Gurucharan Marthi Krishna Kumar, Janine Dale Mendola, Amir Shmueleess.IV cs.CV
Vision language models have transformed 2D medical imaging, yet extending them to 3D white matter tractography remains challenging due to the complex topology of fiber bundles. We introduce TractoGraphVLM, a unified framework for four tasks, bundle classification, text-to-tract retrieval, anatomical captioning, and visual question answering, built on a shared GPS architecture, training procedure, and read-out design. Fiber bundles are represented as streamline graphs whose nodes encode 3D position and tangent orientation. A General, Powerful, Scalable (GPS) graph transformer produces bundle embeddings aligned with a frozen BiomedBERT text encoder via contrastive learning, while a BioGPT decoder with visual prefix tokens generates captions and answers. A single shared encoder and decoder is trained jointly across all four tasks and evaluated from one checkpoint. Trained on HCP Young Adult subjects, TractoGraphVLM achieves 91.8% bundle classification accuracy, 84.7% retrieval R@1, BLEU-4=20.1, ROUGE-L=66.8, and 66.4% VQA accuracy on a held-out test set. The same checkpoints transfer zero-shot to HCP Aging subjects, with a modest drop on discriminative tasks and a larger drop on generative tasks, showing robustness to age and acquisition shift. Language supervision yields richer representations than label-only training, recovering structure like hemisphere and fiber family, carried by captions but never given as a label. Swapping only the visual encoder, graphs preserving fiber orientation outperform volumetric baselines, with GPS giving the best balance. Generative metrics measure consistency with a structured knowledge base rather than independent clinical text; even so, TractoGraphVLM shows that classifying, retrieving, describing, and answering questions about a white matter bundle can be served by one jointly trained model that learns transferable neuroanatomy from language alone.
Transformer-based methods have achieved strong performance in monocular 3D human pose estimation, but most existing approaches organise spatial and temporal reasoning as separate stages, which may weaken unified spatial-temporal interdependencies inherent in human motion and compress frame-level structural information before temporal modelling. In this paper, we propose HSTGFormer, a graph-enhanced Transformer framework that reformulates spatial-temporal reasoning as localised coupled graph aggregation over joint-time nodes. Specifically, HSTGFormer introduces a Hyper Spatial-Temporal Graph (HSTG), which decomposes global spatial-temporal reasoning into local spatial-temporal receptive fields around individual joint-time nodes by extending per-frame skeleton graphs into temporal neighbourhoods, thereby enabling structure-aware coupled reasoning while preserving local structural motion information. It further incorporates an Adaptive Dual-Scale Temporal Graph (ADSTG) to capture joint-specific temporal dependencies over complementary short- and long-range windows. A lightweight node-wise fusion module further adaptively integrates the two graph representations for each joint-time node. Experiments on Human3.6M and MPI-INF-3DHP show that HSTGFormer achieves strong accuracy with high computational efficiency.
Small businesses often have only 12-24 months of accounting history, yet planning and risk workflows require coordinated forecasts across financial statements. We study joint 12-month forecasting of 13 income-statement, balance-sheet, cash-flow, and working-capital key performance indicators (KPIs) from 71 monthly ledger series. We introduce the Accounting Graph Transformer (AGT), which represents each ledger series as a masked token, exchanges information through typed attention on a fixed accounting-relation graph, pools target-specific context, and fuses it with a gated three-month recency path. Across 11,993 forecast origins from 1,060 unseen companies, AGT achieves sample-weighted KPI-macro mean absolute error (MAE) $0.6990 \pm 0.0013$ over three independent seeds, compared with $0.7378 \pm 0.0014$ for the strongest baseline, LightGBM. At the pre-specified seed 42, a paired company-clustered bootstrap gives a LightGBM-minus-AGT difference of 0.0395 with 95% confidence interval (CI) $[0.0350,0.0439]$. AGT is best on all 13 KPIs against LightGBM, TimeMixer, and SOFTS in the matched seed-42 comparison, while final-architecture ablations show that relational attention, accounting topology, and the recency path each improve validation and test accuracy. On 7,094 additional unseen companies with origins sampled from January-May 2025, AGT obtains 0.7548 MAE versus 0.7694 for SOFTS. A single 5.3M-parameter model produces 156 aligned forecasts without company-specific fitting, providing one forecasting layer for integrated planning, liquidity, and working-capital analysis.
Charilaos Papaioannou, Ioannis Tsantilas, Dimitris Giannakakos +9cs.LG cs.AI
Single-task fine-tuning of graph neural networks (GNNs) for power grid problems exhibits a systematic failure mode: models that achieve the lowest in-distribution error degrade the most under topology shift. We term this topology overfitting: the tendency of task-specific gradient signals to encode relational structure particular to the training topologies rather than the underlying physics, causing models to fail on unseen grids despite strong in-distribution performance. To expose and address this failure mode, we introduce MxGPS (Multiplex GPS), a multiplex graph transformer that runs K task-specialised GPS branches over a shared node encoder, jointly trained on Static State Estimation (SSE) and AC Power Flow (PF) via a self-supervised pre-training and multi-task fine-tuning protocol, with a cross-branch attention module evaluated in ablation. The joint SSE+PF objective forces the shared encoder to simultaneously satisfy complementary gradient signals, preventing it from overfitting to topology-specific relational structure. Under a 3-fold sliding-window cross-validation spanning four unseen topologies (14-, 24-, 162-, and 300-bus), MxGPS attains 0% boundary violation rate (BVR) on all four zero-shot Power Flow topologies. Critically, models with substantially lower in-distribution PF error degrade by 190% to 1400% under topology shift, whereas MxGPS degrades by only 39%, an inversion that directly implicates topology overfitting as the failure mechanism rather than insufficient model capacity. With only 1.6M parameters (12x fewer than the GridFM reference baseline), MxGPS demonstrates that multi-task joint training is a principled and parameter-efficient mechanism for topology-agnostic generalisation in power grid foundation models.
Accurate station-level demand forecasting is essential for the efficient operation of bike-sharing systems, yet it remains challenging due to complex spatio-temporal dependencies and the large scale of urban networks. This paper presents STAGformer, a Spatio-Temporal Agent Graph Transformer that achieves efficient global modeling with linear computational complexity. The model introduces a two-step agent attention mechanism, where a small set of learnable spatial and temporal agent tokens first aggregate global information and then broadcast it back to individual stations and time steps, effectively capturing long-range interactions while reducing the quadratic cost of standard self-attention to O(NT). STAGformer integrates four core modules: a spatio-temporal encoder that fuses dynamic node features with external contextual factors (weather, time, points of interest), a graph propagation module for spatial neighbor aggregation, a temporal convolution module for local pattern extraction, and the agent attention module for global dependency modeling. Extensive experiments on two real-world datasets -- NYC Citi-Bike and Chicago Divvy-Bike -- demonstrate that STAGformer consistently outperforms state-of-the-art baselines across multiple prediction horizons, achieving significant improvements in both RMSE and MAE. Ablation studies validate the contribution of each component, with the agent attention mechanism proving critical for modeling global spatio-temporal dependencies.
Transformers have become general-purpose architectures, but their all-to-all self-attention is poorly matched to graph data, whose interactions are sparse, structured and multi-scale. Existing Graph Transformers address this mismatch through structural encodings, hybrid message-passing modules or learned attention constraints, often introducing additional complexity and limited interpretability. Here we introduce X-LogSMask, an explainable multi-head logarithmic structural mask that injects symmetrically normalized graph topology directly into attention logits. The logarithmic transform converts structural connectivity into a topology-aware gating signal, suppressing unsupported node interactions while preserving feature-dependent attention. By assigning different powers of the normalized adjacency matrix to different attention heads, X-LogSMask gives each head a defined structural radius and supports multi-hop information propagation within a single layer. We further show that a standard Transformer encoder can be interpreted as one-step message passing on a complete graph, motivating X-LogSMask as a topology-constrained alternative to unrestricted self-attention. Across 20 node-, edge- and graph-level benchmarks, Transformers equipped with X-LogSMask achieve state-of-the-art performance on 13 datasets and remain competitive in a lightweight one-layer configuration. These results show that simple, interpretable structural masks can make self-attention an effective graph-learning operator without changing the Transformer architecture. The code is available at https://github.com/LiLeyan-0120/X-LogSMask.
Jinke Wu, Yifan Wang, Siyu Yi +5cs.LG cs.AI q-bio.GN
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.
Traffic forecasting is a fundamental component of intelligent transportation systems, yet remains challenging in real-world settings due to irregular sensor distributions and the high computational cost of modeling large-scale spatiotemporal dependencies. In practical traffic networks, sensors are unevenly distributed across regions, leading to non-uniform spatial structures that limit the effectiveness and scalability of existing graph-based and attention-based models. To address these challenges, we propose PatchSTG, a patch-based spatiotemporal graph Transformer designed for efficient forecasting on irregular sensor networks. The key idea is to introduce a hierarchical spatial representation that partitions sensors into balanced, locality-preserving patches based on geographic information. On top of this structure, a dual attention encoder alternates between intra-patch attention for capturing local interactions and inter-patch attention for modeling global dependencies, reducing computational complexity from quadratic to near-linear scaling. We evaluate PatchSTG on real-world traffic data from Rhode Island and additional large-scale datasets. Experimental results demonstrate that the proposed model achieves stable and competitive forecasting performance across multiple horizons, while significantly improving computational efficiency. Ablation studies further validate the effectiveness of spatial partitioning and dual attention in capturing both local and long-range traffic dynamics. These results suggest that patch-based spatiotemporal modeling provides a scalable and effective framework for traffic forecasting under irregular spatial settings.
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.
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.