Graph Transformer

Automated skin cancer classification from dermoscopic images remains challenging due to heterogeneous lesion structure, strong intra-class variability, and subtle visual differences between benign and malignant cases. Existing CNN/ViT pipelines typically rely on global or patch-level features and often combine patient metadata via late fusion, which limits spatially grounded multimodal reasoning. We present a novel region-based graph learning framework that explicitly models lesions as graphs of spatially coherent superpixel regions represented as frozen CNN features. To capture fine-grained lesion arrangements, we encode inter-regional geometry as edge attributes and introduce a dedicated metadata context node connected to all regions, providing structured integration of demographic/clinical variables within the same relational space. Node representations are updated using our edge-aware graph transformer followed by attention-driven propagation, and a final graph-level embedding for benign-malignant classification. Experiments on four public benchmarks demonstrate that explicit region-level relational modeling and graph-native multimodal fusion yield consistent gains over the state-of-the-art. Consequently, we establish a new graph-centric perspective in which CNN features are modeled as relational nodes and improved through contextual integration, yielding more expressive and robust classifications.

Structurally constrained event sequence generation remains challenging because generated paths must preserve transition feasibility, temporal order, termination, and attribute consistency. In predictive process monitoring (PPM), this challenge appears as full event sequence generation, whereas existing work mainly addresses component tasks such as next activity, remaining time, outcome, and attribute prediction. This paper proposes the Graph Grounded Cross Attention Transformer Neural Network (GGATN) for this unified PPM task. GGATN uses a global process graph as structured activity memory, contextualizes sequence positions through Transformer self attention, and injects process topology through graph grounded cross attention. Unlike autoregressive decoding, GGATN generates activities, timestamps, length, and event level and sequence level attributes in a single pass, followed by Viterbi style graph constrained decoding for feasible paths and explicit termination. Experiments on six benchmark event logs show more reliable generation quality than local instruction prompted LLM baselines. GGATN achieves strong performance on sequence similarity, Damerau Levenshtein similarity, bigram based control flow similarity, and duration distribution, while maintaining zero hallucinated activities and zero sequence level attribute inconsistency. Ablation analyses confirm the global graph encoder as a stable structural prior. Interpretability analyses show how graph structure, sequence context, feedback refinement, and constrained decoding shape generation.

Single-cell RNA sequencing (scRNA-seq) serves a pivotal role in characterizing gene expression at the cellular level, enabling the identification of cell types and advancing the understanding of cellular heterogeneity. Despite the significant progress in scRNA-seq data clustering, we argue that current methods always ignore the sparsity and noise, as well as the complex intercellular structural information inherent in scRNA-seq data. Toward this end, in this paper, we propose a novel single-cell RNA-seq clustering framework via deep Siamese Graph Transformer Network (termed scGTN), which explicitly integrates gene expression profile and intercellular structural dependencies for cell clustering. In particular, we formulate scRNA-seq data as a graph and construct two augmented graph views that serve as dual views to capture complementary intercellular information. Then, a Siamese graph transformer network is employed to explicitly incorporate shortest-path information and node-wise distances for capturing richer structural relationships between cells. Finally, we employ an optimal transport strategy to guide the cell clustering in a self-supervised manner. Extensive experiments on multiple benchmark scRNA-seq datasets demonstrate that our scGTN consistently outperforms existing methods. Our code is available at https://github.com/W-RMSL/scGTN.

In this paper, we propose SGFormer++, a novel Semantic Graph Transformer for 3D scene graph generation (SGG), which aims to parse point cloud scenes into semantic structural graphs, where nodes denote detected object instances and edges encode their pairwise relationships, with the core challenge lying in modeling complex global scene structure. While existing graph convolutional network (GCN)-based methods suffer from over-smoothing and limited receptive fields, SGFormer++ leverages Transformer layers as its backbone to enable global message passing. Specifically, we introduce two key components tailored for 3D SGG: (1) a Graph Embedding Layer++ that efficiently integrates edge-aware global context with linear computational complexity, and (2) a Semantic Injection Layer++ that enriches visual features with linguistic priors from large language models (LLMs) and vision-language models (VLMs), boosting semantic representation without introducing extra trainable parameters. To further address the practical challenge of incremental SGG (I-SGG), where new relationship categories arrive sequentially, we equip SGFormer++ with a novel Spatial-guided Feature Adapter, which calibrates predicate features using subject-object spatial geometry to counter scale variation, and a Cascaded Binary Prediction Head that mitigates catastrophic forgetting via task-incremental classifier expansion and logit distillation. Extensive experiments on the 3DSSG benchmark demonstrate that SGFormer++ achieves state-of-the-art performance in both standard and incremental settings: it yields a significant 4.49% absolute improvement in Predicate A@1 under the incremental setting. Code and data are available at: https://github.com/Andy20178/SGFormer.

Transformer architectures have dramatically advanced representation learning and inference in deep models through self-attention mechanisms. In parallel,associative memory (AM) frameworks map representations onto energy landscapes, offering interpretable retrieval mechanisms. However, their continuous-time inference dynamics lack the biological plausibility of classical Continuous Attractor Neural Networks (CANNs). To bridge this gap, we propose Controlled Dynamics Attractor Transformer (CDAT), which couples a mixture von Mises-Fisher (Mo-vMF) attention energy with a Hopfield refinement energy, while augmenting energy descent with a CANN-inspired excitation-inhibition modulation. CDAT instantiates a topology-constrained dynamical system whose couplings encode relational structure among tokens, thereby linking attractor-style dynamics to modern energy-based attention. We further provide a constructive dissipation analysis to formally establish their controlled inference dynamics. Benefiting from these robust and structured dynamics, CDAT achieves state-of-the-art performance across multiple benchmarks in graph anomaly detection and graph classification.

Accurate prediction of absorption, distribution, metabolism, and excretion (ADME) properties is critical to drug discovery, but remains challenging because ADME endpoints are noisy, interdependent, and often data-limited. We propose a molecular graph-transformer pretraining framework that combines chemistry-specific self-supervision with contrastive mutual information machine learning (cMIM). Our method encodes molecular graphs into latent variables, reconstructs SMILES strings from the graph-derived latent codes, and augments the contrastive objective with domain-specific self-supervised chemistry tasks. Rather than treating these tasks as auxiliary regularizers with separately tuned loss weights, we formulate reconstruction, contrastive discrimination, and chemistry-specific supervision as unit-weighted log-probability factors in a single probabilistic latent-variable objective. For fine-tuning, we propose a multi-task GNN readout architecture with task-specific multilayer perceptron heads, preserving shared representation learning while mitigating negative transfer and improving the modeling of heterogeneous, nonlinear task relationships. Across Biogen, ExpansionRX, and ChEMBL-MT, the resulting Contrastive KERMT pretraining improves over the KERMT baseline by 7.6%, 9.9%, and 9.5% respectively (averaged over significantly-improved endpoints). Adding ADME-adjacent molecules to the pretraining corpus further improves transfer, and the contrastive component sharpens chemically meaningful latent neighborhoods.

Metal additive manufacturing enables the fabrication of complex parts, but achieving consistent build quality remains challenging due to interactions induced by repeated layer-wise melting, solidification, and reheating across the 3D build. Advanced sensing provide a great opportunity to collect rich observations of the actual manufacturing process for real-time quality monitoring and control. Yet, existing methods often have limited ability to represent multi-layer interactions and quantify their contributions to quality. In this paper, we develop a novel spatiotemporal graph transformer for modeling 3D neighborhood interactions and learn their effects on build quality in metal additive manufacturing. Specifically, we first introduce a weighted network representation of the manufacturing process, where fusing locations are modeled as nodes, and their spatial- and process-dependent relationships are encoded as edge weights. This representation also enables the integration of multimodal data (e.g., geometric design, process settings, and in-situ sensing data) into a unified structure for downstream learning tasks. Building on this network, we further design a dual-attention graph transformer that captures both within-node feature dependencies and cross-node neighborhood interactions for quality representation learning. Experimental results show that the proposed framework significantly outperforms image-based, sequence-based, and graph-based models in characterizing process-quality relationships. More importantly, the incorporation of cross-layer interactions is critical for improving quality prediction performance. This framework is broadly applicable to other tasks involving network modeling and graph-based representation learning.

We introduce the Graph Set Transformer (GST), a neural network architecture for learning on sets of graphs, designed for tasks in which per-element predictions depend on set-wide context as well as local structure. Existing architectures, including DeepSets and SetTransformer, require pre-encoded graph embeddings from a separate GNN, creating a bottleneck between feature extraction and set-level contextualisation. In contrast, GST interleaves node-level feature propagation and cross-graph contextual modelling at every layer, fusing the two levels of information through a gating mechanism. We evaluate GST on a controlled synthetic suite designed to isolate set-conditional structural reasoning and on three real-data benchmarks spanning per-atom reaction-centre identification, reaction yield prediction, and image classification. Under matched parameter budgets, GST performs better than the baselines across these settings. An architectural ablation strongly suggests that the interleaving of local and set context contributes substantially to this advantage.

Marginal inference in discrete graphical models forces a choice between exactness and scalability: exact algorithms are intractable for high-treewidth graphs, while iterative approximations (Belief Propagation, variational methods) sacrifice convergence guarantees on frustrated topologies. We argue that this dichotomy stems from a mismatched inductive bias: iterative methods abandon the sequential elimination structure that makes exact inference correct. We introduce In-Context Graphical Inference (ICG-I), an autoregressive Graph Transformer that restores this structure by mimicking Variable Elimination with learned, Tensor- Train-compressed intermediate factors, paired with a Dirichlet output layer and Weighted Conformal Prediction for calibrated, distribution-free coverage guarantees under topological shift. We prove that TT compression errors propagate at most lincarly through the autoregressive chain, that the Dirichlet-Multinomial loss is a proper scoring rule, and that WCP maintains coverage with a quantifiable degradation under estimated density ratios. We conducted intensive experiments to evaluate ICG-I and achieved state-of-the-art performance across all benchmarks. ICG-I reduces MAE from 0.041 (best baseline) to 0.020 on standard instances and achieves 0.048 on N=500 frustrated spin glasses where BP diverges entirely.

The graphical representation of the brain offers critical insights into diagnosing and prognosing neurodegenerative disease via relationships between regions of interest (ROIs). Despite recent emergence of various Graph Neural Networks (GNNs) to effectively capture the relational information, there remain inherent limitations in interpreting the brain networks. Specifically, convolutional approaches ineffectively aggregate information from distant neighborhoods, while attention-based methods exhibit deficiencies in capturing node-centric information, particularly in retaining critical characteristics from pivotal nodes. These shortcomings reveal challenges for identifying disease-specific variation from diverse features from different modalities. In this regard, we propose an integrated framework guiding diffusion process at each node by a downstream transformer where both short- and long-range properties of graphs are aggregated via diffusion-kernel and multi-head attention respectively. We demonstrate the superiority of our model by improving performance of pre-clinical Alzheimer's disease (AD) classification with various modalities. Also, our model adeptly identifies key ROIs that are closely associated with the preclinical stages of AD, marking a significant potential for early diagnosis and prevision of the disease.

Relational databases underpin modern enterprise, scientific, and healthcare systems, yet predictive machine learning on such data remains challenging due to their multi-table, heterogeneous, and temporal structure. Relational Deep Learning (RDL) addresses this by representing databases as heterogeneous graphs and applying graph neural networks (GNNs) directly. RelBench v2 recently introduced autocomplete tasks -- a practically motivated task type where the goal is to predict an existing column value from relational context, analogous to an intelligent form-filling assistant. We propose RelGT-AC (Relational Graph Transformer for Autocomplete), extending the RelGT architecture with three targeted contributions: (1) a column masking strategy that prevents trivial solutions by masking the target column during subgraph encoding; (2) a unified task head supporting binary classification, multiclass classification, and regression autocomplete tasks within a single model; and (3) a TF-IDF text encoder that automatically detects and encodes free-text columns, recovering strong lexical signal that categorical encoders discard. Across 7 tasks spanning 3 RelBench v2 datasets (rel-trial, rel-f1, rel-stack), RelGT-AC outperforms the GraphSAGE baseline on all 3 regression autocomplete tasks and achieves up to +10 AUROC points on text-heavy eligibility tasks via the TF-IDF encoder.

Graph Neural Networks (GNNs) are bottlenecked by sparse, irregular memory access. Popular frameworks such as DGL and PyTorch Geometric support general message passing, but complex layers often materialize edge-wise intermediates, increasing memory traffic and limiting scalability on large graphs. We take an I/O- and arithmetic-intensity--centric view and show that widely used layers fall into three kernel families: SpMM-based convolutions, reduction-based aggregations, and attention-based layers (GATv2/Graph Transformer). For each family, we develop GPU kernels that reduce data movement, improve locality, and remain robust across realistic graphs. We also study graph reordering and find that its impact depends on the kernel mapping: it benefits neighbor-parallel (gather-dominated) kernels more consistently than feature-parallel designs. Empirically, our fused attention kernels reach up to $\textbf{3.9}\times$ speedup for Graph Transformer (median $\textbf{1.6}\times$), with Tensor Core (block-sparse) variants up to $\textbf{7.3}\times$ on locally dense graphs; for GATv2 we reach up to $\textbf{8.5}\times$ speedup (median $\textbf{2.0}\times$) while reducing peak memory by up to $\textbf{76}\times$ (median $\textbf{6}\times$). Our degree-aware reduction kernels achieve up to $\textbf{10}\times$ speedup (median $\textbf{2.6}\times$). For SpMM-based layers, properly cached cuSPARSE achieves up to $\textbf{8}\times$ speedup over DGL and outperforms evaluated custom baselines in the majority of evaluations. We release our implementations as drop-in replacements to support reproducible, hardware-aware GNN acceleration.

Transformers have become a central architecture for graph learning, but their application to graphs requires first choosing a tokenization: a graph-to-token map that determines which structural information is exposed at the input. In this work, we show that this choice is a fundamental component of transformer expressivity. We examine three tokenizations that serve as building blocks for many existing graph tokenizations: spectral, random-walk, and adjacency tokenizations. We prove that different tokenizations induce distinct depth regimes: the same graph computation may be realizable by a shallow transformer under one tokenization, while requiring substantially larger depth under another. For example, we prove that random-walk tokenization is lossy for any walk length, making it impossible in general to recover the graph from it, and that while spectral tokenization is lossless, it is ill-conditioned for local tasks. We further show that although both random-walk and spectral tokenizations are derived from adjacency information, it is impossible for a limited-depth transformer to convert between tokenization families in general. In particular, we establish lower bounds and impossibility results showing that unfavorable tokenizations may preclude the efficient recovery of more suitable structural representations. Finally, we complement our theory with controlled experiments on synthetic and real-world tasks, validating the predicted separations and showing that different tasks favor different structural views, and combining complementary tokenizations allows the transformer to leverage distinct signals from each representation.

Aspect-based sentiment analysis (ABSA) requires models to bind sentiment evidence to the correct aspect, making it a natural testbed for fine-grained structural reasoning. We introduce GHI, a Graphormer-over-Conditioned-Hypergraph-Incidence framework that is designed as an incidence-based structural reasoning layer built on a bipartite topology. GHI represents diverse linguistic and semantic evidence as token--hyperedge incidence relations, allowing different structural signals to be incorporated through a unified interface. Extensive experiments on six standard ABSA benchmarks show that GHI outperforms all baselines on the SemEval domains, and multi-seed evaluations show stable improvements over strong DeBERTa. Further experiments show that with only 247M parameters, GHI approaches the performance of 11B Flan-T5 based methods on the ISE benchmark. Moreover, it demonstrates strong robustness on the challenging ARTS datasets, maintaining highly competitive performance where traditional models degrade. These results demonstrate that compact structural reasoning remains a valuable alternative to scale-driven approaches for fine-grained tasks.

Precise measurement of the kinematic Sunyaev-Zel'dovich (kSZ) effect - a probe of the large-scale distribution of baryonic matter, a key observable for cosmological inference - requires accurate reconstruction of galaxy velocities from spectroscopic surveys. The signal-to-noise ratio (SNR) of kSZ measurements scales directly with the correlation coefficient $r$ between reconstructed and true velocities. We introduce Velocityformer, an equivariant graph transformer architecture designed to match the specific symmetry of the observational data. While the underlying physics is equivariant with respect to translations and rotations, observational effects break this symmetry due to the preferred line-of-sight direction. Matching the model's inductive bias to the data's broken symmetry consistently improves performance across all model sizes and training volumes, with Velocityformer improving $r$ by 35% over the standard linear theory baseline and outperforming ML baselines at every data volume. By matching the model's inductive bias to the data and conditioning on the physics-based long-wavelength solution, Velocityformer is highly data-efficient, training to high accuracy on as few as 4 low-fidelity simulations, and generalises zero-shot across input geometry, cosmological parameters, and galaxy sample. On high-fidelity simulated galaxy catalogues, this yields a 30% improvement in $r$ over the physical baseline, directly translating to the same SNR gain on observational data.

We introduce GraViti, a transformer-based graph-level variational autoencoder that encodes entire graphs into single, fixed-dimensional latent vectors rather than per-node embeddings, yielding a graph-level latent space that supports smooth interpolation, property-guided search, and other downstream tasks beyond the reach of node-level approaches. GraViti achieves state-of-the-art reconstruction accuracy on large molecular graph datasets while offering competitive single-step generative performance. Our central finding concerns where permutation invariance is needed in such a model, and where it is not. The encoder remains permutation-invariant throughout, ensuring the model generalizes to graphs regardless of input order. The reconstruction loss, however, does not need to be: when training data is provided in a consistent node order, comparing predictions to targets directly in that order, without a graph-matching step, is sufficient. Relaxing invariance in the loss alone lets GraViti avoid the cubic-cost matching step required by prior graph-level autoencoders, reducing complexity to quadratic while improving reconstruction fidelity. We show the resulting latent space is chemically meaningful, supporting controlled molecular editing and property optimization, recovering established chemical trends, and enabling direct regression of graph-level properties from latent embeddings.

Hypergraphs model higher-order relations that drive real-world decisions, from drug prescriptions to recommendations. A central structural signal in such data, beyond what pairwise relations can express, is interaction compositionality: whether a higher-order relation is compositional, emergent, or inhibitory with respect to its observed or unobserved sets. In polypharmacy, the regime decides whether a drug should be dropped, kept, or excluded: a compositional drug triple can be safely simplified, an emergent triple requires all drugs jointly, and an inhibitory triple flags a drug that disrupts an existing interaction. However, existing hypergraph learning methods, which merely propagate messages over observed hyperedges, leave this compositional signal unmodeled, allowing dangerous drug combinations to slip through and be misclassified. To this end, we propose the Hypergraph Pattern Machine (HGPM), shifting the paradigm from message passing to learning the compositional pattern of subsets. It tokenizes compositional subsets, organizes them in an inclusion DAG, and trains an inclusion-aware Transformer under masked reconstruction. On ten hypergraph benchmarks, HGPM matches or exceeds state-of-the-art methods. Notably, in a real adverse-event prediction case, HGPM correctly identifies the drug addition that inhibits the side effect among feature-identical candidates, a discrimination existing methods cannot make. The code and data are in https://github.com/KryieZhao/HGPM.git.

Relational graph learning enables predictive modeling over relational databases by directly capturing dependencies across interconnected tables. While relational graph Transformers extend the receptive field beyond local message passing, a larger receptive field does not necessarily provide more useful information: sampling must preserve relational structure without introducing excessive semantically irrelevant nodes, while attention must account for the temporal relevance of the retained information. We propose GelGT, a Gaussian relational graph transformer that explicitly addresses these challenges. GelGT introduces a structure-semantic collaborative sampling strategy to preserve structural connectivity while filtering irrelevant semantic information, and incorporates a Gaussian graph attention mechanism with a learnable Gaussian bias on the sampled subgraphs to dynamically encode temporal dependencies. We provide theoretical analysis characterizing the structural preservation, semantic refinement, and temporal discrimination of these mechanisms. Experiments on \textbf{7} real-world relational datasets covering \textbf{21} prediction tasks show that GelGT consistently outperforms existing relational graph learning methods, with improvements of up to \textbf{13.8%}.

Using Large Language Models (LLMs) to process graph-structured data is an active research area, yet current state-of-the-art approaches typically rely on multi-step pipelines with Graph Neural Network (GNN) encoders that compress rich textual attributes into solitary tokens, creating a significant semantic bottleneck. In this paper, we introduce the Graph Transformer Language Model (GTLM), a novel architecture that enables pretrained LLMs to natively process graph topologies while entirely eliminating this compressive bottleneck. GTLM is exceptionally parameter-efficient: by injecting graph-aware attention biases directly into the LLM's attention modules, it introduces only 0.015% additional parameters relative to the base model. We theoretically prove that our bidirectional attention prefix preserves node permutation equivariance while maintaining exact backward compatibility with the pretrained base model. Extensive evaluations demonstrate that a 1B-parameter GTLM matches or exceeds the performance of 7B-parameter state-of-the-art models on standard Text-Attributed Graph benchmarks, while significantly surpassing baselines on GraphQA. Finally, we demonstrate that GTLM attention heads implicitly learn to simulate message passing, explaining its superior performance on algorithmic tasks. This paradigm shift enables true algorithmic reasoning within LLMs and provides a scalable foundation for next-generation GraphRAG and relational deep learning.

Pre-trained language models advance patent classification and retrieval by encoding claims as flat token sequences, but they overlook the dependency hierarchy among claims. Incorporating this hierarchy into self-attention poses two challenges. First, claim dependencies include relation types with different levels of reliability, so treating them uniformly may allow noisy technical relations to interfere with more reliable legal citations. Second, claim dependencies are defined at the claim level, whereas Transformer attention operates over tokens, making direct structural injection nontrivial. We propose the Patent Heterogeneous Attention-Guided Graph Encoder (PHAGE), which constructs a typed claim graph that distinguishes legal citations from technical relations. PHAGE projects this claim-level topology into token-level attention through a connectivity mask and learnable relation-aware biases, and fine-tunes the encoder using a dual-granularity contrastive objective that combines inter-patent taxonomy with intra-patent topology. At inference, the graph-specific attention components are removed, allowing representations to be generated through a standard encoder forward pass without CDG construction. Experiments on patent classification, retrieval, and clustering show that PHAGE consistently outperforms domain-adapted and citation-aware baselines, demonstrating the value of claim-level structural guidance for graph-free patent representation learning.

Graph Neural Networks (GNN) and Transformer-based architectures have achieved remarkable progress in graph learning, yet they still struggle to capture both global structural dependencies and model the dynamic information propagation. In this paper, we propose CTQWformer, a hybrid graph learning framework that integrates continuous-time quantum walks (CTQW) with GNN. CTQWformer employs a trainable Hamiltonian that fuses graph topology and node features, enabling physically grounded modeling of quantum walk dynamics that captures rich and intricate graph structure information. The extracted CTQW-based representations are incorporated into two complementary modules:(i) a Graph Transformer module that embeds final-time propagation probabilities as structural biases in the self-attention mechanism, and (ii) a Graph Recurrent Module that captures temporal evolution patterns with bidirectional recurrent networks. Extensive experiments on benchmark graph classification datasets demonstrate that CTQWformer outperforms graph kernel and GNN-based methods, demonstrating the potential of integrating quantum dynamics into trainable deep learning frameworks for graph representation learning. To the best of our knowledge, CTQWformer is the first hybrid CTQW-based Transformer, integrating CTQW-derived structural bias with temporal evolution modeling to advance graph learning.

Graph neural networks (GNNs) aim to learn well-trained representations in a lower-dimension space for downstream tasks while preserving the topological structures. In recent years, attention mechanism, which is brilliant in the fields of natural language processing and computer vision, is introduced to GNNs to adaptively select the discriminative features and automatically filter the noisy information. To the best of our knowledge, due to the fast-paced advances in this domain, a systematic overview of attention-based GNNs is still missing. To fill this gap, this paper aims to provide a comprehensive survey on recent advances in attention-based GNNs. Firstly, we propose a novel two-level taxonomy for attention-based GNNs from the perspective of development history and architectural perspectives. Specifically, the upper level reveals the three developmental stages of attention-based GNNs, including graph recurrent attention networks, graph attention networks, and graph transformers. The lower level focuses on various typical architectures of each stage. Secondly, we review these attention-based methods following the proposed taxonomy in detail and summarize the advantages and disadvantages of various models. A model characteristics table is also provided for a more comprehensive comparison. Thirdly, we share our thoughts on some open issues and future directions of attention-based GNNs. We hope this survey will provide researchers with an up-to-date reference regarding applications of attention-based GNNs. In addition, to cope with the rapid development in this field, we intend to share the relevant latest papers as an open resource at https://github.com/sunxiaobei/awesome-attention-based-gnns.

Learning-based MIMO detection has shown strong empirical performance, yet existing methods typically rely on fixed-depth architectures without explicitly modeling the progressive refinement of symbol estimates. In this paper, we revisit MIMO detection from a flow matching perspective and propose the Soft Graph Diffusion Transformer (SGDiT), which reformulates detection as a noise-level-conditioned denoising process that progressively transforms a Gaussian initialization toward the posterior conditioned on channel observations. An adaptive layer normalization (AdaLN)-conditioned soft graph transformer is employed to parameterize the denoising dynamics, enabling stage-aware information integration between observation and symbol domains. To better align with the discrete nature of symbol detection, we further adopt a cross-entropy-based training objective that directly models bit-wise posterior probabilities, providing a more suitable inductive bias than conventional regression-based formulations. Experimental results across various MIMO system configurations demonstrate that SGDiT achieves competitive bit error rate (BER) performance compared with representative baselines. Furthermore, the proposed model exhibits good generalization capability across different channel conditions. Overall, the SGDiT framework provides an effective and practical approach for neural MIMO detection.

Accurate end-to-end tail-latency forecasting is critical for proactive SLO management in microservice systems. However, modeling long-range dependency propagation and non-stationary, bursty workloads while maintaining inference efficiency at scale remains challenging. We present STLGT (Scalable Trace-based Linear Graph Transformer), a per-API predictor that encodes traces as span graphs for multi-step p95 tail-latency forecasting. STLGT uses a structure-aware linear graph Transformer to propagate cross-service dependencies with inference time linear in span graph size, and a decoupled temporal module to capture workload dynamics. Across a personalized education microservice application, DeathStarBench, and Alibaba traces, STLGT improves forecasting accuracy over PERT-GNN by 8.5% MAPE on average and achieves up to 12x faster CPU inference at N=32, matching the maximum span graph size after preprocessing the Alibaba traces. Ablation studies further demonstrate the effectiveness of each component, especially under bursty traffic.

Graph Transformers can mix information globally, but this flexibility also creates failure modes: some tasks require long-range communication while others are better served by local interaction. We study this through a synthetic node-classification benchmark on contextual stochastic block model graphs, where labels are generated by a controllable mixture of local and far-shell signals. We define distance-misaligned training as a mismatch between where label-relevant information lies and where the model allocates communication over graph distance. On this benchmark, we find three points. First, the preferred graph-distance bias changes systematically with task locality. Second, an oracle adaptive controller, given offline access to the task-side distance target, nearly matches the best fixed bias across regimes and strongly improves over a neutral baseline on mixed and local tasks. Third, a task-agnostic zero-gap controller is weaker, indicating that adaptation alone is not enough and that the control target matters. These results suggest that distance-resolved diagnosis is useful for understanding Graph Transformer failures and for designing graph-aware control.

3D human pose estimation is a classic and important research direction in the field of computer vision. In recent years, Transformer-based methods have made significant progress in lifting 2D to 3D human pose estimation. However, these methods primarily focus on modeling global temporal and spatial relationships, neglecting local skeletal relationships and the information interaction between different channels. Therefore, we have proposed a novel method,the Dual-stream Spatio-temporal GCN-Transformer Network (MixTGFormer). This method models the spatial and temporal relationships of human skeletons simultaneously through two parallel channels, achieving effective fusion of global and local features. The core of MixTGFormer is composed of stacked Mixformers. Specifically, the Mixformer includes the Mixformer Block and the Squeeze-and-Excitation Layer ( SE Layer). It first extracts and fuses various information of human skeletons through two parallel Mixformer Blocks with different modes. Then, it further supplements the fused information through the SE Layer. The Mixformer Block integrates Graph Convolutional Networks (GCN) into the Transformer, enhancing both local and global information utilization. Additionally, we further implement its temporal and spatial forms to extract both spatial and temporal relationships. We extensively evaluated our model on two benchmark datasets (Human3.6M and MPI-INF-3DHP). The experimental results showed that, compared to other methods, our MixTGFormer achieved state-of-the-art results, with P1 errors of 37.6mm and 15.7mm on these datasets, respectively.

Global self-attention drives modern graph transformers, yet the softmax at its core imposes a structural constraint rarely examined directly: every attention row is non-negative and sums to one, so each per-head output is a mass-conserving convex combination of value vectors. A node can never "attend to nothing." We argue this conservation constraint is a single root cause behind three pathologies usually studied in isolation: the collapse of node representations with depth (over-smoothing), a low-rank bottleneck on per-head outputs, and brittle optimization in deep stacks. Drawing on how sigmoid gating removes analogous attention sinks in language models, we introduce SigGate-GT, a graph transformer that applies a learned, per-head, input-conditioned sigmoid gate to the attention output inside the GraphGPS framework. The gate is a smooth, per-dimension "volume control" that can drive head outputs toward zero, relaxing the constraint without abandoning attention's probabilistic interpretation. Analytically and through synthetic experiments, we show the gate strictly increases the stable rank of per-head outputs, and connect this rank gain to all three manifestations. On five molecular and long-range benchmarks, SigGate-GT matches the prior best on ZINC (0.059 MAE), records the strongest result among the graph-transformer baselines we evaluate on ogbg-molhiv (82.47% ROC-AUC), and is competitive on ogbg-molpcba and the Long-Range Graph Benchmark, with statistically significant gains over GraphGPS on all five datasets (p < 0.05). Mechanism analyses confirm the diagnosis: gating slows over-smoothing (a 30% mean relative gain in representation diversity across 4-16 layers), keeps attention entropy from collapsing, and stabilizes training across a 10x learning-rate range, at about 1% parameter overhead on OGB and under 3% wall-clock cost.

Graph foundation models have demonstrated remarkable adaptability across diverse downstream tasks through large-scale pretraining on graphs. However, existing implementations of the backbone model, graph transformers, are typically limited to single-GPU systems, leading to long training times or out-of-memory issues on large graphs. Moreover, parallelizing graph transformer training over the full graph is challenging, as efficiency depends heavily on both the graph structure and system characteristics, such as bandwidth and memory capacity. In this work, we introduce a distributed training framework for graph transformers, which automatically selects and optimizes parallelization strategies based on the graph structure and hardware configuration. With our implementation of distributed sparse operations, we accelerate sparse graph attention by up to 3.8x and reduce memory consumption by 78% compared to state-of-the-art frameworks. On large graph benchmarks, our proposed framework achieves up to 6x speedup with system scaling up to 8 GPUs. These results demonstrate that the proposed framework improves the scalability of graph transformers, bringing them closer to serving as practical graph foundation models.

Edge classification on directed dynamic graphs requires modeling interactions between source and destination nodes exhibiting asymmetrical behavioral patterns and temporal dynamics. However, existing dynamic graph architectures largely rely on shared parameters for processing source and destination nodes, with limited or no systematic role-aware modeling. We propose DyGnROLE (Dynamic Graph Node-Role-Oriented Latent Encoding), a Transformer-based architecture that disentangles source and destination representations. By using separate embedding tables and role-semantic positional encodings, the model captures the distinct structural and temporal contexts unique to each role. Critical in limited-label settings, which are common in edge classification, is a self-supervised pretraining objective we introduce: Directional Role Alignment (DRA). DRA learns distinct but aligned source and destination embedding spaces by training source representations to retrieve their corresponding destination representations while a historical positive masking strategy excludes previously observed interactions from future negative comparisons. The masks introduce a temporally directional training signal in which node pairs progress monotonically from unseen to observed, after which the relationship is eligible only for further alignment. A comprehensive evaluation on four edge classification tasks across eight datasets demonstrates that DyGnROLE consistently outperforms a wide range of state-of-the-art baselines, highlighting the importance of role-aware representation learning and asymmetric pretraining for modeling complex directed interactions when labeled data is limited.

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 $78.1 \pm 0.5$.