Graph Neural Networks

Accurate prediction of drug-target binding affinity accelerates drug discovery by prioritizing compounds for experimental validation. Current methods face three limitations: sequence-based approaches discard spatial geometric constraints, structure-based methods fail to exploit hydrogen bond features, and conventional loss functions neglect prediction-target correlation, a key factor for identifying high-affinity compounds in virtual screening. We developed HBGSA (Hydrogen Bond Graph with Self-Attention), a 3.06M-parameter model that encodes hydrogen bond spatial features. HBGSA uses graph neural networks to model hydrogen bond spatial topology with self-attention enhancement and Pearson correlation loss. Experimental results on PDBbind Core Set and CSAR-HiQ dataset demonstrate that HBGSA outperforms baseline methods with strong generalization capability. Ablation studies confirm the effectiveness of hydrogen bond modeling and Pearson correlation loss.

Graph neural networks achieve strong node-classification accuracy, but learned message passing entangles ego attributes, neighborhood smoothing, high-pass graph differences, class geometry, and classifier-boundary effects inside opaque representations. This obscures why nodes are classified as they are and which graph-learning mechanisms a dataset requires. We propose WG-SRC, a white-box signal-subspace probe for prediction and graph dataset diagnosis. WG-SRC replaces learned message passing with a fixed, named graph-signal dictionary containing raw features, row- and symmetric-normalized low-pass propagation, and high-pass graph differences. It combines Fisher coordinate selection, class-wise PCA subspaces, closed-form multi-alpha ridge classification, and validation-based score fusion, so prediction and analysis rely on explicit class subspaces, energy-controlled dimensions, and closed-form linear decisions. As a white-box graph-learning instrument, WG-SRC uses predictive performance to validate its diagnostics. Across six node-classification datasets, it remains competitive with reproduced baselines and achieves positive average gain under aligned splits. Its atlas decomposes behavior into raw-feature, low-pass, high-pass, class-geometric, and ridge-boundary components. The resulting fingerprints distinguish low-pass-dominated Amazon graphs, mixed high-pass and class-geometrically complex Chameleon behavior, and raw- or boundary-sensitive WebKB graphs. Aligned interventions show when high-pass blocks act as removable noise, when raw or graph-derived signals should be preserved, and when ridge correction matters. WG-SRC therefore serves both as a functioning white-box classifier and as a dataset-fingerprinting probe, enabling fingerprint-conditioned analysis of how black-box model components behave under different graph-signal conditions.

We propose Mochi, a Graph Foundation Model that addresses task unification and training efficiency by adopting a meta-learning based training framework. Prior models pre-train with reconstruction-based objectives such as link prediction, and assume that the resulting representations can be aligned with downstream tasks through a separate unification step such as class prototypes. We demonstrate through synthetic and real-world experiments that this procedure, while simple and intuitive, has limitations that directly affect downstream task performance. To address these limitations, Mochi pre-trains on few-shot episodes that mirror the downstream evaluation protocol, aligning the training objective with inference rather than relying on a post-hoc unification step. We show that Mochi, along with its more powerful variant Mochi++, achieves competitive or superior performance compared to existing Graph Foundation Models across 25 real-world graph datasets spanning node classification, link prediction, and graph classification, while requiring 8$\sim$27 times less training time than the strongest baseline.

We study the expressive power of message-passing aggregate-combine-readout graph neural networks (ACR-GNNs). Particularly, we focus on the first-order (FO) properties expressible by this formalism. While a tight logical characterisation remains a difficult open question, we make two contributions towards answering it. First, we show that sum aggregation and readout suffice for GNNs to capture FO properties that cannot be expressed in the logic C2 on both directed and undirected graphs. This strengthens known results by Hauke and Wał{\k e}ga (2026) where aggregation and readout functions are specially crafted for the task. Second, we identify two natural ways of restoring characterisability (with regard to C2) for ACR-GNNs. One option is to limit local aggregation (without imposing restrictions on global readout), whilst the second is to run ACR-GNNs over graphs of bounded degree (but unbounded size). In both cases, the FO properties captured by GNNs are exactly those definable by a formula in graded modal logic with global counting modalities. Our results thus establish an innate lower- and upper-bound in terms of how far (fragments of) C2 can be taken to characterise GNNs, and imply that is indeed the unbounded interaction of aggregation and readout that pushes the logical expressive power of GNNs above C2.

Identifying critical nodes in complex networks is a fundamental task in graph mining. Yet, methods addressing an all-or-nothing coverage mechanics in a bipartite dependency network, a graph with two types of nodes where edges represent dependency relationships across the two groups only, remain largely unexplored. We formalize the CriticalSet problem: given an arbitrary bipartite graph modeling dependencies of items on contributors, identify the set of k contributors whose removal isolates the largest number of items. We prove that this problem is NP-hard and requires maximizing a supermodular set function, for which standard forward greedy algorithms provide no approximation guarantees. Consequently, we model CriticalSet as a coalitional game, deriving a closed-form centrality, ShapleyCov, based on the Shapley value. This measure can be interpreted as the expected number of items isolated by a contributor's departure. Leveraging these insights, we propose MinCov, a linear-time iterative peeling algorithm that explicitly accounts for connection redundancy, prioritizing contributors who uniquely support many items. Extensive experiments on synthetic and large-scale real datasets, including a Wikipedia graph with over 250 million edges, reveal that MinCov and ShapleyCov significantly outperform traditional baselines. Notably, MinCov achieves near-optimal performance, within 0.02 AUC of a Stochastic Hill Climbing metaheuristic, while remaining several orders of magnitude faster.

Vision Graph Neural Networks (ViGs) represent an image as a graph of patch tokens, enabling adaptive, feature-driven neighborhoods. Unlike CNNs with fixed grid biases or Vision Transformers with global token interactions, ViGs rely on dynamic graph convolution: at each layer, a feature-dependent graph is built via k-nearest-neighbor (kNN) search on current patch features, followed by message passing. This per-layer graph construction is the main bottleneck, consuming 50--95% of graph convolution time on CPUs and GPUs, scaling as $O(N^2)$ with the number of patches $N$, and creating a sequential dependency between graph construction and feature updates. We introduce GraphLeap, a simple reformulation that removes this dependency by decoupling graph construction from feature update across layers. GraphLeap performs the feature update at layer $\ell$ using a graph built from the previous layer's features, while simultaneously using the current layer's features to construct the graph for layer $\ell+1$. This one-layer-lookahead graph construction enables concurrent graph construction and message passing. Although using prior-layer features can introduce minor accuracy degradation, lightweight fine-tuning for a few epochs is sufficient to recover the original accuracy. Building on GraphLeap, we present the first end-to-end FPGA accelerator for Vision GNNs. Our streaming, layer-pipelined design overlaps a kNN graph construction engine with a feature update engine, exploits node- and channel-level parallelism, and enables efficient on-chip dataflow without explicit edge-feature materialization. Evaluated on isotropic and pyramidal ViG models on an Alveo U280 FPGA, GraphLeap achieves up to $95.7\times$ speedup over CPU and $8.5\times$ speedup over GPU baselines, demonstrating the feasibility of real-time Vision GNN inference.

While LLMs demonstrate remarkable fluency in narrative generation, existing methods struggle to maintain global narrative coherence, contextual logical consistency, and smooth character development, often producing monotonous scripts with structural fractures. To this end, we introduce PLOTTER, a framework that performs narrative planning on structural graph representations instead of the direct sequential text representations used in existing work. Specifically, PLOTTER executes the Evaluate-Plan-Revise cycle on the event graph and character graph. By diagnosing and repairing issues of the graph topology under rigorous logical constraints, the model optimizes the causality and narrative skeleton before complete context generation. Experiments demonstrate that PLOTTER significantly outperforms representative baselines across diverse narrative scenarios. These findings verify that planning narratives on structural graph representations-rather than directly on text-is crucial to enhance the long context reasoning of LLMs in complex narrative generation.

Ramsey-good graphs are graphs that contain neither a clique of size $s$ nor an independent set of size $t$. We study doubly saturated Ramsey-good graphs, defined as Ramsey-good graphs in which the addition or removal of any edge necessarily creates an $s$-clique or a $t$-independent set. We present a method combining SAT solving with bespoke LLM-generated code to discover infinite families of such graphs, answering a question of Grinstead and Roberts from 1982. In addition, we use LLMs to generate and formalize correctness proofs in Lean. This case study highlights the potential of integrating automated reasoning, large language models, and formal verification to accelerate mathematical discovery. We argue that such tool-driven workflows will play an increasingly central role in experimental mathematics.

Graph Neural Networks (GNNs) excel on relational data, but standard benchmarks unrealistically assume the graph is centrally available. In practice, settings such as Federated Graph Learning, distributed systems, and privacy-sensitive applications involve graph data that are localized, fragmented, noisy, and privacy-leaking. We present a unified framework for this setting. We introduce LoGraB (Local Graph Benchmark), which decomposes standard datasets into fragmented benchmarks using three strategies and four controls: neighborhood radius $d$, spectral quality $k$, noise level $σ$, and coverage ratio $p$. LoGraB supports graph reconstruction, localized node classification, and inter-fragment link prediction, with Island Cohesion. We propose AFR (Adaptive Fidelity-driven Reconstruction), a method for noisy spectral fragments. AFR scores patch quality via a fidelity measure combining a gap-to-truncation stability ratio and structural entropy, then assembles fragments using RANSAC-Procrustes alignment, adaptive stitching, and Bundle Adjustment. Rather than forcing a single global graph, AFR recovers large faithful islands. We prove heat-kernel edge recovery under a separation condition, Davis--Kahan perturbation stability, and bounded alignment error. We establish a Spectral Leakage Proposition: under a spectral-gap assumption, polynomial-time Bayesian recovery is feasible once enough eigenvectors are shared, complementing AFR's deterministic guarantees. Experiments on nine benchmarks show that LoGraB reveals model strengths and weaknesses under fragmentation, AFR achieves the best F1 on 7/9 datasets, and under per-embedding $(ε,δ)$-Gaussian differential privacy, AFR retains 75% of its undefended F1 at $ε=2$. Our anonymous code is available at https://anonymous.4open.science/r/JMLR_submission

We introduce TravelFraudBench (TFG), a configurable benchmark for evaluating graph neural networks (GNNs) on fraud ring detection in travel platform graphs. Existing benchmarks--YelpChi, Amazon-Fraud, Elliptic, PaySim--cover single node types or domain-generic patterns with no mechanism to evaluate across structurally distinct fraud ring topologies. TFG simulates three travel-specific ring types--ticketing fraud (star topology with shared device/IP clusters), ghost hotel schemes (reviewer x hotel bipartite cliques), and account takeover rings (loyalty transfer chains)--in a heterogeneous graph with 9 node types and 12 edge types. Ring size, count, fraud rate, scale (500 to 200,000 nodes), and composition are fully configurable. We evaluate six methods--MLP, GraphSAGE, RGCN-proj, HAN, RGCN, and PC-GNN--under a ring-based split where each ring appears entirely in one partition, eliminating transductive label leakage. GraphSAGE achieves AUC=0.992 and RGCN-proj AUC=0.987, outperforming the MLP baseline (AUC=0.938) by 5.5 and 5.0 pp, confirming graph structure adds substantial discriminative power. HAN (AUC=0.935) is a negative result, matching the MLP baseline. On the ring recovery task (>=80% of ring members flagged simultaneously), GraphSAGE achieves 100% recovery across all ring types; MLP recovers only 17-88%. The edge-type ablation shows device and IP co-occurrence are the primary signals: removing uses_device drops AUC by 5.2 pp. TFG is released as an open-source Python package (MIT license) with PyG, DGL, and NetworkX exporters and pre-generated datasets at https://huggingface.co/datasets/bsajja7/travel-fraud-graphs, with Croissant metadata including Responsible AI fields.

Local gauge symmetry underlies fundamental interactions and strongly correlated quantum matter, yet existing machine-learning approaches lack a general, principled framework for learning under site-dependent symmetries, particularly for intrinsically nonlocal observables. Here we introduce a gauge-equivariant graph neural network that embeds non-Abelian symmetry directly into message passing via matrix-valued, gauge-covariant features and symmetry-compatible updates, extending equivariant learning from global to fully local symmetries. In this formulation, message passing implements gauge-covariant transport across the lattice, allowing nonlocal correlations and loop-like structures to emerge naturally from local operations. We validate the approach across pure gauge, gauge-matter, and dynamical regimes, establishing gauge-equivariant message passing as a general paradigm for learning in systems governed by local symmetry.

Semi-supervised node classification is a foundational task in graph machine learning, yet state-of-the-art Graph Neural Networks (GNNs) are hindered by significant computational overhead and reliance on strong homophily assumptions. Traditional GNNs require expensive iterative training and multi-layer message passing, while existing training-free methods, such as Label Propagation, lack adaptability to heterophilo-us graph structures. This paper presents \textbf{F$^2$LP-AP} (Fast and Flexible Label Propagation with Adaptive Propagation Kernel), a training-free, computationally efficient framework that adapts to local graph topology. Our method constructs robust class prototypes via the geometric median and dynamically adjusts propagation parameters based on the Local Clustering Coefficient (LCC), enabling effective modeling of both homophilous and heterophilous graphs without gradient-based training. Extensive experiments across diverse benchmark datasets demonstrate that \textbf{F$^2$LP-AP} achieves competitive or superior accuracy compared to trained GNNs, while significantly outperforming existing baselines in computational efficiency.

Designing and optimizing multi-agent systems (MAS) is a complex, labor-intensive process of "Agent Engineering." Existing automatic optimization methods, primarily focused on flat prompt tuning, lack the structural awareness to debug the intricate web of interactions in MAS. More critically, these optimizers are static; they do not learn from experience to improve their own optimization strategies. To address these gaps, we introduce Textual Parameter Graph Optimization (TPGO), a framework that enables a multi-agent system to learn to evolve. TPGO first models the MAS as a Textual Parameter Graph (TPG), where agents, tools, and workflows are modular, optimizable nodes. To guide evolution, we derive "textual gradients," structured natural language feedback from execution traces, to pinpoint failures and suggest granular modifications. The core of our framework is Group Relative Agent Optimization (GRAO), a novel meta-learning strategy that learns from historical optimization experiences. By analyzing past successes and failures, GRAO becomes progressively better at proposing effective updates, allowing the system to learn how to optimize itself. Extensive experiments on complex benchmarks like GAIA and MCP-Universe show that TPGO significantly enhances the performance of state-of-the-art agent frameworks, achieving higher success rates through automated, self-improving optimization.

An assurance case is a structured argument document that justifies claims about a system's requirements or properties, which are supported by evidence. In regulated domains, these are crucial for meeting compliance and safety requirements to industry standards. We propose a graph diagnostic framework for analysing the structure and provenance of assurance cases. We focus on two main tasks: (1) link prediction, to learn and identify connections between argument elements, and (2) graph classification, to differentiate between assurance cases created by a state-of-the-art large language model and those created by humans, aiming to detect bias. We compiled a publicly available dataset of assurance cases, represented as graphs with nodes and edges, supporting both link prediction and provenance analysis. Experiments show that graph neural networks (GNNs) achieve strong link prediction performance (ROC-AUC 0.760) on real assurance cases and generalise well across domains and semi-supervised settings. For provenance detection, GNNs effectively distinguish human-authored from LLM-generated cases (F1 0.94). We observed that LLM-generated assurance cases have different hierarchical linking patterns compared to human-authored cases. Furthermore, existing GNN explanation methods show only moderate faithfulness, revealing a gap between predicted reasoning and the true argument structure.

In this paper, we propose a proof-of-concept Graph Neural Network model that can successfully predict network flow-level traffic (NetFlow) by accurately modelling the graph structure and the connection features. We use sliding-windows to split the network traffic in equal-sized heterogeneous bidirectional graphs containing IP, Port, and Connection nodes. We then use the GNN to model the evolution of the graph structure and the connection features. Our approach shows superior results when identifying the Port and IP to which connections attach, while feature reconstruction remains competitive with strong forecasting baselines. Overall, our work showcases the use of GNNs for per-flow NetFlow prediction.

Artificial Intelligence (AI) weather models are improving rapidly, and their forecasts are already competitive with long-established traditional Numerical Weather Prediction (NWP). To build confidence in this new methodology, it is critical that we understand how these predictions are generated. This is a huge challenge as these AI weather models remain largely black boxes. In other areas of Machine Learning (ML), mechanistic interpretability has emerged as a framework for understanding ML predictions by analysing the building blocks responsible for them. Here we present an open-source, highly adaptable tool which incorporates concepts from mechanistic interpretability. The tool organises internal latent representations from the model processor and allows for initial analyses, including cosine similarity and Principal Component Analysis (PCA), enabling the user to identify directions in latent space potentially associated with meteorological features. Applying our tool to the graph neural network GraphCast, we present preliminary case studies for mid-latitude synoptic-scale waves and specific humidity. These demonstrate the tool's ability to identify linear combinations of latent channels that appear to correspond to interpretable features.

Fault location in distribution grids is critical for reliability and minimizing outage durations. Yet, it remains challenging due to partial observability, given sparse measurement infrastructure. Recent works show promising results by combining Recurrent Neural Networks (RNNs) and Graph Neural Networks (GNNs) for spatio-temporal learning. Still, many modern GNN architectures remain untested for this grid application, while existing GNN solutions have not explored GNN topology definitions beyond simply adopting the full grid topology to construct the GNN graph. We address these gaps by (i) systematically comparing a newly proposed graph-forming strategy (measured-only) to the traditional full-topology approach, and (ii) introducing STGNN (Spatio-temporal GNN) models based on GraphSAGE and an improved Graph Attention (GATv2), for distribution grid fault location; (iii) benchmarking them against state-of-the-art STGNN and RNN baselines on the IEEE 123-bus feeder. In our experiments, all evaluated STGNN variants achieve high performance and consistently outperform a pure RNN baseline, with improvements up to 11 percentage points F1. Among STGNN models, the newly explored RGATv2 and RGSAGE achieve only marginally higher F1 scores. Still, STGNNs demonstrate superior stability, with tight confidence intervals (within +/- 1.4%) compared to the RNN baseline (up to +/- 7.5%) across different experiment runs. Finally, our proposed reduced GNN topology (measured-only) shows clear benefits in both (i) model training time (6-fold reduction) and (ii) model performance (up to 11 points F1). This suggests that measured-only graphs offer a more practical, efficient, and robust framework for partially observable distribution grids.

Graph neural networks face two fundamental challenges rooted in the linear structure of Euclidean vector spaces: (1) Current architectures represent geometry through vectors (directions, gradients), yet many tasks require matrix-valued representations that capture relationships between directions-such as how atomic orientations covary in a molecule. These second-order representations are naturally captured by points on the symmetric positive definite matrices (SPD) manifold; (2) Standard message passing applies shared transformations across edges. Sheaf neural networks address this via edge-specific transformations, but existing formulations remain confined to vector spaces and therefore cannot propagate matrix-valued features. We address both challenges by developing the first sheaf neural network operates natively on the SPD manifold. Our key insight is that the SPD manifold admits a Lie group structure, enabling well-posed analogs of sheaf operators without projecting to Euclidean space. Theoretically, we prove that SPD-valued sheaves are strictly more expressive than Euclidean sheaves: they admit consistent configurations (global sections) that vector-valued sheaves cannot represent, directly translating to richer learned representations. Empirically, our sheaf convolution transforms effectively rank-1 directional inputs into full-rank matrices encoding local geometric structure. Our dual-stream architecture achieves SOTA on 6/7 MoleculeNet benchmarks, with the sheaf framework providing consistent depth robustness.

The trust in the predictions of Graph Neural Networks is limited by their opaque reasoning process. Prior methods have tried to explain graph networks via concept-based explanations extracted from the latent representations obtained after message passing. However, these explanations fall short of explaining the message passing process itself. To this aim, we propose the Concept Graph Convolution, the first graph convolution designed to operate on node-level concepts for improved interpretability. The proposed convolutional layer performs message passing on a combination of raw and concept representations using structural and attention-based edge weights. We also propose a pure variant of the convolution, only operating in the concept space. Our results show that the Concept Graph Convolution allows to obtain competitive task accuracy, while enabling an increased insight into the evolution of concepts across convolutional steps.

Graph-based techniques and spectral graph theory have enriched the field of machine learning with a variety of critical advances. A central object in the analysis is the graph Laplacian L, which encodes the structure of the graph. We consider the problem of learning over this Laplacian in a distributed streaming setting, where new edges of the graph are observed in real time by a network of workers. In this setting, it is hard to learn quickly or approximately while keeping a distributed representation of L. To address this challenge, we present a novel algorithm, GSQUEAK, which efficiently sparsifies the Laplacian by maintaining a small subset of effective resistances. We show that our algorithm produces sparsifiers with strong spectral approximation guarantees, all while processing edges in a single pass and in a distributed fashion.

Modern artificial intelligence remains fundamentally divided between the continuous, probabilistic spaces of Foundation Models and the discrete, deterministic structures of Knowledge Graphs. While Retrieval-Augmented Generation (RAG) attempts to connect them by serializing graph data into text, we argue this lexical bridging is merely a superficial patch. In this paper, we formalize the underlying structural and geometric friction as the \textit{Impedance Mismatch}. By categorizing current neuro-symbolic integration strategies into a three-tiered hierarchy, we demonstrate that neither surface-level prompt injection nor continuous representation alignment can preserve the strict logical motifs required for reliable multi-hop reasoning. We define the specific mathematical limits, such as the Lexical Bottleneck and Topological Collapse, that show current architectures will eventually hallucinate or conflate semantic nodes. To achieve true semantic fusion, we propose a rigorous theoretical roadmap. We advocate for natively internalizing discrete symbolic structures through Structured Residual Streams, utilizing Vector Symbolic Architectures for latent sub-graph injection, and performing model updates via Orthogonal Subspace Editing. This actionable framework paves the way for models that seamlessly fuse the precision of symbolic logic with the expressivity of parametric memory.

In an election where $n$ voters rank $m$ candidates, a Condorcet winning set is a committee of $k$ candidates such that for any outside candidate, a majority of voters prefer some committee member. Condorcet's paradox shows that some elections admit no Condorcet winning sets with a single candidate (i.e., $k=1$), and the same can be shown for $k=2$. On the other hand, recent work proves that a set of size $k=5$ exists for every election. This leaves an important theoretical gap between the best known lower bound $(k\geq 3)$ and upper bound $(k \leq 5)$ for the number of candidates needed to guarantee existence. We aim to close the gap between the existence guarantees and impossibility results for Condorcet winning sets. We explore an automated reasoning approach to tighten these bounds. We design a mixed-integer linear program (MILP) to search for elections that would serve as counter-examples to conjectured bounds. We employ a number of optimizations, such as symmetry breaking, subsampling, and constraint generation, to enhance the search and model effectively infinite electorates. Furthermore, we analyze the dual of the linear programming relaxation as a path towards obtaining a new upper bound. Despite extensive search on moderate-sized elections, we fail to find any election requiring a committee larger than size 3. Motivated by our experimental results in this direction, we simplify the dual linear program and formulate a conjecture which, if true, implies that a winning set of size 4 always exists. Our automated reasoning results provide strong empirical evidence that the Condorcet dimension of any election may be smaller than currently known upper bounds, at least for small instances. We offer a general-purpose framework for searching elections in ranked voting and a new, concrete analytical path via duality toward proving that smaller committees suffice.

The consensus that GCN, GraphSAGE, GAT, and EvolveGCN outperform feature-only baselines on the Elliptic Bitcoin Dataset is widely cited but has not been rigorously stress-tested under a leakage-free evaluation protocol. We perform a seed-matched inductive-versus-transductive comparison and find that this consensus does not hold. Under a strictly inductive protocol, Random Forest on raw features achieves F1 = 0.821 and outperforms all evaluated GNNs, while GraphSAGE reaches F1 = 0.689 +/- 0.017. A paired controlled experiment reveals a 39.5-point F1 gap attributable to training-time exposure to test-period adjacency. Additionally, edge-shuffle ablations show that randomly wired graphs outperform the real transaction graph, indicating that the dataset's topology can be misleading under temporal distribution shift. Hybrid models combining GNN embeddings with raw features provide only marginal gains and remain substantially below feature-only baselines. We release code, checkpoints, and a strict-inductive protocol to enable reproducible, leakage-free evaluation.

Graph representation learning has achieved notable success in encoding graph-structured data into latent vector spaces, enabling a wide range of downstream tasks. However, these node representations remain opaque and difficult to interpret. Existing explainability methods primarily focus on supervised settings or on explaining individual representation dimensions, leaving a critical gap in explaining the overall structure of node representations. In this paper, we propose TACENR (Task-Agnostic Contrastive Explanations for Node Representations), a local explanation method that identifies not only attribute features but also proximity and structural ones that contribute the most in the representation space. TACENR builds on contrastive learning, through which we learn a similarity function in the representation space, revealing which are the features that play an important role in the representation of a node. While our focus is on task-agnostic explanations, TACENR can be applied to supervised scenarios as well. Experimental results demonstrate that proximity and structural features play a significant role in shaping node representations and that our supervised variant performs comparably to existing task-specific approaches in identifying the most impactful features.

Graph-theoretic approaches offer simplicity, interpretability, and low computational cost for molecular property prediction. Among these, the model proposed by Mukwembi and Nyabadza, based on the external activity $D(G)$ and internal activity $ζ(G)$ indices, achieved strong results on a small flavonoid dataset. However, its ability to generalize to larger and chemically diverse datasets has not been tested. This study evaluates the baseline $D(G)$-$ζ(G)$ polynomial model on five benchmark datasets from MoleculeNet, covering biological activity (BACE, 1,513 molecules), lipophilicity (LogP synthetic, 14,610 molecules; LogP experimental, 753 molecules), aqueous solubility (ESOL, 1,128 molecules), and hydration free energy (SAMPL, 642 molecules). The baseline model achieves an average $R^2 = 0.24$, confirming limited transferability. To address this, a systematic enhancement framework is proposed, progressively incorporating Ridge regularization, additional graph descriptors, physicochemical properties, ensemble learning with Gradient Boosting, Lasso feature selection, and a hybrid approach combining topological indices with Morgan fingerprints. The enhanced models raise the average best $R^2$ to 0.79, with individual improvements ranging from 165% to 274%. All improvements are statistically significant ($p < 0.001$). A direct comparison with a Graph Convolutional Network under identical experimental conditions shows that the enhanced classical models match or outperform deep learning on all five datasets. Comparison with the recent GNN+PGM hybrid of Djagba et al.\ further confirms competitiveness, with the enhanced models achieving the best results on two datasets and tying on one. The entire framework requires no GPU, trains in under five minutes, and uses only open-source tools, making it accessible for researchers in resource-limited settings.

Graph neural networks (GNNs) are the standard for learning on graphs, yet they have limited expressive power, often expressed in terms of the Weisfeiler-Leman (WL) hierarchy or within the framework of first-order logic. In this context, topological neural networks (TNNs) have recently emerged as a promising alternative for graph representation learning. By incorporating higher-order relational structures into message-passing schemes, TNNs offer higher representational power than traditional GNNs. However, a fundamental question remains open: what is the logical expressiveness of TNNs? Answering this allows us to characterize precisely which binary classifiers TNNs can represent. In this paper, we address this question by analyzing isomorphism tests derived from the underlying mechanisms of general TNNs. We introduce and investigate the power of higher-order variants of WL-based tests for combinatorial complexes, called $k$-CCWL test. In addition, we introduce the topological counting logic (TC$_k$), an extension of standard counting logic featuring a novel pairwise counting quantifier $\exists^{N}(x_i,x_j)\, \varphi(x_i,x_j),$ which explicitly quantifies pairs $(x_i, x_j)$ satisfying property $\varphi$. We rigorously prove the exact equivalence: $\text{k-CCWL} \equiv \text{TC}_{k{+}2} \equiv \text{Topological }(k{+}2)\text{-pebble game}.$ These results establish a logical expressiveness theory for TNNs.

Heterophily is a prevalent property of real-world graphs and is well known to impair the performance of homophilic Graph Neural Networks (GNNs). Prior work has attempted to adapt GNNs to heterophilic graphs through non-local neighbor extension or architecture refinement. However, the fundamental reasons behind misclassifications remain poorly understood. In this work, we take a novel perspective by examining recurring inductive subgraphs, empirically and theoretically showing that they act as spurious shortcuts that mislead GNNs and reinforce non-causal correlations in heterophilic graphs. To address this, we adopt a causal inference perspective to analyze and correct the biased learning behavior induced by shortcut inductive subgraphs. We propose a debiased causal graph that explicitly blocks confounding and spillover paths responsible for these shortcuts. Guided by this causal graph, we introduce Causal Disentangled GNN (CD-GNN), a principled framework that disentangles spurious inductive subgraphs from true causal subgraphs by explicitly blocking non-causal paths. By focusing on genuine causal signals, CD-GNN substantially improves the robustness and accuracy of node classification in heterophilic graphs. Extensive experiments on real-world datasets not only validate our theoretical findings but also demonstrate that our proposed CD-GNN outperforms state-of-the-art heterophily-aware baselines.

Heterogeneous graphs have attracted increasing attention for modeling multi-typed entities and relations in complex real-world systems. Multi-label node classification on heterogeneous graphs is challenging due to structural heterogeneity and the need to learn shared representations across multiple labels. Existing methods typically adopt either flexible attention mechanisms or meta-path constrained anchoring, but in heterogeneous multi-label prediction they often suffer from semantic dilution or coverage constraint. Both issues are further amplified under multi-label supervision. We present a theoretical analysis showing that as heterogeneous neighborhoods expand, the attention mass allocated to task-critical (primary) neighborhoods diminishes, and that meta-path constrained aggregation exhibits a dilemma: too few meta-paths intensify coverage constraint, while too many re-introduce dilution. To resolve this coverage-anchoring conflict, we propose FOCAL: Fusion Of Coverage and Anchoring Learning, with two components: coverage-oriented attention (COA) for flexible, unconstrained heterogeneous context aggregation, and anchoring-oriented attention (AOA) that restricts aggregation to meta-path-induced primary semantics. Our theoretical analysis and experimental results further indicates that FOCAL has a better performance than other state-of-the-art methods.

One of the most challenging problems in graph machine learning is generalizing across graphs with diverse properties. Graph neural networks (GNNs) face a fundamental limitation: they require separate training for each new graph, preventing universal generalization across diverse graph datasets. A critical challenge facing GNNs lies in their reliance on labeled training data for each individual graph, a requirement that hinders the capacity for universal node classification due to the heterogeneity inherent in graphs -- differences in homophily levels, community structures, and feature distributions across datasets. Inspired by the success of large language models (LLMs) that achieve in-context learning through massive-scale pre-training on diverse datasets, we introduce NodePFN. This universal node classification method generalizes to arbitrary graphs without graph-specific training. NodePFN learns posterior predictive distributions (PPDs) by training only on thousands of synthetic graphs generated from carefully designed priors. Our synthetic graph generation covers real-world graphs through the use of random networks with controllable homophily levels and structural causal models for complex feature-label relationships. We develop a dual-branch architecture combining context-query attention mechanisms with local message passing to enable graph-aware in-context learning. Extensive evaluation on 23 benchmarks demonstrates that a single pre-trained NodePFN achieves 71.27 average accuracy. These results validate that universal graph learning patterns can be effectively learned from synthetic priors, establishing a new paradigm for generalization in node classification.

Current AI-assisted programming tools are predominantly linear and chat-based, which deviates from the iterative and branching nature of programming itself. Our preliminary study with developers using AI assistants suggested that they often struggle to explore alternatives, manage prompting sequences, and trace changes. Informed by these insights, we created EvoGraph, an IDE plugin that integrates AI interactions and code changes as a lightweight and interactive development graph. EvoGraph automatically records a branching AI-assisted coding history and allows developers to manipulate the graph to compare, merge, and revisit prior collaborative AI programming states. Our user study with 20 participants revealed that EvoGraph addressed developers' challenges identified in our preliminary study while imposing lower cognitive load. Participants also found the graph-based representation supported safe exploration, efficient iteration, and reflection on AI-generated changes. Our work highlights design opportunities for tools to help developers make sense of and act on their problem-solving progress in the emerging AI-mediated programming context.

The reasoning process of Graph Neural Networks is complex and considered opaque, limiting trust in their predictions. To alleviate this issue, prior work has proposed concept-based explanations, extracted from clusters in the model's node embeddings. However, a limitation of concept-based explanations is that they only explain the node embedding space and are obscured by pooling in graph classification. To mitigate this issue and provide a deeper level of understanding, we propose the Subgraph Concept Network. The Subgraph Concept Network is the first graph neural network architecture that distils subgraph and graph-level concepts. It achieves this by performing soft clustering on node concept embeddings to derive subgraph and graph-level concepts. Our results show that the Subgraph Concept Network allows to obtain competitive model accuracy, while discovering meaningful concepts at different levels of the network.

Smooth functions on graphs have wide applications in manifold and semi-supervised learning. In this paper, we study a bandit problem where the payoffs of arms are smooth on a graph. This framework is suitable for solving online learning problems that involve graphs, such as content-based recommendation. In this problem, each item we can recommend is a node and its expected rating is similar to its neighbors. The goal is to recommend items that have high expected ratings. We aim for the algorithms where the cumulative regret with respect to the optimal policy would not scale poorly with the number of nodes. In particular, we introduce the notion of an effective dimension, which is small in real-world graphs, and propose two algorithms for solving our problem that scale linearly and sublinearly in this dimension. Our experiments on real-world content recommendation problem show that a good estimator of user preferences for thousands of items can be learned from just tens of nodes evaluations.

Retrieval-augmented generation (RAG) remains unreliable in long-form settings, where retrieved evidence is noisy or contradictory, making it difficult for RAG pipelines to maintain factual consistency. Existing approaches focus on retrieval expansion or verification during generation, leaving conflict resolution entangled with generation. To address this limitation, we propose ArbGraph, a framework for pre-generation evidence arbitration in long-form RAG that explicitly resolves factual conflicts. ArbGraph decomposes retrieved documents into atomic claims and organizes them into a conflict-aware evidence graph with explicit support and contradiction relations. On top of this graph, we introduce an intensity-driven iterative arbitration mechanism that propagates credibility signals through evidence interactions, enabling the system to suppress unreliable and inconsistent claims before final generation. In this way, ArbGraph separates evidence validation from text generation and provides a coherent evidence foundation for downstream long-form generation. We evaluate ArbGraph on two widely used long-form RAG benchmarks, LongFact and RAGChecker, using multiple large language model backbones. Experimental results show that ArbGraph consistently improves factual recall and information density while reducing hallucinations and sensitivity to retrieval noise. Additional analyses show that these gains are evident under conflicting or ambiguous evidence, highlighting the effectiveness of evidence-level conflict resolution for improving the reliability of long-form RAG. The implementation is publicly available at https://github.com/1212Judy/ArbGraph.

Knowledge Graphs (KGs) are composed of triples, and the goal of Knowledge Graph Completion (KGC) is to infer the missing factual triples. Traditional KGC tasks predict missing elements in a triple given one or two of its elements. As a more realistic task, the Triple Set Prediction (TSP) task aims to infer the set of missing triples conditioned only on the observed knowledge graph, without assuming any partial information about the missing triples. Existing TSP methods predict the set of missing triples in a triple-by-triple manner, falling short in capturing the dependencies among the predicted triples to ensure consistency. To address this issue, we propose a novel discrete diffusion model termed DiffTSP that treats TSP as a generative task. DiffTSP progressively adds noise to the KG through a discrete diffusion process, achieved by masking relational edges. The reverse process then gradually recovers the complete KG conditioned on the incomplete graph. To this end, we design a structure-aware denoising network that integrates a relational context encoder with a relational graph diffusion transformer for knowledge graph generation. DiffTSP can generate the complete set of triples in a one-pass manner while ensuring the dependencies among the predicted triples. Our approach achieves state-of-the-art performance on three public datasets. Code: https://github.com/ADMIS-TONGJI/DiffTSP.

Small language models fine-tuned for graph property estimation have demonstrated strong in-distribution performance, yet their generalization capabilities beyond training conditions remain poorly understood. In this work, we systematically investigate the boundaries of structural inference in fine-tuned small language models along two generalization axes - graph size and graph family distribution - and assess domain-learning capability on real-world graph benchmarks. Using a controlled experimental setup with three instruction-tuned models in the 3-4B parameter class and two graph serialization formats, we evaluate performance on graphs substantially larger than the training range and across held-out random graph families. Our results show that fine-tuned models maintain strong ordinal consistency across structurally distinct graph families and continue to rank graphs by structural properties on inputs substantially larger than those seen during training, with distinct architecture-specific degradation profiles. These findings delineate where fine-tuned small language models generalize reliably, providing empirical grounding for their use in graph-based reasoning tasks.

Sketch-based 3D shape retrieval (SBSR) aims to retrieve 3D shapes that are consistent with the category of the input hand-drawn sketch. The core challenge of this task lies in two aspects: existing methods typically employ simplified aggregation strategies for independently encoded 3D multi-view features, which ignore the geometric relationships between views and multi-level details, resulting in weak 3D representation. Simultaneously, traditional SBSR methods are constrained by visible category limitations, leading to poor performance in zero-shot scenarios. To address these challenges, we propose Multi-View Hierarchical Graph Neural Network (MV-HGNN), a novel framework for SBSR. Specifically, we construct a view-level graph and capture adjacent geometric dependencies and cross-view message passing via local graph convolution and global attention. A view selector is further introduced to perform hierarchical graph coarsening, enabling a progressively larger receptive field for graph convolution and mitigating the interference of redundant views, which leads to more discriminate discriminative hierarchical 3D representation. To enable category agnostic alignment and mitigate overfitting to seen classes, we leverage CLIP text embeddings as semantic prototypes and project both sketch and 3D features into a shared semantic space. We use a two-stage training strategy for category-level retrieval and a one-stage strategy for zero-shot retrieval under the same model architecture. Under both category-level and zero-shot settings, extensive experiments on two public benchmarks demonstrate that MV-HGNN outperforms state-of-the-art methods.

Large Language Models (LLMs) have shown strong potential for recommendation (LLMRec) due to their powerful reasoning and generalization abilities. However, effectively aligning the textual semantics modeled by LLMs with the collaborative signals remains a key challenge. Existing methods either translate collaborative information into textual prompts or inject pre-trained embeddings into the LLM, both of which treat structural information as static input and fail to capture high-order relational dependencies. To bridge this gap, we propose GraphLoRA, a novel framework that generalizes low-rank adaptation from independent to structure-aware propagation. GraphLoRA embeds a trainable graph message-passing network within the low-rank adaptation pathway, enabling structural signals to propagate through the parameter space. This design allows collaborative topology to explicitly guide parameter updates, fostering deep integration between graph-structured and textual semantic information. Extensive experiments on multiple benchmarks demonstrate that GraphLoRA not only outperforms state-of-the-art LLM-based recommendation methods but also achieves superior generalization, effectively balancing structural reasoning capability with computational efficiency. Code is available at \href{https://github.com/wgj15965/GraphLoRA}{https://github.com/wgj15965/GraphLoRA}.

The advent of Large Language Models (LLMs) has fundamentally reshaped the way we interact with graphs, giving rise to a new paradigm called GraphLLM. As revealed in recent studies, graph learning can benefit from LLMs. However, we observe limited benefits when we directly utilize LLMs to make predictions for graph-related tasks within GraphLLM paradigm, which even yields suboptimal results compared to conventional GNN-based approaches. Through in-depth analysis, we find this failure can be attributed to LLMs' limited capability for processing graph data and their tendency to overlook graph information. To address this issue, we propose LoReC (Look, Remember, and Contrast), a novel plug-and-play method for GraphLLM paradigm, which enhances LLM's understanding of graph data through three stages: (1) Look: redistributing attention to graph; (2) Remember: re-injecting graph information into the Feed-Forward Network (FFN); (3) Contrast: rectifying the vanilla logits produced in the decoding process. Extensive experiments demonstrate that LoReC brings notable improvements over current GraphLLM methods and outperforms GNN-based approaches across diverse datasets. The implementation is available at https://github.com/Git-King-Zhan/LoReC.

Persistent homology (PH) encodes global information, such as cycles, and is thus increasingly integrated into graph neural networks (GNNs). PH methods in GNNs typically traverse an increasing sequence of subgraphs. In this work, we first expose limitations of this inclusion procedure. To remedy these shortcomings, we analyze contractions as a principled topological operation, in particular, for graph representation learning. We study the persistence of contraction sequences, which we call Contraction Homology (CH). We establish that forward PH and CH differ in expressivity. We then introduce Hourglass Persistence, a class of topological descriptors that interleave a sequence of inclusions and contractions to boost expressivity, learnability, and stability. We also study related families parametrized by two paradigms. We also discuss how our framework extends to simplicial and cellular networks. We further design efficient algorithms that are pluggable into end-to-end differentiable GNN pipelines, enabling consistent empirical improvements over many PH methods across standard real-world graph datasets. Code is available at \href{https://github.com/Aalto-QuML/Hourglass}{this https URL}.

Text-attributed graphs integrate semantic information of node texts with topological structure, offering significant value in various applications such as document classification and information extraction. Existing approaches typically encode textual content using language models (LMs), followed by graph neural networks (GNNs) to process structural information. However, during the LM-based text encoding phase, most methods not only perform semantic interaction solely at the word-token granularity, but also neglect the structural dependencies among texts from different nodes. In this work, we propose DuConTE, a dual-granularity text encoder with topology-constrained attention. The model employs a cascaded architecture of two pretrained LMs, encoding semantics first at the word-token granularity and then at the node granularity. During the self-attention computation in each LM, we dynamically adjust the attention mask matrix based on node connectivity, guiding the model to learn semantic correlations informed by the graph structure. Furthermore, when composing node representations from word-token embeddings, we separately evaluate the importance of tokens under the center-node context and the neighborhood context, enabling the capture of more contextually relevant semantic information. Extensive experiments on multiple benchmark datasets demonstrate that DuConTE achieves state-of-the-art performance on the majority of them.

Equality saturation (EqSat) is a powerful optimization paradigm that compactly represents many equivalent programs in an e-graph and delays commitment until extraction selects a lowest-cost program. Making EqSat effective, therefore, requires not only domain-specific rewrite rules but also domain-specific strategies. Today, much of this strategy design is still manual, making it a major obstacle to automating e-graph-based compilers. Recent rule-synthesis frameworks can automatically infer large rewrite vocabularies from semantic specifications, but they also enlarge the rewrite space and further exacerbate e-graph explosion. Although large language models (LLMs) make automated strategy synthesis plausible, directly evolving backend code remains ineffective in practice. The search lacks reusable strategy abstractions and actionable feedback, and can easily trigger e-graph explosion or converge to poor designs. We present EggMind, an LLM-guided, end-to-end framework for synthesizing reusable EqSat strategies. At its core, EggMind introduces a domain-specific language, EqSatL, to represent EqSat strategies as explicit and inspectable artifacts. It then proposes an LLM-guided agentic workflow, equipped with novel techniques including proof-derived rewrite motif caching and tractability guidance, to search efficiently for high-quality strategies while keeping synthesis stable under e-graph growth. Evaluation shows that EggMind substantially improves the resource-quality trade-off on vectorization benchmarks, reducing final cost by 45.1% and peak RAM by 69.1% relative to full EqSat. We further show that the same methodology transfers effectively to an XLA-based tensor compiler, and demonstrate its practical potential in a logic-synthesis case study with augmented rewrite spaces.

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

Copy-move forgery, where a region within an image is duplicated to hide or fabricate content, remains a persistent threat to visual media integrity. We introduce GraphSpecForge, a training-free framework that detects copy-move forgery by analysing the spectral structure of attention graphs from a pretrained Stable Diffusion U-Net. Our central insight is that copy-move manipulation induces approximate subgraph duplication in the self-attention graph, leading to measurable spectral redistribution in the normalized graph Laplacian. We formalise this link with perturbation-based arguments and build an image-level anomaly detector using Wasserstein distances between per-image Laplacian spectra and an authentic reference distribution. We evaluate GraphSpecForge on four copy-move benchmarks without forgery-specific retraining. On RecodAI-LUC (5,128 images), our best configuration achieves AUROC = 0.606 (95% CI: 0.580-0.638; permutation p = 0.005), and the normalized Laplacian outperforms raw attention spectra by +0.057 AUROC. On MICC-F220, CoMoFoD, and COVERAGE, the same pipeline attains AUROCs of 0.752, 0.774, and 0.673, respectively; on CoMoFoD it also reaches AUPRC = 0.833, balanced accuracy = 0.712, MCC = 0.499, and TPR@1%FPR = 32.5%. Additional ablation and falsification experiments confirm the signal's specificity and sensitivity to manipulation strength, while null-graph controls rule out trivial-statistic explanations.

Node classification on text-attributed graphs (TAGs) is a fundamental task with broad applications in citation analysis, social networks, and recommendation systems. Current GNN-based approaches suffer from shallow text encoding and heavy dependence on labeled data, limiting their effectiveness in label-scarce settings. While large language models (LLMs) naturally address the text understanding gap with deep semantic reasoning, existing LLM-for-graph methods either still require abundant labels during training or fail to exploit the rich structural signals freely available in graph topology. Our key observation is that, in many real-world TAGs, edges predominantly connect similar nodes under the homophily principle, meaning graph topology inherently encodes class structure without any labels. Building on this insight, we reformulate node classification as a link prediction task and present HopRank, a fully self-supervised LLM-tuning framework for TAGs. HopRank constructs preference data via hierarchical hop-based sampling and employs adaptive preference learning to prioritize informative training signals without any class labels. At inference, nodes are classified by predicting their connection preferences to labeled anchors, with an adaptive early-exit voting scheme to improve efficiency. Experiments on three TAG benchmarks show that HopRank matches fully-supervised GNNs and substantially outperforms prior graph-LLM methods, despite using zero labeled training data.

Current knowledge graph (KG) construction methods are confirmatory, focusing on recovering known relationships rather than identifying novel or context-dependent nodes. This paper proposes a phenotype-driven and evidence-governed framework that shifts the paradigm toward structured hypothesis discovery and controlled KG expansion. The approach integrates graph neural networks (GNNs) for phenotype discovery, causal inference, probabilistic reasoning and large language models (LLMs) for hypothesis generation and claim extraction within a unified pipeline. The framework prioritizes relationships that are both structurally supported by data and underexplored in the literature. KG expansion is formulated as a multi-objective optimization problem, where candidate claims are jointly evaluated in terms of relevance, structural validation and novelty. Pareto-optimal selection enables the identification of non-dominated claims that balance confirmation and discovery, avoiding trivial or redundant knowledge inclusion. Experiments on heterogeneous population datasets demonstrate that the proposed framework produces more interpretable phenotypes, reveals context-dependent causal structures and generates high-quality claims that align with both data and scientific evidence. Compared to rule-based and LLM-only baselines, the method achieves the best trade-off across plausibility, novelty, validation and relevance. In retrieval-augmented settings, it significantly improves performance (Recall@5=0.98) while reducing hallucination rates (0.05), highlighting its effectiveness in grounding LLM outputs.

The paper considers the computation of L1 regularization paths in a state space setting, which includes L1 regularized Kalman smoothing, linear SVM, LASSO, and more. The paper proposes two new algorithms, which are duals of each other; the first algorithm applies to L1 regularization of independent variables while the second applies to L1 regularization of dependent variables. The heart of the proposed algorithms is parametric Gaussian message passing (i.e., Kalman-type forward-backward recursions) in the pertinent factor graphs. The proposed methods are broadly applicable, they (usually) require only matrix multiplications, and their complexity can be competitive with prior methods in some cases.

Low-altitude Gaussian splatting (LAGS) facilitates 3D scene reconstruction by aggregating aerial images from distributed drones. However, as LAGS prioritizes maximizing reconstruction quality over communication throughput, existing low-altitude resource allocation schemes become inefficient. This inefficiency stems from their failure to account for image diversity introduced by varying viewpoints. To fill this gap, we propose a groupwise heterogeneous graph neural network (GW-HGNN) for LAGS resource allocation. GW-HGNN explicitly models the non-uniform contribution of different image groups to the reconstruction process, thus automatically balancing data fidelity and transmission cost. The key insight of GW-HGNN is to transform LAGS losses and communication constraints into graph learning costs for dual-level message passing. Experiments on real-world LAGS datasets demonstrate that GW-HGNN significantly outperforms state-of-the-art benchmarks across key rendering metrics, including PSNR, SSIM, and LPIPS. Furthermore, GW-HGNN reduces computational latency by approximately 100x compared to the widely-used MOSEK solver, achieving millisecond-level inference suitable for real-time deployment.

Accurate traffic forecasting is crucial for intelligent transportation systems, supporting effective traffic management, congestion reduction, and informed urban planning. However, traditional models often fail to adequately capture the intricate spatio-temporal dependencies present in traffic data. To overcome these limitations, we introduce GAMMA-Net, a novel approach that integrates Graph Attention Networks (GAT) with multi-axis Selective State Space Models (Mamba). The GAT component uses a self-attention mechanism to dynamically adjust the influence of nodes within the traffic network, enabling adaptive spatial dependency modeling based on real-time conditions. Simultaneously, the Mamba module efficiently models long-term temporal and spatial dynamics without the heavy computational cost of conventional recurrent architectures. Extensive experiments on several benchmark traffic datasets, including METR-LA, PEMS-BAY, PEMS03, PEMS04, PEMS07, and PEMS08, show that GAMMA-Net consistently outperforms existing state-of-the-art models across different prediction horizons, achieving up to a 16.25% reduction in Mean Absolute Error (MAE) compared to baseline models. Ablation studies highlight the critical contributions of both the spatial and temporal components, emphasizing their complementary role in improving prediction accuracy. In conclusion, the GAMMA-Net model sets a new standard in traffic forecasting, offering a powerful tool for next-generation traffic management and urban planning. The code for this study is available at https://github.com/hdy6438/GAMMA-Net

Quantum error mitigation (QEM) provides a practical route for estimating reliable observables on noisy intermediate-scale quantum (NISQ) devices. Traditional QEM strategies, including zero-noise extrapolation (ZNE) and Clifford data regression (CDR), rely on noise scaling or global regression, and their performance is constrained by the exponential growth of the system degrees of freedom. We construct a graph-enhanced mitigation (GEM) framework, which incorporates physical information into the model representation. In this work, quantum circuits are encoded as attributed graphs. Hardware-level physical information is mapped to node and edge features: local noise parameters such as calibration parameters $T_1$, $T_2$, and readout errors are encoded at nodes, while coupling-related information such as two-qubit gate errors is encoded as edge features. Graph neural networks are used to model how errors propagate along the physical coupling structure and build up into non-local correlations. This allows the model to capture local interactions and part of the resulting non-local correlations across qubits. A dual-branch affine correction is applied to maintain consistency with physical constraints. Experiments on 10-qubit and 16-qubit random circuits executed on superconducting quantum processors show that GEM provides a level of accuracy comparable to CDR at small scales, while yielding lower mean absolute error and improved stability in zero-shot transfer to larger systems. Results of the traditional QEM strategy indicate that global regression methods remain effective in low-dimensional settings but become less reliable as system degrees of freedom grow. In contrast, GEM makes use of local physical structures to show better scalability and generalization, while preserving the overall error propagation patterns. This work provides a practical scalable approach to QEM for NISQ devices.

Chromatic Correlation Clustering (CCC) extends Correlation Clustering by assigning semantic colors to edges and requiring each cluster to receive a single color label. Unlike standard CC, whose LP relaxation has integrality gap 2 on complete graphs and admits a 2.06-approximation, the analogous LP for CCC has a strict lower bound of 2.11, and the best known LP-rounding algorithm achieves 2.15. We explain this gap by isolating the source of difficulty: cross-edge chromatic interference. Neutral edges, whose color does not match the candidate cluster color, create an irreducible cost absent from standard CC and force any color-independent rounding scheme to pay an additional mismatch penalty. We make four contributions. First, we prove a Global Integrality Gap Decomposition Theorem showing that the gap of any color-independent CCC rounding algorithm equals the standard CC gap plus an irreducible chromatic penalty Delta(L) > 0. Second, we solve the associated min-max problem and derive the staircase formula Delta(L) = ((L-1)/L) Delta_infinity, where Delta_infinity is approximately 0.0734. In particular, the two-color gap is 2.0967, separating CCC from standard CC already at L = 2. Third, we introduce Color-Coupled Correlation Clustering (C4). Adding the valid global constraint sum_c x_uv^c >= L-1 and a correlated interval-packing rounding scheme makes neutral edges behave like classical negative edges, recovering the optimal 2.06 approximation and bypassing the 2.11 lower bound for the uncoupled LP. Fourth, experiments on extremal instances, real multi-relational networks, and fairness benchmarks validate the theory: empirical LP gaps follow the predicted staircase, and C4 matches the unconstrained approximation ratio under fairness constraints.

Graph self-supervised learning can reduce the need for labeled graph data and has been widely used in recommendation, social networks, and other web applications. However, existing methods often underuse high-frequency signals and may overfit to specific local patterns, which limits representation quality and generalization. We propose Frequency-Corrupt Based Graph Self-Supervised Learning (FC-GSSL), a method that builds corrupted graphs biased toward high-frequency information by corrupting nodes and edges according to their low-frequency contributions. These corrupted graphs are used as inputs to an autoencoder, while low-frequency and general features are reconstructed as supervision targets, forcing the model to fuse information from multiple frequency bands. We further design multiple sampling strategies and generate diverse corrupted graphs from the intersections and unions of the sampling results. By aligning node representations from these views, the model can discover useful frequency combinations, reduce reliance on specific high-frequency components, and improve robustness. Experiments on 14 datasets across node classification, graph prediction, and transfer learning show that FC-GSSL consistently improves performance and generalization.

Graph anomaly detection aims to identify irregular patterns in graph-structured data. Most unsupervised GNN-based methods rely on the homophily assumption that connected nodes share similar attributes. However, real-world graphs often exhibit attribute-level heterophily, where connected nodes have dissimilar attributes. Our analysis of attribute-level heterophily graphs reveals two phenomena indicating that current approaches are not practical for unsupervised graph anomaly detection: 1) attribute similarities between connected nodes show nearly identical distributions across different connected node pair types, and 2) anomalies cause consistent variation trends between the graph with and without anomalous edges in the low- and high-frequency components of the spectral energy distributions, while the mid-part exhibits more erratic variations. Based on these observations, we propose NK-GAD, a neighbor knowledge-enhanced unsupervised graph anomaly detection framework. NK-GAD integrates a joint encoder capturing both similar and dissimilar neighbor features, a neighbor reconstruction module modeling normal distributions, a center aggregation module refining node features, and dual decoders for reconstructing attributes and structures. Experiments on seven datasets show NK-GAD achieves an average 3.29% AUC improvement.

Hyperbolic conservation laws govern a wide range of transport-driven dynamics featuring shocks, contact discontinuities, and complex wave interactions, posing distinct challenges for deep-learning-based surrogate modeling. While classical numerical methods provide robust and physically admissible solutions, their computational cost restricts applicability in many-query tasks such as parametric studies and design optimization. Conversely, existing neural surrogates offer rapid inference but often fail to respect intrinsic PDE structures, leading to non-physical artifacts, rollout instability, and poor generalization. We present an interpretable, structure-preserving graph neural solver that bridges classical numerical principles with graph neural networks (GNNs). The network is designed as a learned reconstruction-and-flux operator rather than a black-box state updater, thereby inherently preserving key properties such as local conservation and upwinding. Inspired by Arbitrary high-order DERivatives schemes, we further recast message-passing GNNs as high-order space-time predictors, enabling conservative and stable neural updates with large time steps. Evaluation is performed on challenging supersonic flow benchmarks spanning broad parametric variations in geometry, initial/boundary conditions, and flow regimes. The neural solver achieves superior long-horizon rollout stability and accuracy compared with strong surrogate baselines, outperforms low-order discretizations, and delivers orders-of-magnitude runtime speedups over high-resolution simulations.

Node embeddings act as the information interface for graph neural networks, yet their empirical impact is often reported under mismatched backbones, splits, and training budgets. This paper provides a controlled benchmark of embedding choices for graph classification, comparing classical baselines with quantum-oriented node representations under a unified pipeline. We evaluate two classical baselines alongside quantum-oriented alternatives, including a circuit-defined variational embedding and quantum-inspired embeddings computed via graph operators and linear-algebraic constructions. All variants are trained and tested with the same backbone, stratified splits, identical optimization and early stopping, and consistent metrics. Experiments on five different TU datasets and on QM9 converted to classification via target binning show clear dataset dependence: quantum-oriented embeddings yield the most consistent gains on structure-driven benchmarks, while social graphs with limited node attributes remain well served by classical baselines. The study highlights practical trade-offs between inductive bias, trainability, and stability under a fixed training budget, and offers a reproducible reference point for selecting quantum-oriented embeddings in graph learning.

Graph Neural Networks (GNNs) conventionally rely on standard Laplacian or adjacency matrices for structural message passing. In this work, we substitute the traditional Laplacian with a Doubly Stochastic graph Matrix (DSM), derived from the inverse of the modified Laplacian, to naturally encode continuous multi-hop proximity and strict local centrality. To overcome the intractable $O(n^3)$ complexity of exact matrix inversion, we first utilize a truncated Neumann series to scalably approximate the DSM, which serves as the foundation for our proposed DsmNet. Furthermore, because algebraic truncation inherently causes probability mass leakage, we introduce DsmNet-compensate. This variant features a mathematically rigorous Residual Mass Compensation mechanism that analytically re-injects the truncated tail mass into self-loops, strictly restoring row-stochasticity and structural dominance. Extensive theoretical and empirical analyses demonstrate that our decoupled architectures operate efficiently in $O(K|E|)$ time and effectively mitigate over-smoothing by bounding Dirichlet energy decay, providing robust empirical validation on homophilic benchmarks. Finally, we establish the theoretical boundaries of the DSM on heterophilic topologies and demonstrate its versatility as a continuous structural encoding for Graph Transformers.

Pareto optimization via evolutionary multi-objective algorithms has been shown to efficiently solve constrained monotone submodular functions. Traditionally when solving multiple problems, the algorithm is run for each problem separately. We introduce multitasking formulations of these problems that are an effective way to solve multiple related problems with a single run. In our setting the given problems share a monotone submodular function $f$ but have different knapsack constraints. We examine the case where elements within a constraint have the same cost and show that our multitasking formulations result in small Pareto fronts. This allows the population to share solutions between all problems leading to significant improvements compared to running several classical approaches independently. Using rigorous runtime analysis, we analyze the expected time until the introduced multitasking approaches obtain a $(1-1/e)$-approximation for each of the given problems. Our experimental investigations for the maximum coverage problem give further insight into the dynamics behind how the approach works and doesn't work in practice for problems where elements within a constraint also have varied costs.

Proteins carry out biological functions through the coordinated action of groups of residues organized into structural arrangements. These arrangements, which we refer to as protein units, exist at an intermediate scale, being larger than individual residues yet smaller than entire proteins. A deeper understanding of protein function can be achieved by identifying these units and their associations with function. However, existing approaches either focus on residue-level signals, rely on curated annotations, or segment protein structures without incorporating functional information, thereby limiting interpretable analysis of structure-function relationships. We introduce PUFFIN, a data-driven framework for discovering protein units by jointly learning structural partitioning and functional supervision. PUFFIN represents proteins as residue-level structure graphs and applies a graph neural network with a structure-aware pooling mechanism that partitions each protein into multi-residue units, with functional supervision that shapes the partition. We show that the learned units are structurally coherent, exhibit organized associations with molecular function, and show meaningful correspondence with curated InterPro annotations. Together, these results demonstrate that PUFFIN provides an interpretable framework for analyzing structure-function relationships using learned protein units and their statistical function associations. We made our source code available at https://github.com/boun-tabi-lifelu/puffin.

The rapid expansion of gaming industry requires advanced recommender systems tailored to its dynamic landscape. Existing Graph Neural Network (GNN)-based methods primarily prioritize accuracy over diversity, overlooking their inherent trade-off. To address this, we previously proposed CPGRec, a balance-oriented gaming recommender system. However, CPGRec fails to account for critical disparities in player-game interactions, which carry varying significance in reflecting players' personal preferences and may exacerbate over-smoothness issues inherent in GNN-based models. Moreover, existing approaches underutilize the reasoning capabilities and extensive knowledge of large language models (LLMs) in addressing these limitations. To bridge this gap, we propose two new modules. First, Preference-informed Edge Reweighting (PER) module assigns signed edge weights to qualitatively distinguish significant player interests and disinterests while then quantitatively measuring preference strength to mitigate over-smoothing in graph convolutions. Second, Preference-informed Representation Generation (PRG) module leverages LLMs to generate contextualized descriptions of games and players by reasoning personal preferences from comparing global and personal interests, thereby refining representations of players and games. Experiments on \textcolor{black}{two Steam datasets} demonstrate CPGRec+'s superior accuracy and diversity over state-of-the-art models. The code is accessible at https://github.com/HsipingLi/CPGRec-Plus.

Generating synthesizable Verilog for large, hierarchical hardware designs remains a significant challenge for large language models (LLMs), which struggle to replicate the structured reasoning that human experts employ when translating complex specifications into RTL. When tasked with producing hierarchical Verilog, LLMs frequently lose context across modules, hallucinate interfaces, fabricate inter-module wiring, and fail to maintain structural coherence - failures that intensify as design complexity grows and specifications involve informal prose, figures, and tables that resist direct operationalization. To address these challenges, we present VeriGraphi, a framework that introduces a spec-anchored Knowledge Graph as the architectural substrate driving the RTL generation pipeline. VeriGraphi constructs a HDA, a structured knowledge graph that explicitly encodes module hierarchy, port-level interfaces, wiring semantics, and inter-module dependencies as first-class graph entities and relations. Built through iterative multi-agent analysis of the specification, this Knowledge Graph provides a deterministic, machine-checkable structural scaffold before code generation. Guided by the KG, a progressive coding module incrementally generates pseudo-code and synthesizable RTL while enforcing interface consistency and dependency correctness at each submodule stage. We evaluate VeriGraphi on a benchmark of three representative specification documents from the National Institute of Standards and Technology and their corresponding implementations, and we present a RV32I processor as a detailed case study to illustrate the full pipeline. The results demonstrate that VeriGraphi enables reliable hierarchical RTL generation with minimal human intervention for RISC-V, marking a significant milestone for LLM-generated hardware design while maintaining strong functional correctness.

Ollivier-Ricci curvature (ORC), defined via the Wasserstein distance that captures rich geometric information, has received growing attention in both theory and applications. However, the high computational cost of Wasserstein distance evaluation has significantly limited the broader practical use of ORC. To alleviate this issue, previous work introduced a computationally efficient lower bound as a proxy for ORC based on 1-hop random walks, but this approach empirically exhibits large gaps from the exact ORC. In this paper, we establish a substantially tighter lower bound for ORC than the existing lower bound, while retaining much lower computational cost than exact ORC computation, with practical speedups of tens of times. Moreover, our bound is not restricted to 1-hop random walks, but also applies to k-hop random walks (k > 1). Experiments on several fundamental graph structures demonstrate the effectiveness of our bound in terms of both approximation accuracy and computational efficiency.