Graph Transformer

Prioritizing disease-associated genes is central to understanding the molecular mechanisms of complex disorders such as Alzheimer's disease (AD). Traditional network-based approaches rely on static centrality measures and often fail to capture cross-modal biological heterogeneity. We propose NETRA (Node Evaluation through Transformer-based Representation and Attention), a multimodal graph transformer framework that replaces heuristic centrality metrics with attention-driven relevance scoring. Using AD as a case study, gene regulatory networks are independently constructed from microarray, single-cell RNA-seq, and single-nucleus RNA-seq data. Random-walk sequences derived from these networks are used to train a BERT-based model for learning global gene embeddings, while modality-specific gene expression profiles are compressed using variational autoencoders. These representations are integrated with auxiliary biological networks, including protein-protein interactions, Gene Ontology semantic similarity, and diffusion-based gene similarity, into a unified multimodal graph. A graph transformer assigns NETRA scores that quantify gene relevance in a disease-specific and context-aware manner. Gene set enrichment analysis shows that NETRA achieves a normalized enrichment score of about 3.9 for the Alzheimer's disease pathway, substantially outperforming classical centrality measures and diffusion models. Top-ranked genes enrich multiple neurodegenerative pathways, recover a known late-onset AD susceptibility locus at chr12q13, and reveal conserved cross-disease gene modules. The framework preserves biologically realistic heavy-tailed network topology and is readily extensible to other complex disorders.

Edge classification on directed dynamic graphs is critical for understanding evolving user-item interactions and behavioral patterns in recommender systems and social platforms. Existing dynamic graph architectures typically process these interactions using shared parameters for nodes with semantically distinct roles, including source, destination, query, and neighbor. While abundant supervision in tasks such as link prediction provides sufficient gradient signal for models to implicitly deduce role semantics and overcome this conflation, there are often far fewer labels available for edge classification. We hypothesize that in such regimes, the ability of models to implicitly separate roles is restricted, degrading downstream performance. To empirically investigate this relationship, we introduce an experimental framework for sequence-based models that explicitly disentangles functional roles using targeted embeddings and an asymmetric pretraining objective. By providing architectural priors for these roles, the framework serves as an evaluative vehicle to isolate and measure the resulting performance delta across a range of label budgets. Our empirical evaluation demonstrates that this explicit role disentanglement yields substantial and consistent relative performance gains over baselines. Furthermore, representational analyses reveal that the mechanism by which the framework provides these benefits is a bifurcation of source and destination latent spaces that improves linear separability.

Curvature notions on graphs provide a theoretical description of graph topology, highlighting bottlenecks and denser connected regions. Artifacts of the message passing paradigm in Graph Neural Networks, such as oversmoothing and oversquashing, have been attributed to these regions. However, it remains unclear how the topology of a graph interacts with the learned preferences of GNNs. Through Massive Activations, which correspond to extreme edge activation values in Graph Transformers, we probe this correspondence. Our findings on synthetic graphs and molecular benchmarks reveal that MAs do not preferentially concentrate on curvature extremes, despite their theoretical link to information flow. On the Long Range Graph Benchmark, we identify a systemic curvature shift: global attention mechanisms exacerbate topological bottlenecks, drastically increasing the prevalence of negative curvature. Our work reframes curvature as a diagnostic probe for understanding when and why graph learning fails.

Graph Transformer has demonstrated impressive capabilities in the field of graph representation learning. However, existing approaches face two critical challenges: (1) most models suffer from exponentially increasing computational complexity, making it difficult to scale to large graphs; (2) attention mechanisms based on node-level operations limit the flexibility of the model and result in poor generalization performance in out-of-distribution (OOD) scenarios. To address these issues, we propose VecFormer (the Vector Quantized Graph Transformer), an efficient and highly generalizable model for node classification, particularly under OOD settings. VecFormer adopts a two-stage training paradigm. In the first stage, two codebooks are used to reconstruct the node features and the graph structure, aiming to learn the rich semantic Graph Codes. In the second stage, attention mechanisms are performed at the Graph Token level based on the transformed cross codebook, reducing computational complexity while enhancing the model's generalization capability. Extensive experiments on datasets of various sizes demonstrate that VecFormer outperforms the existing Graph Transformer in both performance and speed.

Graph neural networks frequently encounter significant performance degradation when confronted with structural noise or non-homophilous topologies. To address these systemic vulnerabilities, we present AdvSynGNN, a comprehensive architecture designed for resilient node-level representation learning. The proposed framework orchestrates multi-resolution structural synthesis alongside contrastive objectives to establish geometry-sensitive initializations. We develop a transformer backbone that adaptively accommodates heterophily by modulating attention mechanisms through learned topological signals. Central to our contribution is an integrated adversarial propagation engine, where a generative component identifies potential connectivity alterations while a discriminator enforces global coherence. Furthermore, label refinement is achieved through a residual correction scheme guided by per-node confidence metrics, which facilitates precise control over iterative stability. Empirical evaluations demonstrate that this synergistic approach effectively optimizes predictive accuracy across diverse graph distributions while maintaining computational efficiency. The study concludes with practical implementation protocols to ensure the robust deployment of the AdvSynGNN system in large-scale environments.

Whole-slide images (WSIs) from cancer patients contain rich information that can be used for medical diagnosis or to follow treatment progress. To automate their analysis, numerous deep learning methods based on convolutional neural networks and Vision Transformers have been developed and have achieved strong performance in segmentation and classification tasks. However, due to the large size and complex cellular organization of WSIs, these models rely on patch-based representations, losing vital tissue-level context. We propose using scalable Graph Transformers on a full-WSI cell graph for classification. We evaluate this methodology on a challenging task: the classification of healthy versus tumor epithelial cells in cutaneous squamous cell carcinoma (cSCC), where both cell types exhibit very similar morphologies and are therefore difficult to differentiate for image-based approaches. We first compared image-based and graph-based methods on a single WSI. Graph Transformer models SGFormer and DIFFormer achieved balanced accuracies of $85.2 \pm 1.5$ ($\pm$ standard error) and $85.1 \pm 2.5$ in 3-fold cross-validation, respectively, whereas the best image-based method reached $81.2 \pm 3.0$. By evaluating several node feature configurations, we found that the most informative representation combined morphological and texture features as well as the cell classes of non-epithelial cells, highlighting the importance of the surrounding cellular context. We then extended our work to train on several WSIs from several patients. To address the computational constraints of image-based models, we extracted four $2560 \times 2560$ pixel patches from each image and converted them into graphs. In this setting, DIFFormer achieved a balanced accuracy of $83.6 \pm 1.9$ (3-fold cross-validation), while the state-of-the-art image-based model CellViT256 reached $78.1 \pm 0.5$.

Transformers have achieved remarkable success across domains, motivating the rise of Graph Transformers (GTs) as attention-based architectures for graph-structured data. A key design choice in GTs is the use of Graph Neural Network (GNN)-based positional encodings to incorporate structural information. In this work, we study GTs through the lens of manifold limit models for graph sequences and establish a theoretical connection between GTs with GNN positional encodings and Manifold Neural Networks (MNNs). Building on transferability results for GNNs under manifold convergence, we show that GTs inherit transferability guarantees from their positional encodings. In particular, GTs trained on small graphs provably generalize to larger graphs under mild assumptions. We complement our theory with extensive experiments on standard graph benchmarks, demonstrating that GTs exhibit scalable behavior on par with GNNs. To further show the efficiency in a real-world scenario, we implement GTs for shortest path distance estimation over terrains to better illustrate the efficiency of the transferable GTs. Our results provide new insights into the understanding of GTs and suggest practical directions for efficient training of GTs in large-scale settings.

This paper proposes a joint multi-objective optimization framework for strategic sensor placement in power systems to enhance attack detection. A novel physics-informed graph transformer network (PIGTN)-based detection model is proposed. Non-dominated sorting genetic algorithm-II (NSGA-II) jointly optimizes sensor locations and the PIGTN's detection performance, while considering practical constraints. The combinatorial space of feasible sensor placements is explored using NSGA-II, while concurrently training the proposed detector in a closed-loop setting. Compared to baseline sensor placement methods, the proposed framework consistently demonstrates robustness under sensor failures and improvements in detection performance in seven benchmark cases, including the 14, 30, IEEE-30, 39, 57, 118 and the 200 bus systems. By incorporating AC power flow constraints, the proposed PIGTN-based detection model generalizes well to unseen attacks and outperforms other graph network-based variants (topology-aware models), achieving improvements up to 37% in accuracy and 73% in detection rate, with a mean false alarms rate of 0.3%. In addition, optimized sensor layouts significantly improve the performance of power system state estimation, achieving a 61%--98% reduction in the average state error.

Link prediction is a core challenge in graph machine learning, demanding models that capture rich and complex topological dependencies. While Graph Neural Networks (GNNs) are the standard solution, state-of-the-art pipelines often rely on explicit structural heuristics or memory-intensive node embeddings -- approaches that struggle to generalize or scale to massive graphs. Emerging Graph Transformers (GTs) offer a potential alternative but often incur significant overhead due to complex structural encodings, hindering their applications to large-scale link prediction. We challenge these sophisticated paradigms with PENCIL, an encoder-only plain Transformer that replaces hand-crafted priors with attention over sampled local subgraphs, retaining the scalability and hardware efficiency of standard Transformers. Through experimental and theoretical analysis, we show that PENCIL extracts richer structural signals than GNNs, implicitly generalizing a broad class of heuristics and subgraph-based expressivity. Empirically, PENCIL outperforms heuristic-informed GNNs and is far more parameter-efficient than ID-embedding--based alternatives, while remaining competitive across diverse benchmarks -- even without node features. Our results challenge the prevailing reliance on complex engineering techniques, demonstrating that simple design choices are potentially sufficient to achieve the same capabilities. Our code is publicly available at https://github.com/quang-truong/pencil.

Multi-agent reinforcement learning (MARL) has shown promise for large-scale network control, yet existing methods face two major limitations. First, they typically rely on an exponential decay property of agent interactions on far-away nodes, which can be exploited to develop more efficient and tractable MARL algorithms. When this exponential decay property does not hold, these algorithms do not account for long-range interactions such as epidemic outbreaks or cascading power failures. Second, existing approaches lack network generalizability, or the ability to generalize to networks of different topological structure and scale than those seen during training. In this work, we first present a mean-field stability analysis and empirical study investigating the conditions for long-range network interactions. These results motivate our primary contribution: STACCA (Shared Transformer Actor-Critic with Counterfactual Advantage), a transformer-based MARL framework that addresses both long-range interactions and network generalizability. STACCA employs a centralized Graph Transformer Critic to model long-range dependencies and provide system-level feedback, while its shared Graph Transformer Actor learns a generalizable policy capable of adapting across diverse network topologies. To improve credit assignment during training, STACCA integrates a novel counterfactual advantage estimator that is compatible with state-value critic estimates. We evaluate STACCA on epidemic containment and rumor-spreading network control tasks, demonstrating improved performance and network generalizability. These results highlight the potential of transformer-based MARL architectures to achieve generalizable control in large-scale networked systems.

We study the extent to which rotary position encodings (RoPE), a recent transformer position encoding algorithm broadly adopted in large language models (LLMs) and vision transformers (ViTs), can be applied to graph-structured data. We find that rotating tokens depending on the spectrum of the graph Laplacian efficiently injects structural information into the attention mechanism, boosting performance in synthetic and real-world graph learning tasks. This approach, coined Wave-Induced Rotary Encodings (WIRE), enjoys intriguing theoretical properties: it recovers regular RoPE on grids, and depends asymptotically on the graph effective resistance. Unlike bias-based relative position encodings, WIRE is compatible with linear attention.