Graph Neural Networks

User modeling is a critical task in a variety of personalized systems. Recognizing their effectiveness in learning from graph-structured data, Graph Neural Networks (GNNs), particularly Graph Convolutional Networks (GCNs), are increasingly employed for user modeling. However, existing approaches typically treat different relation types in a graph as homogeneous, limiting their ability to capture richer semantics and construct more informative user models. While multi-relational GNNs (MR-GNNs) have been adopted for representation learning and recommendation, their application for user modeling remains unexplored. Moreover, existing GNN-based user modeling approaches ignore the user interaction sequence. To address these research gaps, in this work we propose MR-ConceptGCN, a novel fully unsupervised approach focused on concept-based sequential learner modeling using multi-relational GCNs (MR-GCNs). MR-ConceptGCN effecively combines Personal Knowledge Graphs (PKGs), MR-GCNs, and the pre-trained language model SBERT to obtain enhanced relation- and semantic-aware representations of the PKG items. The enriched embeddings of the knowledge concepts that a learner did not understand when interacting with learning materials in CourseMapper are then used to construct a sequential learner model that combines long-term and short-term learner interactions. We report the results of an online user study (n = 31), demonstrating the benefits of MR-ConceptGCN in terms of several important user-centric aspects including accuracy, usefulness, diversity, and satisfaction with an educational recommender system.

Vision-language models (VLMs) provide a unified representation space for textual and visual information, yet their potential as general-purpose backbones for graph-structured data remains largely unexplored. In practice, attributed graphs exhibit substantial modality heterogeneity: some graphs contain only textual node attributes, others only visual attributes, while still others provide both. Existing graph learning approaches are typically designed for fixed modality schemas, requiring separate models for different settings and limiting scalability and cross-graph generalization. To bridge this gap, we present OMG-VLM (One Model, Many Graphs with Vision-Language Models), a unified framework for learning over attributed graphs across heterogeneous modality schemas. OMG-VLM leverages a pretrained VLM as a shared backbone and introduces structure-aware graph adapters that integrate neighborhood information while remaining compatible with the VLM's native embedding space. This design enables effective learning over text-attributed, image-attributed, and multimodal-attributed graphs within a single model. Extensive experiments across diverse domains show that OMG-VLM consistently outperforms state-of-the-art GNN- and LLM-based baselines on attributed graph learning tasks such as node classification and link prediction, while exhibiting strong generalization to unseen graphs and varying modality schemas. The source code is available at https://github.com/Jo-eyang/OMG-VLM.

Neural Markov Logic Networks (NMLNs) are a flexible neurosymbolic relational model. Previous work has shown that, although NMLNs achieve strong performance as generative models for small relational structures, they underperform diffusion-based generative graph models on larger structures. In this paper, we strengthen NMLNs along two main dimensions: (i) we increase the expressive capacity of their potential functions using graph neural networks, and (ii) we develop a new training and inference algorithm inspired by parallel-tempering Markov chain Monte Carlo methods, which we name parallel noising. Together, these enhancements enable NMLNs to attain strong performance in graph generation relative to general diffusion-based generative graph models. Furthermore, they allow NMLNs to match the performance of specialized text-based recurrent models when generating small molecular structures.

Text-attributed graphs (TAGs) are an important graph data form that combine relational structure with rich node text. However, real-world TAGs are often imperfect, with quality issues arising from text, structure, and labels, and typically manifesting as sparsity, noise, and imbalance. These dimensions define nine representative degradation scenarios that can substantially affect TAG learning. Although prior studies have explored specific mitigation strategies, existing evidence remains fragmented across degradation types, datasets, tasks, and model families, leaving TAG robustness insufficiently understood. To address this gap, we present OpenRTAG, a robustness benchmark for text-attributed graph learning. OpenRTAG organizes TAG quality issues into a unified 3 * 3 taxonomy and supports standardized evaluation across nine TAG datasets and three downstream tasks. It systematically evaluates scenario validity and model sensitivity, compares traditional GNNs, LLM-GNNs, and a representative GFM, investigates the effectiveness, efficiency, and robustness of scenario-matched baselines, and further examines model behavior under composite degradation scenarios. OpenRTAG provides a standardized testbed for understanding robustness in TAG learning under realistic low-quality settings.

Equivariant graph neural networks provide a powerful modeling language for three-dimensional scientific data, but their reuse is often limited by implementations tied to specific tasks, outputs, and training regimes. We present GEqTrain, a configuration-driven framework that separates dataset semantics, model composition, and training objectives. Raw data are mapped to typed node-, edge-, and graph-level fields, while model stacks, losses, and training workflows are assembled declaratively through Hydra configurations. A shared equivariant backbone and training infrastructure can therefore be retargeted to a new task primarily through configuration. We demonstrate this flexibility on three different problems handled within one software stack: coarse-grained-to-atomistic backmapping of biomolecular systems, prediction of NMR chemical shifts in molecular solids, and equivariant generative modeling. Our aim is not to surpass individually optimized task-specific systems, but to show that a shared representation and training infrastructure can achieve competitive accuracy across qualitatively different tasks at the cost of a configuration change. We further introduce GEqDiff, a generative extension based on equivariant flow matching. GEqDiff treats user-defined equivariant fields as first-class generation targets, jointly transporting Cartesian positions and non-scalar node fields spanning representations up to l=3 within a single equivariant flow. We validate this capability on a controlled synthetic benchmark inspired by protein secondary-structure motifs, showing that fields with heterogeneous transformation properties can be reconstructed jointly and with high fidelity. By reducing the software overhead of moving between predictive and generative, scalar and tensorial settings, GEqTrain aims to make equivariant modeling more reproducible, extensible, and reusable.

This paper explores Relative Positional Encoding (RPE) as an additive bias in Transformer architectures to solve the Team Orienteering Problem. By embedding in the attention mechanism pairwise spatial relationships among nodes of the graph that represents the routing problem, the transformer encoder can compute a richer spatial-aware graph embedding that allows the decoder to estimate better routes. Experimental results involving instances up to 100 nodes demonstrate consistent improvements in collected rewards and optimality gaps over vanilla Transformer architectures used by other state-of-the-art works. These findings highlight that explicit relational modeling significantly enhances scalability and generalization for complex combinatorial optimization.

A central aim of unsupervised learning is to uncover latent factors that explain dependencies among observations. Probabilistic models typically achieve this by introducing multiple latent variables linked through a graph of conditional relationships, with distributional parameters and their dependence learnt from data. Learning relies either on distributional choices that allow tractable belief propagation, or on approximations that scale poorly with model size and complexity. We build on the recently developed recognition-parametrised modelling paradigm to propose an alternative approach: RAMP, a method that implicitly defines latent structure by learning a flexible, nonlinear, amortised message-passing framework. We show that RAMP enables efficient likelihood-based recovery of latent-variable distributions within expressive nonlinear models acting on complex high-dimensional data.

Automated Algorithm Selection (AS) aims to improve problem-solving performance by selecting, for each problem instance, the most suitable algorithm from a predefined portfolio. This is particularly relevant to the Traveling Salesman Problem (TSP), where solver performance is strongly instance-dependent. We introduce GNNAS-TSP, a Graph Neural Network (GNN)-based AS framework that learns TSP instance representations directly from raw graph data, avoiding manual feature engineering. GNNAS-TSP formulates AS as a joint cost-prediction and ranking task. We evaluate cost-based (mean squared error (MSE), mean absolute error (MAE), and Huber), rank-based (RankNet, ListNet, and LambdaRank), and hybrid learning objectives for a portfolio comprising Chained Lin-Kernighan, Edge Assembly Crossover, Lin-Kernighan-Helsgaun, Multiagent Optimization System, and Concorde. Experiments use fixed computational budgets of 10 and 60 seconds. On the held-out test set, the selected configurations improve on the Single Best Solver (SBS) in normalized solution cost at both budgets. For the 10s budget, AS achieves substantial and statistically significant cost improvement over SBS. Overall, the results suggest that GNNAS-TSP is a useful meta-solving strategy when exploitable variation exists across solver performance.

In recent years, interest in single-atom catalysts supported on carbon-based structures has grown considerably due to their high catalytic activity and efficient uses of metal atoms. However, the design and characterization of these materials through first-principles calculations are computationally expensive, limiting the exploration of a large number of possible configurations. Here, we developed a framework based on graph neural networks (GNNs) to predict the adsorption energies of transition metals on graphene quantum dots (GQDs). The model was trained using data obtained from density functional theory calculations and achieved an $R^2$ of 0.906 with an MAE of 0.101 eV, while reducing computational cost by roughly six orders of magnitude relative to DFT. This methodology provides an efficient tool for the accelerated screening and rational design of new catalysts based on carbon nanostructures.

A graph foundation model generalizes across graph domains by mapping every input into one shared representation before any task reasoning. We call this map the alignment layer, the component that separates a graph foundation model from a graph neural network, and we show it is a distinct attack surface that prior work has not studied. We attack it at inference time, with no access to training, on six public models spanning spectral tokenizers, text embedding spaces, and a discrete codebook. A directed representation-space perturbation collapses every model, but at a budget comparable to the representation norm a plain graph network also needs, with one exception: OpenGraph, whose spectral tokenizer collapses at a fifth of that budget, an alignment-specific fragility a plain network does not share and which a same-representation control traces to the tokenizer rather than the decoder. A realizable input-space attack that edits edges, features, or text removes at least half the correct predictions on three of the six models at peak. How much of this fragility an input-access attacker realizes tracks how directly the decoder reads the representation, and not the clean accuracy a task leaves; we measure this carrier gain structurally from the decoder's local Lipschitz sensitivity, and report clean-accuracy headroom as a within-model ordering heuristic that does not survive on realizable attacks.

Gaussian graphical model selection is usually studied under independent sampling, but in many applications the data arise as a single trajectory of a dependent stochastic process. We study exact recovery of the graph from one trajectory of random-scan Gaussian Glauber dynamics. Existing techniques for this problem either inherit the mixing time of the chain, which can be super-polynomial in the dimension $p$ without strong assumptions, or are suboptimal in the minimum normalized edge strength $κ$. We propose two algorithms that are mixing-free and attain the $κ^{-2}$ dependence of the information-theoretic lower bounds. Both instantiate a shared dueling-neighborhood search meta-algorithm with a local statistic built directly from the update sequence. For every fixed precision matrix and deterministic initialization, the first algorithm fits a least-squares regression at the updates of each node and has pointwise recovery horizon $\widetilde O(pd^{2}/κ^{2})$, where $d$ is the maximum degree. Its horizon depends logarithmically on a local conditioning quantity and on the initialization potential. The second algorithm is based on counting occurences of a specific update pattern and requires $\widetilde O(pd^{4}/κ^{2})$ updates, with no dependence on any condition number. The central technical challenge is that both statistics are built from dependent, non-stationary observations. Our analysis tackles this by demonstrating how to extract fresh Gaussian innovations from the update sequence, which yields mixing-free control of appropriate quantities. Neither the algorithms nor their analyses invoke stationarity, a spectral gap, or mixing conditions.

Machine olfaction for gas unmixing is an underconstrained inverse problem in which gas compositions must be inferred from low-dimensional, delayed, and entangled sensor responses produced by interacting chemical transport, surface adsorption, and sensor transduction. One of the key obstacles is physics closure misspecification, where a neural network is designed to fit sensor traces rather than infer a physically closed olfactory process. In this work, we formulate gas unmixing as a multi-physics-constrained inverse problem governed by Maxwell--Stefan multicomponent transport PDEs, competitive adsorption ODEs, and nonlinear sensor transduction ODEs. Directly solving such a high-dimensional coupled system is computationally expensive and often numerically unstable. To this end, we propose UnMixNet, a physics-closed graph neural solver that embeds this multi-physics forward process into end-to-end gas unmixing. UnMixNet discretizes Maxwell--Stefan cross-diffusion on spatial graphs and formulates the multicomponent flux on each edge. This design enables local, differentiable, and flux-conservative inference for multicomponent cross-diffusion. Evaluations on SmellNet show improved single-odor recognition, seen-mixture unmixing, and unseen-mixture generalization. In addition, an external validation on UCI Dynamic Gas Mixtures shows that the inferred concentration process agrees with ground truth concentration set points under dynamic transitions. Process-consistency diagnostics further show that the proposed model learns transferable dynamic physical fingerprints that better satisfies transport, conservation, adsorption, and readout closure.

Equivariant graph neural networks repeatedly apply edge-conditioned tensor-product convolutions over graph edges. Conventional implementations materialize edge-specific weights, messages, and adjoints, causing tensor-product workspace and memory traffic to grow rapidly with graph size and operator width. This limits feasible workloads and can prevent larger problems from fully utilizing the GPU. We show that these edge-sized intermediates are artifacts of the execution schedule, not requirements of the equivariant operator. By reassociating radial projection, spherical-harmonic coupling, and graph aggregation, edge-local products can be consumed directly into bounded receiver-side state. The resulting streaming formulation preserves fully connected multiplicity mixing and extends through forward, backward, and double backward. We implement this formulation in Sobek, a generated-CUDA backend, and evaluate it across edge-scaling regimes and varied feature structures. Across two operator families and all three differentiation orders, Sobek is faster in all 75 capacity-matched comparisons, with speedups ranging from $1.2\times$ to $49.7\times$, and reduces peak allocated memory by up to 99%. It also executes workloads up to two orders of magnitude beyond OpenEquivariance's capacity while retaining near-peak throughput. These results show that edge-scaled tensor-product workspace is a property of the conventional schedule, not of equivariant convolution itself.

Bayesian inference provides a principled foundation for reasoning under uncertainty, but its computational cost hinders deployment on resource-constrained edge devices. In this paper, we present a hardware-oriented methodology for accelerating discrete Bayesian inference on commercial off-the-shelf embedded GPUs. We identify that the latency of a broad class of variational message-passing algorithms is dominated by tensor contractions. Our approach restructures the memory layout of these operations using two complementary merging strategies that produce compact, regularly-shaped primitives better suited for efficient GPU execution. We then introduce optional sparse array representations and a tensor-clustering scheme to reduce the memory footprint. We instantiate the methodology and produce optimized variants of three message-passing algorithms for Hidden Markov Models (HMMs), namely variational filtering, variational message passing, and marginal message passing. Furthermore, we complement this with a machine-learning-based autotuner that automatically selects the best-performing algorithmic variant for a given generative model specification. Benchmarked on an NVIDIA Jetson Orin AGX across 770 randomly sampled realistic Partially Observable Markov Decision Process (POMDP) configurations, our implementations achieve speedups of up to 5x, with typical gains of 2-2.5x, while producing numerically identical outputs to the baseline implementations.

Graph Neural Network (GNN) inference on billion-scale graphs is challenging due to the large memory footprint of features and embeddings and high disk I/O costs in out-of-core settings. Existing distributed GNN systems incur high communication times and infrastructure costs, while disk-based GNN systems are primarily tailored to training and experience massive wasted reads during inference on the entire graph. We present Taurus, a single-machine system for GNN inference on graphs that do not fit in RAM, supporting both \textit{exact} full-graph inference and fanout-sampled inference. To avoid random and repeated feature gathers, Taurus reformulates layer-wise inference as source-centric broadcasts over sequential SSD scans, backed by a pipelined GPU-CPU-SSD hierarchy, topology-aware reordering, pending-message eviction, and a GPU-resident store for high-degree vertices. It further uses non-buffered sequential reads and GPU-backed writes to reduce page-cache pollution, host-memory pressure, and write overheads. On out-of-core graphs with up to $269M$ vertices, $4B$ edges, and $514$ GiB of features, Taurus outperforms the strongest layer-wise baseline, DGI, by $7$-$25\times$, and vertex-wise baselines by $40$-$140\times$.

High quality temporal graph benchmarks with rich semantics and ground-truth anomaly labels are essential for training graph neural networks, yet remain scarce due to privacy constraints and annotation costs. We present SAGA (Synthetic Agentic Graph Architecture), a system for generating large-scale, semantically rich temporal graphs via a four-phase pipeline. Our Skeleton-First, Semantics-Second architecture decouples structure from semantics: (S) an O(1)-per-edge skeleton generator produces power-law graphs; (A) a dispatcher partitions causally ordered time blocks for parallel execution; (G) LLM agents inject domain semantics using RAG-based rule bases across four domains; and (A) a state alignment engine resolves conflicts via temporal replay, yielding anomaly labels as natural byproducts. Unlike structural generators (e.g., LDBC SNB, Kronecker/R-MAT) or purely LLM-based approaches, SAGA achieves structural realism, semantic richness, and automatic anomaly labeling in a unified framework. On a single H100 GPU with vLLM batching, SAGA generates 500,000 temporal edges with controlled anomalies in under 90 minutes, scaling to 100,000 nodes while maintaining clustering coefficients above 0.99. The system supports real-time pipeline visualization, interactive multi-domain tuning (Finance/AML, Network/IDS, Cyber/APT, Transportation), and a CLI for large-scale GPU-based experiments.

Node representation learning has advanced rapidly, yet most existing methods rely on per-dataset training and hyperparameter tuning. This dataset-specific optimization comes from the difficulty of designing reusable graph models that generalize across diverse graph datasets. In this work, we introduce Node4All, a node representation learner applicable to arbitrary graph datasets without any dataset-specific optimization. Node4All is built on two complementary ideas. At the architectural level, we introduce the Channel Graph Transformer (CGT), which enables a single fixed parameterization to process arbitrary graph datasets. At the learning level, we propose a self-supervised learning based on a series of synthetic graphs. Together, these components enable generalization beyond individual datasets, which is infeasible with existing architectures and learning frameworks. We extensively evaluate Node4All on node classification across 25 benchmarks against 21 baselines, covering both supervised and self-supervised methods. Despite all baselines being trained and optimized for each dataset, a single Node4All, applied uniformly across the datasets, achieves a competitive ranking of 5th among 21 baselines. Moreover, Node4All supports one-shot and in-context learning with an appropriate predictor and outperforms recent graph foundation models (GFMs) in these settings. These results demonstrate that Node4All not only achieves reusability across arbitrary graph datasets, but also remains an effective solution in practice. Code and model checkpoints are available in https://github.com/dooho00/node4all.

In many cases, the outage of one transmission line in a system can be localized by monitoring the power flow of another line, and machine learning methods can be used to distinguish the cases under uncertainty. In this study, we examine the improvements in line outage localization performance achieved by various ensemble classifiers compared to single-model methods. In the case studies, we compared the classification results with measurement data collected at observed transmission lines (OTLs) selected using three algorithms, i.e, greedy maximum coverage problem (MCP), high-eta, and random selection, based on two sensitivity factors, i.e., line outage distribution factors (LODFs) and line outage impact factors (LOIFs). We found that the OTLs selected by the greedy MCP algorithm yielded the highest F1 score and the ensemble classifiers significantly outperformed a base kNN classifier. The extra-trees bagging technique achieved the highest F1 score in many instances. All the findings were statistically significant.

Indoor robots are increasingly employed for facility management tasks such as cleaning and inspection. These applications primarily rely on navigation and can be effectively supported by predefined routes or perception-driven Simultaneous Localization and Mapping (SLAM) techniques. However, more complex tasks, such as locating and repairing leaking pipes, require not only navigation but also access to building information, including the location, geometry, material, and operational attributes of components. Existing navigation approaches provide only limited environmental understanding and cannot readily supply such information. In contrast, Building Information Modeling (BIM) contains rich geometric, semantic, and operational information that remains largely underutilized in robotic applications. This study proposes a BIM-enabled, agent-based simulation platform for knowledge-driven indoor robot navigation and operation planning. Within the framework, indoor environments are discretized into grid cells that are mapped to graph nodes and classified as target, obstacle, or regular nodes according to their spatial relationships with building elements. Traversal costs are assigned to edges connecting neighboring nodes, enabling graph-theoretic algorithms to compute efficient and collision-free navigation paths while avoiding obstacles. Simulation results demonstrate that the proposed graph representation enables efficient and collision-free navigation. A key limitation associated with coarse discretization, namely overlap between target-occupied and obstacle-occupied cells, is identified and mitigated through grid refinement, improving spatial accuracy and path feasibility. The proposed platform supports virtual evaluation of robotic operations prior to deployment and provides a foundation for BIM-informed robotic systems in facility management.

Graph Neural Networks (GNNs) have emerged as a powerful, differentiable class of learning models for graph-structured systems. Their ability to generalize across topologies opens the prospect of a surrogate for combined structural and parametric optimization, which classical metamodels cannot offer. Supply chains are a natural target, yet the use of GNN surrogates for supply chain problems is largely unexplored. This paper lays the foundation, presents initial steps, and discusses key research directions. As a foundation, we formulate the problem and create a large public training dataset of programmatically generated supply chain graphs with input parameters and steady-state performance metrics obtained using our SupplyNetPy simulation library. As initial steps, we explore GNN architectures that work well as surrogates for node- and network-level predictions, and analyze their accuracy-compute trade-off against simulation. Most importantly, we outline the exciting directions this opens, namely gradient-based optimization over topology, fast design-space exploration, and sensitivity analysis.

How deep does a graph neural network need to be on a sparse graph? We study its purest statistical form: node classification on the sparse contextual stochastic block model (CSBM) with average degree $Δ=O(1)$, whose local weak limit is a broadcast-labelled Poisson Galton-Watson tree. Prior work derived a message-passing classifier $h_\ell$ that aggregates from each vertex at distance $k\le\ell$ the attenuated evidence $2\operatorname{artanh}(γ^k t(X_v))$, with $γ$ the edge signal and $t$ a bounded likelihood-ratio transform of the feature. We prove that the value of depth is governed by a single number, the Kesten-Stigum ratio $κ=γ^2Δ$. Below the threshold ($κ<1$), the error sequence is Cauchy at a geometric rate, $|\mathcal{E}(\ell)-\mathcal{E}(\ell')|\le Cκ^{(\ell+1)/3}$ for all $\ell'>\ell$, so all layers beyond depth $O(\log(1/ε))$ change the error by less than $ε$; conversely, under mild regularity each sufficiently deep layer still flips the decision with probability at least $cκ^{\ell/2}$, the empirically sharp exponent. Above the threshold ($κ>1$), depth is geometrically productive: $\mathcal{E}(\ell)$ is driven to a branching-process floor of order at most $1/(κ-1)$ at any geometric rate $κ^{-s\ell}$, $s<1$ (this bound has content only for $κ>17$). No local classifier of any depth beats the universal floor $e^{-Δ}Φ(-ζ)$ set by isolated roots ($ζ$ the feature signal-to-noise ratio), while the first layer provably helps by an explicit total-variation amount. Simulations with an exact belief-propagation baseline on the same trees show that the pairwise rule's error curve is mildly non-monotone in $\ell$, so an optimal finite depth exists (an exact instance is certified in the appendix), while BP saturates strictly faster, at an effective per-layer ratio below $κ$ that we identify.

Safe and socially compliant navigation in open human-robot environments requires robots to reason about heterogeneous participants with different dynamics, autonomy levels, and social roles. Existing trajectory prediction and planning methods often rely on homogeneous interaction assumptions or enforce only geometric collision constraints, making it difficult to jointly model asymmetric interactions, coupled prediction-planning, and soft social norms. This paper proposes SAGE, a socially-aware generative engine for heterogeneous multi-agent navigation. SAGE represents robots and surrounding entities as a directed heterogeneous graph and employs a Heterogeneous Graph Transformer (HGT) to encode type-specific asymmetric interactions. Conditioned on the resulting context, a diffusion-based generative module jointly models future entity trajectories and robot trajectory plans. During inference, a training-free safety-social energy guidance mechanism refines sampled robot trajectories using differentiable collision, kinematic, task-progress, and role-conditioned social-compliance terms. Extensive experiments on real-world (ETH/UCY and SDD) and synthetic datasets verify the effectiveness of SAGE in improving safety and social compliance while maintaining task performance. The proposed guidance mechanism consistently reduces collision and social-violation rates, scales to teams of up to 20 robots, and enables explicit control of the safety-accuracy-task trade-off without retraining. These findings demonstrate the potential of SAGE as a scalable framework for socially-aware multi-agent navigation in complex environments.

Large language models (LLMs) are increasingly used to automate data-processing workflows, yet coding agents typically produce scripts that are not automatically materialized as persistent, editable platform artifacts. We call this disconnect the \textit{NL2Pipeline gap}. To bridge it, we introduce \textsc{DataFlow-Harness}, a platform that guides an LLM agent to construct platform-native directed acyclic graphs (DAGs) through typed, incremental mutations rather than free-form scripts. The platform combines \textsc{DataFlow-Skills} for procedural guidance, a Model Context Protocol (MCP) layer that exposes the live operator registry and current pipeline state, and \textsc{DataFlow-WebUI}, which synchronizes conversational authoring with a visual DAG editor. On a 12-task data-engineering benchmark, \textsc{DataFlow-Harness} achieves a 93.3% observed end-to-end pass rate. Relative to Vanilla Claude Code, it reduces measured monetary cost by 72.5% and generation latency by 49.9%; its observed pass rate is within 0.9 percentage points of the Context-Aware Claude Code baseline while its cost is 42.8% lower. Per-task analysis indicates that Skills are most useful when construction depends on implicit procedural knowledge. These results show that live platform grounding can produce persistent, editable workflow artifacts with an observed reliability close to script-generation baselines and with lower measured construction cost and latency.

Exhaustive site-by-site interventions on a neural network's computational graph -- activation-patching sweeps, circuit-discovery searches, systematic ablation studies -- mutate the graph at every candidate site, and their cost is dominated by recomputation after each mutation. On a reactive graph engine whose invalidation provably touches exactly the downstream cone of a mutated node, we give a complete cost accounting for such workloads. First, the aggregate speedup of an exhaustive sweep over independent full recomputations is not a universal constant: if per-layer weight varies regularly with depth at Karamata index q, the ratio converges to (q+2)/(q+1) when weight concentrates near the output and to q+2 near the input, recovering 2 only in the depth-uniform case; a wall-clock corollary predicts a ceiling of about 1.79, below 2, until interpreter overhead is compiled away. Second, we prove the exact cost of a sequence of persistent mutations, never undone between insertions: the interleaved cost exceeds the isolated sum by an exact overcount summed over comparable site pairs, with closed-form extremes over insertion orders, while batched application is order-independent and sub-additive, costing exactly the union of the sites' cones plus the fresh nodes. Third, we prove the exact mirror of forward locality for the backward pass, showing it collapses the aggregate speedup to 1 under backpropagation on architectures without long skip connections. Every identity is validated on NeuroDSL, a reactive graph engine in Julia: measured sweep ratios converge to the predicted limits under four cost profiles; the training-mode ratio collapses to 1 at the predicted rate; and all 18 per-graft sequential costs and the batched total match the closed forms at zero tolerance across three insertion orders.

Function-preserving network growth techniques such as Net2Net and progressive stacking expand a model's capacity without destroying its learned function, but existing formulations either tolerate numerical perturbations or require a full rebuild of the training program. We formalize Exact Network Surgery: the in-place insertion of a residual block into a live computational graph such that (i) the network function is preserved -- bit-exactly under explicit floating-point hypotheses -- and (ii) inserted parameters remain trainable immediately after insertion. We prove an identity-morphism theorem for gated residual blocks, a structural-locality theorem showing that a reactive invalidation engine recomputes exactly the downstream cone of the insertion point, leaving every other node's value and optimizer state untouched, and an escape-from-initialization proposition showing that the Gradient Shadowing gate alpha, initialized at zero over a randomly initialized branch, receives a generically non-zero gradient at insertion time. We identify a degenerate configuration -- zero-initialized output projections combined with a zero gate -- that is an exact saddle point gradient descent cannot escape. Every claim is validated on the reference implementation in NeuroDSL, a reactive graph engine in Julia: grafting is bit-exact on every logit tested (0 mismatches out of 1600); the gate escapes zero at the first optimizer step and unlocks branch gradients at the second, exactly as predicted; the degenerate configuration exhibits gradients identically zero for the entire 600-step run; surgery cost tracks downstream cone size with r = 0.9992 while graft-plus-invalidation bookkeeping is constant (about 0.75 ms) across insertion depths; and training resumes bit-identically across a real process restart. A flagged preliminary appendix reports first single-seed observations on post-insertion gate dynamics.

Protein fold classification can be approached via sequence-based representations or structural descriptors, but direct comparisons between lightweight handcrafted descriptors and pretrained protein language model embeddings remain limited. We investigate discrete Ricci curvature on Calpha contact graphs as a lightweight structural descriptor for fold classification. Each protein domain is represented by a 22-dimensional fixed-length feature derived from summary statistics and quantiles of Ollivier-Ricci and Forman-Ricci edge curvature distributions. We evaluate on CATH top-10 Topology classification and on the ASTRAL 40%-identity SCOPe top-10 Fold benchmark, comparing against geometry, contact-graph statistics, persistent homology, and mean-pooled ESM-2 (150M) baselines. On both datasets, lightweight structural descriptors substantially outperform mean-pooled ESM-2 embeddings, with a larger performance gap on the ASTRAL 40% SCOPe benchmark. Ricci alone uses 22 dimensions, or 3.4% of the ESM-2 baseline dimensionality, and already outperforms mean-pooled ESM-2 on both datasets. Combining Ricci with persistent homology yields the strongest performance, achieving macro-F1 of 0.71 on CATH and 0.68 on SCOPe with a 112-dimensional feature vector. These results identify a regime where lightweight interpretable graph descriptors offer a practical alternative to pretrained protein language model embeddings.

Automated individual animal re-identification is essential for large-scale biodiversity monitoring; however, field imagery complicates separating identity cues from nuisance variation in pose, illumination, background, resolution, and species-specific morphology. The DS@GT ARC submission to AnimalCLEF 2026 introduces a multi-species image-clustering system for re-identifying Eurasian lynx, fire salamanders, loggerhead sea turtles, and Texas horned lizards. Instead of relying on a single descriptor or nearest-neighbor retrieval, this approach formulates re-identification as species-aware graph construction over candidate image pairs. The pipeline integrates tailored preprocessing, global candidate retrieval, LightGlue-based local verification with multiple keypoint families, LightGBM pair scoring, conservative edge admission, and Leiden community detection. This design directly addresses a primary failure mode of clustering-based re-identification: high-scoring false pairs that act as bridge edges and merge distinct individuals through transitive closure. Across species, ablation studies demonstrate that local feature support, foreground-aware preprocessing, and species-specific backbone selection enhance pair evidence, while graph operating points determine the trade-off between fragmentation and over-merging. The selected submission achieved a public ARI of 0.733 and a private ARI of 0.674, ranking fifth among 230 teams. These results indicate that robust wildlife re-identification requires not only strong visual representations but also calibrated integration of global similarity, local identity markings, neighborhood context, and graph-level constraints. The code can be found at https://github.com/dsgt-arc/animalclef-2026.

Comparing phylogenetic tree topologies is essential for understanding epidemic dynamics, yet biologically meaningful distances such as the Subtree Prune and Regraft (SPR) distance are NP-hard to compute and intractable on large datasets. We investigate whether a Graph Neural Network (GNN) can approximate SPR distances in near-constant time per comparison after training. Our contributions are fourfold. First, we build and publicly release a dataset of 864 phylogenetic trees inferred with UPGMA and Neighbor-Joining over four bacterial species, spanning up to 9{,}500 isolates, together with 388 labelled tree pairs. Second, we establish a reproducible pre-processing pipeline including midpoint re-rooting, which reduces tree depth and supplies the rooting required for exact distance computation and for the model's root-based features. Third, we validate the supervision target: on small trees, where exact SPR is tractable, the unrooted phangorn::SPR.dist heuristic correlates almost perfectly with the exact rooted distance computed by rspr (Pearson $0.98$--$0.99$), making it an excellent monotonic surrogate. Lastly, we train a Siamese Graph Isomorphism Network (GIN) regressor. In-distribution, i.e., held-out trees from the same species and size range as training, it explains roughly 87--90% of the variance ($R^2 \approx 0.87$ on a held-out split; $0.90 \pm 0.19$ under stratified cross-validation), with about four times lower error than a mean-predictor baseline, and shows partial transfer to unseen species ($R^2 \approx 0.37$). Its main limitation is extrapolation to trees larger than those seen in training, where accuracy collapses. The released dataset and the validated heuristic versus exact relationship provide a reproducible basis for scaling learned SPR approximation.

Unsteady aerodynamic phenomena, such as gusts, turbulence, and fluid-structure interactions affect an aircraft during flight. For design, optimisation and certification, it is indispensable to quantify such unsteady aerodynamic effects. Industry-standard computational fluid dynamics methods, such as solving the unsteady Reynolds-averaged Navier-Stokes equations or the linearized frequency domain method, are either computationally expensive or restricted by assumptions like linearity. Once trained, machine learning methods are capable of computing non-linear relationships very fast, making them suitable as surrogate models. By autoregressively applying graph neural networks (GNNs), operating on a discretised spatial domain, spatio-temporal predictions can be made. However, autoregressive GNNs suffer from error accumulation leading to unstable rollouts over time. Here we show that combining GNNs with augmented Neural Ordinary Differential Equations yields temporally stable predictions of the surface forces on a pitching airfoil. We found that our approach, called GNODE, based on Graph Neural Ordinary Differential Equations, provides temporally more stable, spatially smoother, and overall more accurate results than an autoregressive GNN baseline. Tests are conducted on a dataset consisting of a simulations of a pitching airfoil, including transonic shocks, transient behaviour and dynamic non-linearities. Augmenting GNODEs with additional latent dimensions improves the expressivity and accuracy by capturing underlying history effects. The developed method demonstrates an approach that is suitable to model non-linear spatio-temporal systems with exogenous inputs.

Industrial processes often generate complex, interdependent time-series data from multiple sensors across multiple stages, forming complex dependencies among variables and process stages. Effective monitoring and timely anomaly detection of these time series through multivariate time series anomaly detection (MTAD) is crucial for preventing failures and ensuring the reliability of automated systems. Graph neural networks (GNNs) have advanced MTAD by leveraging data-driven graphs to model complex dependencies among variables, effectively capturing relational structures within multivariate time series to enhance anomaly detection performance. However, existing GNN-based approaches often overlook critical process knowledge, and even when this knowledge is considered, seamlessly incorporating it into existing models remains inherently challenging, leading to suboptimal performance. To address this limitation, we propose a knowledge-assisted multi-graph framework for modeling sensor dependencies in multi-stage industrial processes for MTAD, which explicitly incorporates process knowledge into graph learning to enhance dependency modeling and improve anomaly detection performance. Our method constructs three complementary graphs: one purely data-driven and two refined by integrating structural constraints derived from process knowledge. To effectively leverage these graphs for anomaly detection, we employ a multi-graph attention network, enabling a more accurate and robust representation of complex dependencies. Comprehensive experiments on two real-world, multi-stage industrial datasets demonstrate that incorporating process knowledge substantially enhances anomaly detection performance.

Accurate prediction of crystal properties remains a key challenge in computational materials science. While graph neural networks (GNNs) such as CGCNN, MEGNet, ALIGNN, and SchNet have shown strong performance, they primarily represent crystals at the atomic level and implicitly learn local chemical environments through message passing. However, many material properties are governed by coordination polyhedra, the fundamental structural units formed by atoms and their neighboring atoms. To address this limitation, we propose the Coordination Polyhedron Graph Network (CPGN), a multi-scale GNN that jointly learns atomic, bond, and coordination-polyhedron representations. CPGN constructs three coupled graphs: an atom graph encoding elemental and bonding information, a line graph capturing angular interactions, and a coordination polyhedron graph describing Voronoi-derived local environments through corner-, edge-, and face-sharing relationships. Physically meaningful geometric descriptors are incorporated for each polyhedron, while an interleaved message-passing mechanism with bidirectional cross-attention enables effective information exchange across structural levels. Extensive evaluations on the Materials Project, JARVIS-DFT, and QM9 benchmark datasets demonstrate that CPGN outperforms existing state-of-the-art GNN models. It achieves a formation-energy MAE of 0.060 eV/atom and a band-gap MAE of 0.292 eV on the Materials Project, while providing competitive multi-property prediction on JARVIS-DFT and superior HOMO prediction on QM9. The results highlight that explicit modeling of coordination polyhedra improves crystal representation learning and enables accurate, physically interpretable prediction of material properties.

Multimodal-attributed graphs (MAGs), whose nodes carry modalities such as images and text alongside topological structure, now pervade applications including social platforms, e-commerce, and biomedical networks, offering richer semantic signals than single-modality graphs. In practice, such graphs are fragmented across privacy-restricted silos owned by different platforms and institutions, so learning a broadly transferable model over them demands collaborative training that never exposes raw data. This places the task at the intersection of multimodal graph learning and federated learning, yet existing methods cover only one side of it. To address the challenges from these two perspectives, we propose FedGAMMA, casting federated multimodal graph foundation learning as a two-stage semantic-structural alignment problem of federated pre-training and prompt-based fine-tuning. During pre-training, a shared-private semantic enhancer disentangles cross-modal commonality from modality-specific information, aligning it through optimal transport, a topology-aware graph fusion module decouples semantic and structural views via semantic residual graphs and dual positional encodings, and a dual-channel affinity-aware aggregation mechanism estimates client similarity from feature and graph centroids without exposing raw data. During fine-tuning, FedGAMMA adapts the pretrained encoder through lightweight graph-aware prompts, a shared prompt pool with controlled exploration, and channel-wise prompt synchronization. Experiments on twelve multimodal graph datasets show FedGAMMA consistently surpassing a broad range of baselines across downstream tasks, with gains of up to 12.96%. FedGAMMA further outperforms competitive baselines accross multi-domain datasets on multiple tasks with up to 5.71% under few-shot learning scenario.

Graph neural networks (GNNs) frequently encounter group fairness issues, often yielding biased predictions against specific demographic groups defined by sensitive attributes such as gender or race. While this challenge has motivated extensive research, most existing solutions rely on the strong assumption that demographics are fully available. To bypass this strict requirement, a few recent studies have attempted to use predicted demographics as proxies to enforce fairness constraints. However, predicted demographics may be inaccurate, resulting in the failure to improve fairness. In this work, we investigate the problem of graph fairness without demographic information and avoid the utilization of predicted demographics. Motivated by our observation that the gradient distributions of misclassified nodes implicitly encode demographic information, we first propose GradDist, a gradient-based metric that quantifies bias by measuring the distance between local modes within these distributions. To mitigate this bias, we propose Gradient-to-Fairness (Grad2Fair), a gradient-guided approach for group fairness without demographics. Due to the potential demographics in gradients, Grad2Fair directly leverages gradients to debias and eliminates demographic prediction, thereby enabling stable fairness performance. Experiments on several real-world datasets demonstrate the effectiveness of Grad2Fair, as evidenced by superior performance over baselines in most cases. Our code is available at https://github.com/ZzoomD/Grad2Fair.

Egocentric Visual Question Answering (VQA) has attracted widespread attention as an important task for enabling Multimodal Large Language Models (MLLMs) to interact with the real world. However, existing MLLMs struggle to perform effective spatial reasoning in complex egocentric scenes due to their limited spatial perception capabilities. To this end, we introduce Ego Scene Augmentation (ESA), an egocentric spatial perception framework, which actively enhances the spatial perception capabilities from the egocentric perspective, powered by the proposed Ego-element Graph. Our core insight is leveraging the Ego-element Graph as an intermediary representation to augment the egocentric spatial perception of MLLMs via visual foundational models. Specifically, we 1) construct the Ego-element Graph, which encapsulates and integrates egocentric spatial features enabled by visual foundational models; 2) enhance the spatial perception capabilities of MLLMs via the Ego-element Graph for ego-perspective scenes. Our proposed ESA framework presents significant performance improvement on the EgoTextVQA benchmark. We achieve an 8.14% gain on the indoor setting and an 8.72% gain on the outdoor setting. Furthermore, our ESA shows the most impressive performance improvement in the shopping subset of the indoor setting. The project code is publicly available.

We study sparse random geometric graphs generated by connecting pairs of high-dimensional vectors whose inner product exceeds a threshold. The latent vectors are sampled either uniformly from the sphere or from a standard Gaussian distribution. Although every edge appears with probability $p$, the edges are dependent through their shared latent vectors. For the spherical model, at the connectivity scale $np=Ω(\log n)$, we prove $\|A-\mathbb E A\|=O\left(\sqrt{np\log n}+npτ\right)$, with high probability, where $τ$ is the cap threshold. This sharpens the spectral norm bound of Liu, Mohanty, Schramm, and Yang (2023) under weaker assumptions. An analogous result holds for the Gaussian model after removing the fluctuations of the vector norms, yielding improved global synchronization guarantees for the homogeneous Kuramoto model. We then recover the latent geometry from the leading eigenspace. When $np\gg\log n$, both the latent vector and relative Gram matrix errors vanish provided $d\ll np\log(1/p)/\log n$. The required lower dimension is only $d\gg\log(1/p)$ for the spherical model and $d\gg\log^2(1/p)\log n$ for the Gaussian model, improving the recovery guarantees of Li and Schramm (2023). Finally, we prove the first exact recovery result for the Gaussian mixture block model of Li and Schramm (2023). At the optimal connectivity scale $np=Ω(\log n)$, a polynomial-time semidefinite program exactly recovers all labels in a moderate-separation regime, whereas larger separation makes exact recovery impossible because isolated vertices appear with high probability. Our proofs combine orthogonal polynomial expansions, decoupling, and matrix concentration, avoiding the trace-moment arguments used in previous work.

In real-world applications, node classification on graphs often faces the challenge of class imbalance, where majority classes dominate training, resulting in biased model performance. Traditional GNNs often struggle in such scenarios, as they tend to overfit to majority classes while underrepresenting minority classes. Existing solutions, which either prioritize nodes based on class size or synthesize new nodes for minority classes, often fall short of effectively addressing this imbalance issue. This paper introduces an approach to class-imbalanced node classification by utilizing a balanced meta-set for importance measurement, where a training node is considered significant if it enhances model performance under an unbiased setting. Our method identifies important nodes that can counteract class imbalance and utilizes them for model training, allowing for fine-grained and dynamic node selection throughout the training process. We theoretically derive a formula to directly assess node importance, reducing computational overhead and providing an intuitive threshold for node selection. Guided by this metric, we develop a novel framework that filters valuable labeled, unlabeled, and synthetic nodes that enhance model performance in an unbiased context. A key advantage of this framework is its separation of the synthetic node generation process from the filtering process, ensuring compatibility with various node generation methods. Furthermore, we introduce a strategy to construct a high-quality meta-set that closely approximates the overall feature distribution, ensuring robust representation of each class. We evaluate our framework, NodeImport, across multiple datasets using popular GNN architectures, demonstrating its superiority over existing baselines. Our results highlight the flexibility and effectiveness of the framework in mitigating class imbalance, leading to improved outcomes.

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.

Recovering a latent potential from observed flow on a directed graph (a discrete Poisson problem with Dirichlet boundaries) is ill-posed, and the standard fix backfires: ridge regularization shrinks toward a gauge-meaningless origin, collapsing and reversing the recovered ordering ($+0.81\to-0.42$ rank correlation against a planted ground truth). The gauge-invariant graph Dirichlet energy removes the hazard and delivers parameter-insensitivity: the estimate is stable across four orders of magnitude in $λ$, whereas ridge inverts the ordering for every $λ>0$. We prove the reduced solve is SPD and preserves dynamic range exactly where ridge collapses it, and localize absorbing boundaries from flow alone via a Poisson residual. The $H^1$ seminorm is classical; what is new is the gauge diagnosis, the parameter-insensitivity it buys, and an ablation showing the result is robust to the extraction method. On three public clickstream corpora the gauge-invariant estimate retains $28$--$41\%$ of the interior dynamic range while ridge collapses to as little as $0.2\%$. The same gauge invariance carries into graph neural networks -- neutralizing the constant mode per layer prevents the oversmoothing that collapses a deep directed GCN -- linking this classical inverse problem to a central question in graph learning.

Traffic forecasting is highly challenging due to complex and nonlinear spatial and temporal dependencies. Self-attention mechanisms have been widely adopted to model dynamic and long-range dependencies, achieving state-of-the-art performance, but suffer from limited scalability due to quadratic computational and memory complexity. To address this, we propose an Efficient Multi-Attention Graph Network (EMAGN) that linearises the spatial attention mechanism itself, inspired by the theory of fast high-dimensional Gaussian filtering. Two learned clustering matrices C_k and C_v adaptively group key and value vectors into M super-clusters, reducing complexity from O(N^2 d) to O(NMd) without sacrificing the flexibility of attention for dynamic dependency modelling. Experimental results on PEMS-BAY and METR-LA show that EMAGN achieves accuracy within 2.7-3.2% MAE of full-attention GMAN while reducing training time by 32%, inference time by 38%, and GPU memory by 58%. Critically, at K=16 attention heads, full-attention GMAN runs out of memory on a standard 11 GB GPU entirely while EMAGN continues to operate, demonstrating a categorical expansion of feasible model configurations. EMAGN also surpasses Linformer and Performer in both accuracy and efficiency within the same backbone, owing to its traffic-network-aware adaptive clustering.

We present cayleyR, an R package for solving permutation puzzles by detecting cycle intersections in Cayley graphs. The core algorithm performs an iterative bidirectional search: from both the initial and target permutation states, random operation sequences generate cycles in the Cayley graph of the symmetric group Sn; their intersection yields a connecting path. When no direct intersection is found, a distance-guided bridge selection narrows the gap, and the process repeats. The package targets the TopSpin(n,k) puzzle, whose state space is a Cayley graph of Sn generated by a cyclic shift and a prefix reversal. We describe the mathematical framework, the algorithm, and its implementation, which combines a C++ hash-indexed state store with optional Vulkan GPU acceleration. The software is publicly available on CRAN.

In this work, we study various graph partitioning problems under a general demand model. In each such task, we are given a graph $G=(V,E,c,w)$ with a capacity function $c\colon E\to \mathbb{N}$ and a demand function $w\colon V\times V\to \mathbb{N}$. Our main focus is the problem of finding a cut $(S, \bar{S})$ minimizing the quantity $$ψ_w( S ) = \frac{c( S, \bar{S} )}{w( S, V )\cdot w( \bar{S}, V )}.$$ Here, $c( S, \bar{S} )$ is the cost of edges between $S$ and the complement of $S$, $\bar{S}$, and $w( S, V )=w( S )+w( S, \bar{S} )$ is the sum of the internal demand within $S$, $w( S )$, and the demand between vertices of $S$ and $\bar{S}$, $w( S, \bar{S} )$. We call $ψ_w( S )$ the \emph{generalized conductance} of the cut $(S, \bar{S})$, and the task of minimizing $ψ_w( S )$ the Generalized Conductance Problem. Our main contribution is an algorithm with an $\mathcal{O}(\log n)$-approximation guarantee for this objective. Our result is achieved via a two-way reduction: first to the well-known Generalized $k$-Multicut Problem, and then to a constrained variant of the classic Sparsest-Cut Problem, with an additional upper-bound constraint on the amount of demand that may be cut. Moreover, we show that the above procedure can be used to obtain an $\mathcal{O}(\log n)$-bicriteria approximation for Graph Partitioning with Demands, where the goal is to find a minimum-cost subset of edges $C$ such that for every component $H$ of $G\setminus C$, $w( H )\leq ρ\cdot w( V )$. This, in turn, yields an $\mathcal{O}(\log n)$-approximation for Hierarchical Clustering with Demands, the problem of finding a hierarchy of cuts that partitions the graph into increasingly refined clusters. For multiplicative demand functions, we improve these guarantees to $\mathcal{O}(\sqrt{\log n})$ and for trees we get an $\mathcal{O}(1)$-approximation for all of our objectives.

Small language models (SLMs) have shown promise for zero-shot molecular property prediction from SMILES strings, yet they often suffer from structural blindness because sequence representations under-specify key graph-topological cues. We propose a modular Context-Augmented Prompting framework that enables agentic tool use at inference time: a trained GNN expert model provides a predictive hint with confidence, and a GNN extracts an instance-specific explanatory subgraph (e.g., a subgraph SMILES and an accompanying explanatory paragraph). We evaluate three commonly used SLMs on MUTAG and Tox21 under five prompting configurations ranging from SMILES-only to using all available tools at hand. Across two datasets, enriching prompts with graph-derived context yields substantial accuracy gains, often exceeding 25% relative improvement and up to 74% on Tox21. We further validate the functional relevance of the extracted motifs via a necessity-based edge-drop intervention. Despite the observed gains, a persistent gap remains to specialized GNN models, highlighting both the value and limits of text-conditioned reasoning for molecular structure.

Multi-agent language-model systems increasingly route local interactions, yet the runtime interaction graph is often treated as an implementation detail. We study convention formation in open-weight LM populations spanning 1.1B-32B parameters with a naming-game protocol. Restricted first-token scores over tokenizer-safe labels let us measure prompt-conditioned score-state distributions, construct state-similarity graphs, and separate sampled-label agreement from latent state-space consensus. Across controlled interventions, in the main open-weight repair grids, retained partner-label evidence is necessary but not sufficient: homophilous threshold-similarity routing deletes cross-basin exposure and amplifies fragmentation, while bridge-seeking routing often repairs fragmentation when memory is available. In a three-seed mixed four-model grid, threshold-similarity produces no final behavioral or state consensus in 189 setting-seed runs, whereas state-component and label-disagreement bridges recover final behavioral consensus in 14/18 retained-memory runs. Across homogeneous model populations, retained history generally shifts fragmented dynamics toward consensus; the clearest case is Qwen2.5-32B, which reaches stable behavioral and final state consensus in all 18 retained-history well-mixed settings, while threshold-similarity reaches neither form of consensus in 189 settings. Robustness over state thresholds, population size, and vocabulary size preserves the qualitative ordering, and early-window graph-energy features provide useful within-grid diagnostics.

Finite groups are rigid algebraic objects, whose Cayley graphs expose a rich network geometry through which group-theoretic structure can be measured, compared, and learned. In this paper, a dataset of $131{,}406$ Cayley graphs is constructed, covering all groups of order at most $767$ except order $512$, recording exact algebraic labels for group properties together with a broad collection of graph, cycle, distance, and spectral statistics. This census aims to provide novel benchmarks for studying how finite-group properties are reflected in Cayley graph observables. It also yields new enumerative contributions: alongside recovering known OEIS sequences for standard group classes, new sequences for monolithic groups and for groups generated by at most three, four, and five elements are contributed to the OEIS. The accompanying network analysis identifies several empirical regularities and formulates testable conjectures, including relationships involving square clustering, Cayley graph diameter, average graph disorder, and spectral eigengaps of nilpotent groups. Finally, a comparison between classical models, an MLP, and graph neural network architectures is performed for predicting algebraic group properties directly from Cayley graph data. The results show that engineered graph statistics are highly informative, while GNNs, especially GIN and in some fixed-order settings GCN, can recover substantial structural signal directly from the graph. Such that graph-aware architectures show phases of optimality on these group-theoretic graph representations.

Industrial design in fields such as vehicle and aerospace engineering often relies on large-scale numerical simulations to evaluate fluid dynamics performance, which can incur substantial computational costs. Deep neural networks have shown promise in improving simulation efficiency, especially graph neural networks (GNNs), which demonstrate great potential due to their flexibility with unstructured data. However, GNNs face challenges when dealing with tasks involving complex geometries and large-scale meshes. In this paper, we propose the Multi-scale Feature Enhanced Graph Neural Network (ME-GNN) to tackle these challenges. ME-GNN employs a graph neural network with a two-step message-passing mechanism to capture detailed local features effectively. Additionally, it integrates an Attention U-Net with uniform grid discretization, enabling the extraction of both fine and coarse features. The model also utilizes K-hop sampling to construct subgraphs, facilitating efficient training on large datasets while preserving detailed local features. We evaluated ME-GNN on three benchmark datasets and achieved state-of-the-art results: a relative L2 error of 0.0196 for the velocity field and 0.0556 for the surface pressure on ShapeNet-Car, a normalized mean squared error of 0.0033 for the flow field on AirfRANS, and a relative L2 error of 0.1416 for the surface pressure on DrivAerNet.

We introduce a constrained two-view framework for node prediction that aligns structure-conditioned GNN embeddings with a structure-free feature prior learned by an anchor model. Conventional Graph Neural Networks (GNNs) couple feature transformation and neighborhood aggregation, which renders them vulnerable to topology noise and heterophilous connections. To decouple this dependency, our framework utilizes an independent anchor network to capture intrinsic attribute features via a self-supervised reconstruction objective. Furthermore, we propose a Channel-Split Adaptive Gated GNN (CSAG-GNN) that dynamically routes representations between global spectral smoothing and local spatial discrimination through a node-wise gating mechanism. We propose a stable cyclic alternating optimization strategy to solve the resulting coupled bi-level objective, preventing mutual representation drift during training. Empirical results on both homophilous and heterophilous benchmarks show balanced performance gains and structural robustness over competitive baselines.

Graph Foundation Models (GFMs) have emerged as a promising paradigm for learning transferable representations across diverse graph domains. Recent advancements in GFMs have been largely dominated by two paradigms: Graph Neural Network and Large Language Model (LLM) based methods. However, these methods often face a fundamental dilemma between training with limited data and a heavy reliance on textual attributes. Tabular foundation models (TFMs) offer a potential alternative, as node features and representations can be naturally organized in a tabular form. However, how to enable TFMs to effectively capture structural information of graphs remains largely unexplored. The key challenge is to learn a graph-to-table alignment mechanism that enables graph structural understanding for TFMs. To address this, we propose GTAlign, a surprisingly simple yet effective Graph-to-Table Alignment framework for text-free Graph Foundation Model. Specifically, we first pretrain a graph encoder that maps diverse graphs into a unified latent space to capture domain-agnostic graph representations. To further bridge the gap between graph topology and the tabular representation space, we propose community-guided continual pre-training, where pseudo-labels derived from graph community are used to construct few-shot prediction episodes. Lastly, we adapt the graph encoder for an unseen target domain and perform in-context inference. Extensive experiments on five benchmark datasets demonstrate that GTAlign significantly outperforms state-of-the-art baselines on both node and graph classification, offering a simple, effective, and text-free GFM model. Code will be released upon acceptance.

Like many optimization-driven domains, railway rescheduling relies on Mixed-Integer Linear Programming (MILP), yet the field's modeling knowledge is scattered across hundreds of papers in incompatible notations, and narrative surveys organize it subjectively: they classify models by vocabulary rather than by structure, and reproduce neither. We present LP Mining with LP2Graph, a method that mines the structure of published LP and MILP formulations into a reproducible dataset and an induced taxonomy. Its core, LP2Graph, represents each formulation admitted by its canonical grammar as a typed variable--equation graph derived from a single canonical model; once a source is extracted into that model, everything downstream is deterministic. Each source is parsed into this model, homologized, and clustered bottom-up (over variables, then constraints and the objective, then whole-model structure) and, separately, by application domain and solution approach; the resulting groups are labeled by a rule-seeded, self-updating classifier. We validate the representation rather than assume it: per-cluster representatives are regenerated as independent LaTeX and re-solved across CBC, HiGHS and Gurobi against the optimum reported in the source paper. The outcome is an objective, repeatable taxonomy of variables, constraints and model types: the principled foundation on which our raiLPminer line of automated railway-rescheduling model development builds.

Determining whether one finite group is isomorphic to a subgroup of another is a fundamental problem in computational group theory. In this work, we propose a Siamese Graph Neural Network (Siamese GNN) for subgroup prediction using Cayley graph representations of finite groups. Each input group is represented by its undirected Cayley graph and encoded by one branch of a Siamese GNN to produce a graph embedding. The resulting graph embeddings are combined with algebraic features derived directly from the input groups to construct a joint feature vector, which is processed by a fully connected classifier to predict subgroup relations between finite groups. By integrating graph-based structural representations with algebraic features, the proposed framework provides a unified approach for learning subgroup relations from finite groups. Experimental results demonstrate the effectiveness of the proposed architecture, achieving a test accuracy of 95.9% (47/49) on an independent test set and illustrating the potential of geometric deep learning for subgroup prediction.

Graph fraud detection plays a pivotal role in safeguarding the security and integrity of modern digital ecosystems. Graph Neural Networks (GNNs) are commonly adopted for graph fraud detection. However, the practical performance of existing GNN-based detectors is severely hindered by incomplete node attributes and extreme class imbalance within graphs. To mitigate these limitations, this paper proposes a novel framework for Graph Fraud Detection with Grouped attribute completion and Confidence-aware Contrastive learning, named GFD-GC. Specifically, it first imitates heterogeneous neighborhood structures to implement group-wise aggregation, which obtains informative complete node features by capturing fine-grained graph contextual patterns. Further, it introduces a confidence-aware supervised contrastive learning strategy to augment scarce labeled fraud nodes with high confidence pseudo-fraud nodes, which enhances the compactness of fraud representations and their separability from non-fraud nodes. Extensive experiments demonstrate the superiority of the proposed GFD-GC over state-of-the-art baselines on the graph fraud detection task, thereby providing an effective solution for real-world fraud scenarios.

Indoor spatial understanding remains a fundamental challenge for intelligent systems operating in physical environments. Traditional RFID localization techniques typically estimate positions of tags using signal strength measurements but fail to capture higher-order spatial relationships between objects and infrastructure. Recent work on RFID and wireless indoor localization has increasingly emphasized robust learning under noisy propagation, while recent graph-based localization methods demonstrate the value of relational modeling over isolated samples. This paper introduces a graph-based learning framework that leverages Graph Neural Networks (GNNs) to infer spatial geometry from RFID observations. Rather than predicting isolated coordinates, the proposed system models relationships between RFID readings, antennas, and physical structures within an indoor floorplan. This framing is aligned with recent graph-based indoor positioning and graph construction literature, where topology is a first-class source of information for downstream inference. The approach integrates signal strength data, floorplan semantics, and spatial constraints into a graph representation where nodes correspond to RFID observations and edges encode proximity and contextual relationships. A GNN is then trained to predict geometric patterns such as linear trajectories, rectangular bounding regions, and movement paths of objects in space.

Graph neural networks (GNNs) are increasingly deployed in real-world applications where distribution shift is un-avoidable. However, how such shifts affect model calibration, defined as the agreement between predictive confidence and actual accuracy, remains poorly understood, and existing graph calibration methods typically rely on labeled validation data from the deployment distribution. In this work, I present the first closed-form theoretical characterization of GNN calibration under distribution shift. I show that calibration is governed by a single scalar quantity that explicitly depends on structural changes between the source and target graphs, as well as feature quality. This characterization precisely identifies when a model becomes over-confident, under-confident, or remains calibrated, and directly yields the optimal temperature scaling strategy. I further extend the analysis to graph convolutional networks with symmetric normalization, multi-class classification, and covariate shift, and derive a theoretical upper bound on the expected calibration error. My analysis also reveals that, under homogeneous distribution shift, a single global temperature is theoretically optimal, providing a principled explanation for why more complex node-wise recalibration methods offer no additional benefit. Building on these theoretical insights, I propose STAC, a source-free, label-free calibration method. Experiments on synthetic benchmarks demonstrate substantial calibration improvements, while evaluations on five real-world graph datasets show that reliable calibration without target labels remains challenging despite the strong predictive power of the theory.

Self-attention is a ubiquitous primitive in modern sequence models, yet its operator-level geometry is only partially understood. We view a token sequence as a vector field over the token-position graph and identify attention as a connection walk: messages are aggregated by a nonnegative walk matrix while being transported along each edge by a learned linear map. Within this framework, we prove that single-head attention (SHA) is exactly a connection propagation step with constant transport, and that multi-head attention (MHA) is exactly a single edge-dependent connection walk whose effective transport is an attention-gated mixture of headwise transports. We further clarify the conditions under which the corresponding generator reduces to a random-walk connection Laplacian, highlighting the roles of stochasticity, reversibility, and metric-compatible transports. Empirically, we find that trained Transformers across scales (from 124M to 8B) and structures (encoder/decoder) exhibit geometric structure consistent with our theory: effective attention graphs converge to stable geometric operators in deeper layers, learned transports self-organize into approximate scaled isometries, and both phenomena strengthen consistently with scale. Overall, the paper provides a precise connection-walk formalism that links self-attention to classical geometric operators, along with a set of operator-level tools for analyzing transformer models from a geometric perspective.

Brain field potentials are scale-free: their power spectra follow a $1/f^β$ law whose aperiodic exponent $β$ tracks cortical state, and sleep depth in particular is a shift in $β$. We ask whether a transformer endowed with an explicit renormalization-group (RG) inductive bias the RG-Flow Transformer, which couples ordinary self-attention to a scale-aware stream with a learnable anomalous dimension $γ$, block-spin coarse-graining, and an entropy-gated synchronization bridge has an advantage over a parameter-matched vanilla transformer on \emph{real, scarce} EEG. Using the PhysioNet Sleep-EDF corpus with a strict leakage-free by-subject hold-out, we (i) benchmark RG-Flow against a param-matched vanilla transformer and a hierarchy-only ablation on 5-class AASM sleep staging, (ii) sweep the per-subject data budget to look for the inductive-bias crossover predicted when data are scarce, and (iii) test whether RG-Flow's learned $γ$ tracks the measured spectral exponent $β$ out-of-sample a quantity the vanilla model does not possess. Across $5$ subjects and $5$ seeds under leave-one-subject-out cross-validation, RG-Flow and the vanilla transformer are statistically indistinguishable on 5-class staging (77.3% vs 77.0% accuracy; paired $p=0.294$), and the predicted scarce-data crossover does not appear: vanilla is numerically ahead at every data-limited budget. What does separate the models is interpretability RG-Flow recovers the continuous spectral exponent out-of-sample ($β$-recovery $R^2 = 0.416$), a capability the vanilla architecture has no analogue for.

Raag classification is a fundamental MIR task for Hindustani Music, with applications in recommendation, education, archiving, and intelligent search. However, raag clustering remains underexplored, as most existing approaches rely on annotated audio or labeled datasets. While annotated melodic phrases capture characteristic patterns, complete note sequences preserve temporal structure and contextual dependencies, making them more suitable for data-driven modeling. In this work, we introduce RaagBase, a notation-based text dataset consisting of note sequences from compositions by Pt. Bhatkhande. Furthermore we propose a novel graph-based representation of raag structures by modeling the dominance and absence of notes in compositions. Each composition is represented as a node, and the edges between two compositions corresponds the similarities between them based on the note frequency distribution. Further, we apply established graph clustering techniques to identify groups of similar raag compositions. Experimental results demonstrate highly coherent clusters with strong agreement to ground-truth raag labels, thereby validating both the dataset and the proposed representation. The dataset is publicly available at https://anonymous.4open.science/r/RaagBase-5427.

Money laundering threatens financial stability and exposes institutions to penalties, motivating automated detection. Because laundering schemes often emerge through relational patterns, graph neural networks (GNNs) are increasingly used for anti-money laundering (AML). Yet AML GNNs are typically evaluated with aggregate metrics such as overall F1 score, which hide an operational issue: high-activity recipient accounts concentrate many incoming transactions, making suspicious signals harder to isolate and costlier to investigate. We introduce a recipient-degree stratified evaluation that reports standard AML metrics across recipient-context density. Across three datasets (HI-Small, HI-Medium, and AMLSim-32k-5%), it reveals consistent degradation in dense recipient contexts, which we trace to three GNN characteristics: two known limitations that AML amplifies, i.e., (1) multiset non-discriminability and (2) cardinality blindness, and (3) an attention-specific effect: in dense neighborhoods, normalized attention attenuates weak but pattern-relevant multi-hop signals. Guided by this diagnosis, we propose SALT-GNN, a lightweight statistics-aware architecture that fuses degree-aware statistical aggregation with attention at each message-passing layer, so distributional and cardinality information shapes the node states used by subsequent attention steps. Ablations support fusion placement as a key factor in dense-context performance. On HI-Small and HI-Medium, SALT-GNN uses up to 77% fewer parameters than task-specific graph-transformer baselines while improving dense-context F1 score by 3-6 points; on AMLSim-32k-5%, it improves highest-degree F1 score by 16-20 points. The gains hold for both Transformer- and GAT-style attention, indicating that the benefit comes from where statistical and attentional evidence is fused rather than from a specific attention operator.

Graph machine learning provides powerful tools for understanding complex networks and learning meaningful node representations. A central challenge, however, is designing embeddings with minimal distortion of both local and global functionals, such as shortest path lengths. Prior distortion guarantees for distance-preserving embeddings are worst-case in nature, producing overly pessimistic bounds that fail to capture the structure of typical large-scale networks. To address this, we analyze shortest-path approximation via landmark-based embeddings on inhomogeneous random graphs, a general model with type-dependent edge probabilities. By retaining shortest paths to a small set of reference nodes called landmarks, landmark-based methods effectively function as virtual graph spanners, where structural heterogeneity and controlled neighborhood expansion modeled via multi-type branching processes enable significantly tighter dimension-distortion trade-offs than classical worst-case bounds. We extend these guarantees to global, component-wide averages and unify the analysis across finite-type and continuous latent spaces through a novel metric sandwiching framework, establishing universal distortion bounds for general $L^2$ kernel models, including heavy-tailed and power-law networks. Finally, we introduce a GNN-augmented variant that replaces rigid, computationally expensive exact shortest-path queries with flexible, structure-aware neural surrogates. By leveraging the inherent alignment between graph neural message-passing and the dynamic programming principles of shortest-path algorithms, our approach demonstrates that models trained on small-scale random graphs learn to extract universal distance-preserving features, achieving robust generalization to large-scale, real-world networks that match or exceed the fidelity of classical, exact landmark-based embeddings.

Here, we present a platform built on our inverted Graph Transformer Network, IMPRESSION-G2, which can accurately and rapidly reconstruct molecular bonding directly from experimental nuclear magnetic resonance (NMR) spectroscopic information. It comprises three interconnected stages: a one-shot model that predicts bond connectivity between atoms; a structure-correction stage that corrects the predicted structures by removing uncertain bonds and iteratively reassigning them; noise-augmented multi-shot prediction, generating an ensemble of candidate structures, which are ranked to identify the best-fit structure. By integrating a range of $^{1}$H and $^{13}$C NMR data, including two-dimensional (2D) experiments such as COSY, HSQC, and HMBC, the inverse-IMPRESSION platform correctly identifies the structures of 77.8% of molecules with up to 30 heavy atoms (H, C, N, O and F) using simulated NMR data, and 10 of 19 (53%) molecules using experimental NMR data. The experimental structures solved have molecular weights of up to 480 Da and are representative of the complex structures in synthetic and natural products that routinely challenge chemists. The inverse-IMPRESSION framework thus provides the first effective approach for automated molecular structure elucidation using graph-based machine learning on experimental data.

We present an interpretable network-based framework for representing idiomatic and figurative meaning across eight typologically diverse languages, totaling 160 conventional expressions, the large majority of which are idiomatic. Each expression is annotated with binary conceptual features (containment, concealment, emotional, social, etc.) derived from cognitive-linguistic theory, and pairwise Jaccard similarities define a weighted graph. Community detection reveals that idioms cluster by conceptual schema rather than by language, producing a structure consistent with cognitive-linguistic predictions. The conceptual network captures unique semantic information not present in distributional embeddings, can be scaled via automatic annotation with LLMs, improves downstream idiom detection, and remains robust when enriched with corpus frequencies. Cross-lingual transfer experiments show that conceptual proximity alone can identify acceptable translation equivalents across five language families, with substantial gains over embedding-based baselines. Ablation studies demonstrate that all three feature dimensions -- schemas, roles, and valence -- contribute non-redundantly to both the network's organizational properties and its performance on idiom detection, and that specific graph-derived signals (community membership, neighbor similarity) are particularly informative. The framework offers an interpretable, cross-linguistically stable representation of idiomatic meaning, combining theoretical grounding with practical utility.

Graph Neural Networks (GNNs) provide a learning-based framework for approximating graph quantities that are expensive to compute exactly. This paper investigates GNNs for scalable approximation of betweenness and closeness centrality, formulated as a node-ranking problem. Exact centrality values are used as supervision, and ranking quality is evaluated using Kendall's tau rank correlation. We study whether message-passing GNNs can learn transferable structural representations across different graph topologies rather than only fitting the distribution used during training. On unseen Erdos renyi graphs, the proposed models achieve tau = 0.851 for betweenness and tau = 0.894 for closeness. A large-scale betweenness model trained on graphs with N = 5,000 nodes achieves tau = 0.938, demonstrating scalability. Mixed-distribution training on Erdos renyi, Barabasi-Albert, and Gaussian Random Partition graphs improves betweenness transfer across graph families. In contrast, closeness centrality remains more sensitive to community-structured graphs and shows reduced transfer to real-world topologies. Finally, GNN inference achieves up to a 97.7x speedup over exact computation. These results show that mixed-distribution training can improve structural transfer in GNN-based centrality approximation, while identifying closeness centrality's sensitivity to topology as an open challenge.