's robustness, exploratory nature, and tolerance for delayed rewards, GATES achieves stable policy learning in CADWS. Extensive experimental results demonstrate the superiority of the proposed GATES in CADWS, outperforming several state-of-the-art algorithms. The source code is available at: https://github.com/YaShen998/GATES.
Link prediction in unmanned aerial vehicle (UAV) ad hoc networks (UANETs) aims to predict the potential formation of future links between UAVs. In adversarial environments where the route information of UAVs is unavailable, predicting future links must rely solely on the observed historical topological information of UANETs. However, the highly dynamic and sparse nature of UANET topologies presents substantial challenges in effectively capturing meaningful structural and temporal patterns for accurate link prediction. Most existing link prediction methods focus on temporal dynamics at a single structural scale while neglecting the effects of sparsity, resulting in insufficient information capture and limited applicability to UANETs. In this paper, we propose a multi-scale structural-temporal link prediction model (MUST) for UANETs. Specifically, we first employ graph attention networks (GATs) to capture structural features at multiple levels, including the individual UAV level, the UAV community level, and the overall network level. Then, we use long short-term memory (LSTM) networks to learn the temporal dynamics of these multi-scale structural features. Additionally, we address the impact of sparsity by introducing a sophisticated loss function during model optimization. We validate the performance of MUST using several UANET datasets generated through simulations. Extensive experimental results demonstrate that MUST achieves state-of-the-art link prediction performance in highly dynamic and sparse UANETs.
3D visual grounding aims to localize the unique target described by natural languages in 3D scenes. The significant gap between 3D and language modalities makes it a notable challenge to distinguish multiple similar objects through the described spatial relationships. Current methods attempt to achieve cross-modal understanding in complex scenes via a target-centered learning mechanism, ignoring the perception of referred objects. We propose a novel 2D-assisted 3D visual grounding framework that constructs semantic-spatial scene graphs with referred object discrimination for relationship perception. The framework incorporates a dual-branch visual encoder that utilizes 2D pre-trained attributes to guide the multi-modal object encoding. Furthermore, our cross-modal interaction module uses graph attention to facilitate relationship-oriented information fusion. The enhanced object representation and iterative relational learning enable the model to establish effective alignment between 3D vision and referential descriptions. Experimental results on the popular benchmarks demonstrate our superior performance compared to state-of-the-art methods, especially in addressing the challenges of multiple similar distractors.
Spoilers in movie reviews are important on platforms like IMDb and Rotten Tomatoes, offering benefits and drawbacks. They can guide some viewers' choices but also affect those who prefer no plot details in advance, making effective spoiler detection essential. Existing spoiler detection methods mainly analyze review text, often overlooking the impact of movie genres and user bias, limiting their effectiveness. To address this, we analyze movie review data, finding genre-specific variations in spoiler rates and identifying that certain users are more likely to post spoilers. Based on these findings, we introduce a new spoiler detection framework called GUSD (The code is available at https://github.com/AI-explorer-123/GUSD) (Genre-aware and User-specific Spoiler Detection), which incorporates genre-specific data and user behavior bias. User bias is calculated through dynamic graph modeling of review history. Additionally, the R2GFormer module combines RetGAT (Retentive Graph Attention Network) for graph information and GenreFormer for genre-specific aggregation. The GMoE (Genre-Aware Mixture of Experts) model further assigns reviews to specialized experts based on genre. Extensive testing on benchmark datasets shows that GUSD achieves state-of-the-art results. This approach advances spoiler detection by addressing genre and user-specific patterns, enhancing user experience on movie review platforms.
To reduce the reliance on large-scale annotations, self-supervised RGB-T tracking approaches have garnered significant attention. However, the omission of the object region by erroneous pseudo-label or the introduction of background noise affects the efficiency of modality fusion, while pseudo-label noise triggered by similar object noise can further affect the tracking performance. In this paper, we propose GDSTrack, a novel approach that introduces dynamic graph fusion and temporal diffusion to address the above challenges in self-supervised RGB-T tracking. GDSTrack dynamically fuses the modalities of neighboring frames, treats them as distractor noise, and leverages the denoising capability of a generative model. Specifically, by constructing an adjacency matrix via an Adjacency Matrix Generator (AMG), the proposed Modality-guided Dynamic Graph Fusion (MDGF) module uses a dynamic adjacency matrix to guide graph attention, focusing on and fusing the object's coherent regions. Temporal Graph-Informed Diffusion (TGID) models MDGF features from neighboring frames as interference, and thus improving robustness against similar-object noise. Extensive experiments conducted on four public RGB-T tracking datasets demonstrate that GDSTrack outperforms the existing state-of-the-art methods. The source code is available at https://github.com/LiShenglana/GDSTrack.
Recent advances in machine learning have demonstrated an enormous utility of deep learning approaches, particularly Graph Neural Networks (GNNs) for materials science. These methods have emerged as powerful tools for high-throughput prediction of material properties, offering a compelling enhancement and alternative to traditional first-principles calculations. While the community has predominantly focused on developing increasingly complex and universal models to enhance predictive accuracy, such approaches often lack physical interpretability and insights into materials behavior. Here, we introduce a novel computational paradigm, Self-Adaptable Graph Attention Networks integrated with Symbolic Regression (SA-GAT-SR), that synergistically combines the predictive capability of GNNs with the interpretative power of symbolic regression. Our framework employs a self-adaptable encoding algorithm that automatically identifies and adjust attention weights so as to screen critical features from an expansive 180-dimensional feature space while maintaining O(n) computational scaling. The integrated SR module subsequently distills these features into compact analytical expressions that explicitly reveal quantum-mechanically meaningful relationships, achieving 23 times acceleration compared to conventional SR implementations that heavily rely on first principle calculations-derived features as input. This work suggests a new framework in computational materials science, bridging the gap between predictive accuracy and physical interpretability, offering valuable physical insights into material behavior.
This paper addresses the joint transceiver design, including pilot transmission, channel feature extraction and feedback, as well as precoding, for low-overhead downlink massive multiple-input multiple-output (MIMO) communication in frequency-division duplex (FDD) systems. Although deep learning (DL) has shown great potential in tackling this problem, existing methods often suffer from poor scalability in practical systems, as the solution obtained in the training phase merely works for a fixed feedback capacity and a fixed number of users in the deployment phase. To address this limitation, we propose a novel DL-based framework comprised of choreographed neural networks, which can utilize one training phase to generate all the transceiver solutions used in the deployment phase with varying sizes of feedback codebooks and numbers of users. The proposed framework includes a residual vector-quantized variational autoencoder (RVQ-VAE) for efficient channel feedback and an edge graph attention network (EGAT) for robust multiuser precoding. It can adapt to different feedback capacities by flexibly adjusting the RVQ codebook sizes using the hierarchical codebook structure, and scale with the number of users through a feedback module sharing scheme and the inherent scalability of EGAT. Moreover, a progressive training strategy is proposed to further enhance data transmission performance and generalization capability. Numerical results on a real-world dataset demonstrate the superior scalability and performance of our approach over existing methods.
Graph Neural Networks (GNNs) have emerged as the de facto standard for modeling graph data, with attention mechanisms and transformers significantly enhancing their performance on graph-based tasks. Despite these advancements, the performance of GNNs on heterogeneous graphs often remains complex, with networks generally underperforming compared to their homogeneous counterparts. This work benchmarks various GNN architectures to identify the most effective methods for heterogeneous graphs, with a particular focus on node classification and link prediction. Our findings reveal that graph attention networks excel in these tasks. As a main contribution, we explore enhancements to these attention networks by integrating positional encodings for node embeddings. This involves utilizing the full Laplacian spectrum to accurately capture both the relative and absolute positions of each node within the graph, further enhancing performance on downstream tasks such as node classification and link prediction.
Action quality assessment (AQA) is critical for evaluating athletic performance, informing training strategies, and ensuring safety in competitive sports. However, existing deep learning approaches often operate as black boxes and are vulnerable to spurious correlations, limiting both their reliability and interpretability. In this paper, we introduce FineCausal, a novel causal-based framework that achieves state-of-the-art performance on the FineDiving-HM dataset. Our approach leverages a Graph Attention Network-based causal intervention module to disentangle human-centric foreground cues from background confounders, and incorporates a temporal causal attention module to capture fine-grained temporal dependencies across action stages. This dual-module strategy enables FineCausal to generate detailed spatio-temporal representations that not only achieve state-of-the-art scoring performance but also provide transparent, interpretable feedback on which features drive the assessment. Despite its strong performance, FineCausal requires extensive expert knowledge to define causal structures and depends on high-quality annotations, challenges that we discuss and address as future research directions. Code is available at https://github.com/Harrison21/FineCausal.
Node classification in graphs aims to predict the categories of unlabeled nodes by utilizing a small set of labeled nodes. However, weighted graphs often contain noisy edges and anomalous edge weights, which can distort fine-grained relationships between nodes and hinder accurate classification. We propose the Edge Weight-aware Graph Structure Learning (EWGSL) method, which combines weight learning and graph structure learning to address these issues. EWGSL improves node classification by redefining attention coefficients in graph attention networks to incorporate node features and edge weights. It also applies graph structure learning to sparsify attention coefficients and uses a modified InfoNCE loss function to enhance performance by adapting to denoised graph weights. Extensive experimental results show that EWGSL has an average Micro-F1 improvement of 17.8% compared with the best baseline.
Studying peer relationships is crucial in solving complex challenges underserved communities face and designing interventions. The effectiveness of such peer-based interventions relies on accurate network data regarding individual attributes and social influences. However, these datasets are often collected through self-reported surveys, introducing ambiguities in network construction. These ambiguities make it challenging to fully utilize the network data to understand the issues and to design the best interventions. We propose and solve two variations of link ambiguities in such network data -- (i) which among the two candidate links exists, and (ii) if a candidate link exists. We design a Graph Attention Network (GAT) that accounts for personal attributes and network relationships on real-world data with real and simulated ambiguities. We also demonstrate that by resolving these ambiguities, we improve network accuracy, and in turn, improve suicide risk prediction. We also uncover patterns using GNNExplainer to provide additional insights into vital features and relationships. This research demonstrates the potential of Graph Neural Networks (GNN) to advance real-world network data analysis facilitating more effective peer interventions across various fields.
While deep learning models play a crucial role in predicting antibody-antigen interactions (AAI), the scarcity of publicly available sequence-structure pairings constrains their generalization. Current AAI methods often focus on residue-level static details, overlooking fine-grained structural representations of antibodies and their inter-antibody similarities. To tackle this challenge, we introduce a multi-modality representation approach that integates 3D structural and 1D sequence data to unravel intricate intra-antibody hierarchical relationships. By harnessing these representations, we present MuLAAIP, an AAI prediction framework that utilizes graph attention networks to illuminate graph-level structural features and normalized adaptive graph convolution networks to capture inter-antibody sequence associations. Furthermore, we have curated an AAI benchmark dataset comprising both structural and sequence information along with interaction labels. Through extensive experiments on this benchmark, our results demonstrate that MuLAAIP outperforms current state-of-the-art methods in terms of predictive performance. The implementation code and dataset are publicly available at https://github.com/trashTian/MuLAAIP for reproducibility.
The histopathological classification of whole-slide images (WSIs) is a fundamental task in digital pathology; yet it requires extensive time and expertise from specialists. While deep learning methods show promising results, they typically process WSIs by dividing them into artificial patches, which inherently prevents a network from learning from the entire image context, disregards natural tissue structures and compromises interpretability. Our method overcomes this limitation through a novel graph-based framework that constructs WSI graph representations. The WSI-graph efficiently captures essential histopathological information in a compact form. We build tissue representations (nodes) that follow biological boundaries rather than arbitrary patches all while providing interpretable features for explainability. Through adaptive graph coarsening guided by learned embeddings, we progressively merge regions while maintaining discriminative local features and enabling efficient global information exchange. In our method's final step, we solve the diagnostic task through a graph attention network. We empirically demonstrate strong performance on multiple challenging tasks such as cancer stage classification and survival prediction, while also identifying predictive factors using Integrated Gradients. Our implementation is publicly available at https://github.com/HistoGraph31/pix2pathology
Protein-protein interaction (PPI) prediction is an instrumental means in elucidating the mechanisms underlying cellular operations, holding significant practical implications for the realms of pharmaceutical development and clinical treatment. Presently, the majority of research methods primarily concentrate on the analysis of amino acid sequences, while investigations predicated on protein structures remain in the nascent stages of exploration. Despite the emergence of several structure-based algorithms in recent years, these are still confronted with inherent challenges: (1) the extraction of intrinsic structural information of proteins typically necessitates the expenditure of substantial computational resources; (2) these models are overly reliant on seen protein data, struggling to effectively unearth interaction cues between unknown proteins. To further propel advancements in this domain, this paper introduces a novel PPI prediction method jointing masked reconstruction and contrastive learning, termed JmcPPI. This methodology dissects the PPI prediction task into two distinct phases: during the residue structure encoding phase, JmcPPI devises two feature reconstruction tasks and employs graph attention mechanism to capture structural information between residues; during the protein interaction inference phase, JmcPPI perturbs the original PPI graph and employs a multi-graph contrastive learning strategy to thoroughly mine extrinsic interaction information of novel proteins. Extensive experiments conducted on three widely utilized PPI datasets demonstrate that JmcPPI surpasses existing optimal baseline models across various data partition schemes. The associated code can be accessed via https://github.com/lijfrank-open/JmcPPI.