Graph Neural Networks

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Mechanistic understanding and rational design of complex chemical systems depend on fast and accurate predictions of electronic structures beyond individual building blocks. However, if the system exceeds hundreds of atoms, first-principles quantum mechanical (QM) modeling becomes impractical. In this study, we developed FB-GNN-MBE by integrating a fragment-based graph neural network (FB-GNN) into the many-body expansion (MBE) theory and demonstrated its capacity to reproduce first-principles potential energy surfaces (PES) for hierarchically structured systems with manageable accuracy, complexity, and interpretability. Specifically, we divided the entire system into basic building blocks (fragments), evaluated their one-fragment energies using a QM model, and addressed many-fragment interactions using the structure-property relationships trained by FB-GNNs. Our investigation shows that FB-GNN-MBE achieves chemical accuracy in predicting two-body (2B) and three-body (3B) energies across water, phenol, and mixture benchmarks, as well as the one-dimensional dissociation curves of water and phenol dimers. To transfer the success of FB-GNN-MBE across various systems with minimal computational costs and data demands, we developed and validated a teacher-student learning protocol. A heavy-weight FB-GNN trained on a mixed-density water cluster ensemble (teacher) distills its learned knowledge and passes it to a light-weight GNN (student), which is later fine-tuned on a uniform-density (H2O)21 cluster ensemble. This transfer learning strategy resulted in efficient and accurate prediction of 2B and 3B energies for variously sized water clusters without retraining. Our transferable FB-GNN-MBE framework outperformed conventional non-FB-GNN-based models and provided a scalable and accurate route toward interaction energies of large molecular assemblies.

Generative models for crystalline materials often rely on equivariant graph neural networks, which capture geometric structure well but are costly to train and slow to sample. We present Crystalite, a lightweight diffusion Transformer for crystal modeling built around two simple inductive biases. The first is Subatomic Tokenization, a compact chemically structured atom representation that replaces high-dimensional one-hot encodings and is better suited to continuous diffusion. The second is the Geometry Enhancement Module (GEM), which injects periodic minimum-image pair geometry directly into attention through additive geometric biases. Together, these components preserve the simplicity and efficiency of a standard Transformer while making it better matched to the structure of crystalline materials. Crystalite achieves state-of-the-art results on crystal structure prediction benchmarks, and de novo generation performance, attaining the best S.U.N. discovery score among the evaluated baselines while sampling substantially faster than geometry-heavy alternatives.

With the advent of system-in-package (SiP) chiplet-based design and heterogeneous 2.5D/3D integration, thermal-induced warpage has become a critical reliability concern. While conventional numerical approaches can deliver highly accurate results, they often incur prohibitively high computational costs, limiting their scalability for complex chiplet-package systems. In this paper, we present WarPGNN, an efficient and accurate parametric thermal warpage analysis framework powered by Graph Neural Networks (GNNs). By operating directly on graphs constructed from the floorplans, WarPGNN enables fast warpage-aware floorplan exploration and exhibits strong transferability across diverse package configurations. Our method first encodes multi-die floorplans into reduced Transitive Closure Graphs (rTCGs), then a Graph Convolution Network (GCN)-based encoder extracts hierarchical structural features, followed by a U-Net inspired decoder that reconstructs warpage maps from graph feature embeddings. Furthermore, to address the long-tailed pattern of warpage data distribution, we developed a physics-informed loss and revised a message-passing encoder based on Graph Isomorphic Network (GIN) that further enhance learning performance for extreme cases and expressiveness of graph embeddings. Numerical results show that WarPGNN achieves more than 205.91x speedup compared with the 2-D efficient FEM-based method and over 119766.64x acceleration with 3-D FEM method COMSOL, respectively, while maintaining comparable accuracy at only 1.26% full-scale normalized RMSE and 2.21% warpage value error. Compared with recent DeepONet-based model, our method achieved comparable prediction accuracy and inference speedup with 3.4x lower training time. In addition, WarPGNN demonstrates remarkable transferability on unseen datasets with up to 3.69% normalized RMSE and similar runtime.

We define an information-complexity property for aggregation functions, capturing a vast range of practical aggregations, and prove that any Message-Passing Graph Neural Network (MP-GNN) model with such aggregations induces only a polynomial number of equivalence classes on all graphs - while the number of non-isomorphic graphs is super-exponential (in number of vertices). Adding a familiar perspective, we observe that merely 2 iterations of Color Refinement (CR) induce at least an exponential number of equivalence classes, making the aforementioned MP-GNNs relatively infinitely weaker. Previous studies state that sum-aggregation MP-GNNs match full CR however they consider a weak, 'non-uniform', notion of distinguishing-power where each graph size may require a different MP-GNN to distinguish graphs up to that size. Our results concern both distinguishing between non-equivariant vertices and distinguishing between non-isomorphic graphs.

In this paper, we propose a fast method for estimating the condition number of sparse matrices using graph neural networks (GNNs). For efficient deployment of GNNs, we introduce a graph feature construction with $\mathrm{O}(\mathrm{nnz} + n)$ complexity, where $\mathrm{nnz}$ is the number of non-zero elements in the matrix and $n$ denotes the matrix dimension. We propose two schemes for estimating the matrix condition number using GNNs; one follows by decomposing the condition number and predicts the relatively more computationally intensive part $\|\mathbf{A}^{-1}\|$, without explicitly forming the inverse, while the other is to predict the whole condition number $κ$. Our approach can be extended to an arbitrary norm. Extensive experiments are conducted for the estimation of the 1-norm and 2-norm condition numbers, which show that our method achieves a significant speedup over the traditional numerical estimation methods. Our software for GNN condition number estimator is made publicly available at https://github.com/inEXASCALE/sparse-kappa.

Micro-expression Action Unit (AU) detection identifies localized AUs from subtle facial muscle activations, providing a foundation for decoding affective cues. Previous methods face three key limitations: (1) heavy reliance on low-density visual information, rendering discriminative evidence vulnerable to background noise; (2) coarse-grained feature processing that misaligns with the demand for fine-grained representations; and (3) neglect of inter-AU correlations, restricting the parsing of complex expression patterns. We propose AULLM++, a reasoning-oriented framework leveraging Large Language Models (LLMs), which injects visual features into textual prompts as actionable semantic premises to guide inference. It formulates AU prediction into three stages: evidence construction, structure modeling, and deduction-based prediction. Specifically, a Multi-Granularity Evidence-Enhanced Fusion Projector (MGE-EFP) fuses mid-level texture cues with high-level semantics, distilling them into a compact Content Token (CT). Furthermore, inspired by micro- and macro-expression AU correspondence, we encode AU relationships as a sparse structural prior and learn interaction strengths via a Relation-Aware AU Graph Neural Network (R-AUGNN), producing an Instruction Token (IT). We then fuse CT and IT into a structured textual prompt and introduce Counterfactual Consistency Regularization (CCR) to construct counterfactual samples, enhancing the model's generalization. Extensive experiments demonstrate AULLM++ achieves state-of-the-art performance on standard benchmarks and exhibits superior cross-domain generalization.

This work formulates and solves optimization problems to generate input points that yield high errors between a neural network's predicted AC power flow solution and solutions to the AC power flow equations. We demonstrate this capability on an instance of the CANOS-PF graph neural network model, as implemented by the PF$Δ$ benchmark library, operating on a 14-bus test grid. Generated adversarial points yield errors as large as 3.7 per-unit in reactive power and 0.08 per-unit in voltage magnitude. When minimizing the perturbation from a training point necessary to satisfy adversarial constraints, we find that the constraints can be met with as little as an 0.04 per-unit perturbation in voltage magnitude on a single bus. This work motivates the development of rigorous verification and robust training methods for neural network surrogate models of AC power flow.

The Winner Determination Problem (WDP) in combinatorial auctions is NP-hard, and no existing method reliably predicts which instances will defeat fast greedy heuristics. The ML-for-combinatorial-optimization community has focused on learning to \emph{replace} solvers, yet recent evidence shows that graph neural networks (GNNs) rarely outperform well-tuned classical methods on standard benchmarks. We pursue a different objective: learning to predict \emph{when} a given instance is hard for greedy allocation, enabling instance-dependent algorithm selection. We design a 20-dimensional structural feature vector and train a lightweight MLP hardness classifier that predicts the greedy optimality gap with mean absolute error 0.033, Pearson correlation 0.937, and binary classification accuracy 94.7% across three random seeds. For instances identified as hard -- those exhibiting ``whale-fish'' trap structure where greedy provably fails -- we deploy a heterogeneous GNN specialist that achieves ${\approx}0\%$ optimality gap on all six adversarial configurations tested (vs.\ 3.75--59.24% for greedy). A hybrid allocator combining the hardness classifier with GNN and greedy solvers achieves 0.51% overall gap on mixed distributions. Our honest evaluation on CATS benchmarks confirms that GNNs do not outperform Gurobi (0.45--0.71 vs.\ 0.20 gap), motivating the algorithm selection framing. Learning \emph{when} to deploy expensive solvers is more tractable than learning to replace them.

Graph neural networks are usually treated as auxiliaries for combinatorial optimization: they imitate algorithms, guide search, or supply scores to classical procedures. We show that this auxiliary role is not intrinsic. A GNN can itself be a heuristic. For the Euclidean Travelling Salesman Problem, we train a non-autoregressive GNN with no labels, rewards, sequential decoding, search, or local improvement. A differentiable Hamiltonian-cycle objective is the only supervision. The trained model produces a complete tour in one forward pass, while dropout and snapshots from a single training trajectory provide solution diversity without engineered moves. The heuristic is therefore learned, not programmed. It is also fast: batched inference remains in the millisecond regime on GPUs. Experiments on TSP100, TSP200, and TSP500 show that the model consistently improves over nearest-neighbor greedy baselines. These results identify unsupervised GNNs as a class of fast learned heuristics for combinatorial optimization.

Mixed-integer linear programming (MILP) is a foundational framework for combinatorial optimization across science and engineering, but remains hard to solve at scale due to NP-hardness. Recent learning-based methods typically model MILP instances as variable-constraint bipartite graphs and use Graph Neural Networks (GNNs) for representation learning, yet their locality limits representation power. We propose an attention-driven neural backbone that adopts an element-centric view of variables and constraints, with dual attention performing parallel intra-type self-attention and inter-type cross-attention. Across three representative tasks at the instance, element, and solving-state levels, our model consistently outperforms conventional GNN-based architectures, highlighting attention-based, element-centric modeling as a powerful foundation for learning-enhanced combinatorial optimization.

Quantum circuit design is a key bottleneck for practical quantum machine learning on complex, real-world data. We present an automated framework that discovers and refines variational quantum circuits (VQCs) using graph-based Bayesian optimization with a graph neural network (GNN) surrogate. Circuits are represented as graphs and mutated and selected via an expected improvement acquisition function informed by surrogate uncertainty with Monte Carlo dropout. Candidate circuits are evaluated with a hybrid quantum-classical variational classifier on the next generation firewall telemetry and network internet of things (NF-ToN-IoT-V2) cybersecurity dataset, after feature selection and scaling for quantum embedding. We benchmark our pipeline against an MLP-based surrogate, random search, and greedy GNN selection. The GNN-guided optimizer consistently finds circuits with lower complexity and competitive or superior classification accuracy compared to all baselines. Robustness is assessed via a noise study across standard quantum noise channels, including amplitude damping, phase damping, thermal relaxation, depolarizing, and readout bit flip noise. The implementation is fully reproducible, with time benchmarking and export of best found circuits, providing a scalable and interpretable route to automated quantum circuit discovery.

Algorithmic reasoning -- the ability to perform step-by-step logical inference -- is a synthetic benchmark for evaluating multi-step reasoning abilities, designed for graph neural networks and also for transformer models. Prior work has evaluated reasoning for executing a single algorithmic task, whereas a more desirable objective is to perform multiple algorithmic reasoning tasks simultaneously. We start by noting that this is inherently difficult due to differences arising from the execution traces of the algorithms (such as depth- vs. breadth-first search), which cause interference when they are trained together. In this paper, we introduce {branching neural networks}, a new architecture for multitask algorithmic reasoning. The main idea is to search for a recursive tree-structured partition of $n$ algorithmic tasks into a $k$-ary tree (divided into $L$ layers). Naive search requires $O(k^{nL})$ complexity; we develop an algorithm that reduces this to $O(nL)$ by solving a convex relaxation at each layer to approximate an optimal partition. Our approach clusters these tasks using gradient-based affinity and can be used on top of any base model. We validate our approach on algorithmic reasoning benchmarks and their extensions with text descriptions. We show that gradient-based affinity scores help estimate true performance with less than 5% error, measured across eight different architectures with up to 34 billion parameters. On the CLRS benchmark, our approach outperforms existing graph neural networks by 3.7% and baselines by 1.2%, while reducing runtime by 48% and memory usage by 26%. The learned branching structure shows a hierarchical clustering of related algorithms. On three text-based graph reasoning benchmarks, our approach improves over baseline methods by 3.2%. Finally, we validate our approach for overlapping community detection.

Graph neural networks (GNNs) have become an indispensable tool for analyzing relational data. Classical GNNs are broadly classified into three variants: convolutional, attentional, and message-passing. While the standard message-passing variant is expressive, its typical pair-wise messages only consider the features of the center node and each neighboring node individually. This design fails to incorporate contextual information contained within the broader local neighborhood, potentially hindering its ability to learn meaningful relationships within the entire set of neighboring nodes. To address this, the paper first refines the concept of neighborhood-contextualization within GNNs, leveraging ideas from set-based aggregation methods and a key property of the attentional variant. This then serves as the basis for generalizing the message-passing variant to the proposed neighborhood-contextualized message-passing (NCMP) framework. To demonstrate its utility, a simple, mathematically grounded method to parametrize and operationalize NCMP is presented, leading to the development of the proposed Soft-Isomorphic Neighborhood-Contextualized Graph Convolution Network (SINC-GCN). Across a diverse set of synthetic and benchmark datasets, SINC-GCN strikes a highly favorable balance between expressivity and efficiency. Notably, while more complex models incur significant computational overhead, SINC-GCN delivers substantial performance gains with considerable effect sizes over baseline GNN models while maintaining a highly efficient asymptotic runtime complexity, further underscoring the distinctive utility of neighborhood-contextualization. Overall, by integrating multiset neighborhood context, the proposed NCMP framework serves as a practical and scalable path toward enhancing the graph representational power of classical GNNs.

Limited-Area Models (LAMs) enable weather forecasting over regional domains at higher resolutions than what is computationally feasible for global models. At such high resolutions, machine learning approaches for weather prediction increasingly rely on ensemble methods to produce probabilistic forecasts. However, existing machine learning LAMs are not scalable due to relying on computationally costly diffusion models or inefficient graph neural networks. We tackle this by introducing a new hybrid CNN/GNN architecture, tailored to the LAM weather forecasting problem. Using this architecture, we construct the DET-LAM deterministic model, producing LAM forecasts both more efficiently and accurately than its graph-based competitor. We then tackle the ensemble forecasting problem, by using this architecture as a backbone for the generative model CRPS-LAM. CRPS-LAM is trained using a Continuous Ranked Probability Score (CRPS) objective, enabling efficient training and sampling in a single forward pass. This yields a speedup of $\approx \times 39$ compared to diffusion-based baselines. We evaluate our approach on regional domains in northern Europe, demonstrating that CRPS-LAM produces skillful and well-calibrated forecasts across a range of atmospheric variables.

The class imbalance problem refers to the disproportionate distribution of samples across different classes within a dataset, where the minority classes are significantly underrepresented. This issue is also prevalent in graph-structured data. Most graph neural networks (GNNs) implicitly assume a balanced class distribution and therefore often fail to account for the challenges introduced by class imbalance, which can lead to biased learning and degraded performance on minority classes. We identify a quality inconsistency problem in synthesized nodes, which leads to suboptimal performance under graph imbalance conditions. To mitigate this issue, we propose GraphIFE (Graph Invariant Feature Extraction), a novel framework designed to mitigate quality inconsistency in synthesized nodes. Our approach incorporates two key concepts from graph invariant learning and introduces strategies to strengthen the embedding space representation, thereby enhancing the model's ability to identify invariant features. Extensive experiments demonstrate the framework's efficiency and robust generalization, as GraphIFE consistently outperforms various baselines across multiple datasets. The code is publicly available at https://github.com/flzeng1/GraphIFE.

Mixed bundle pricing is a classic revenue management problem arising in industries such as e-commerce, tourism, and video games. It refers to designing product combinations (i.e., bundles) and determining their prices to maximize expected profit. Exact mixed-bundling formulations capture this structure but are computationally intractable because the number of possible bundles grows exponentially with the number of products. We propose a graph neural network (GNN)-guided pruning framework for scalable (non-)additive bundle pricing. Instead of learning on the exponential bundle-level formulation, we encode each instance as a compact customer-product graph and train an edge-output GNN to learn the product-assignment probabilities from optimal mixed-bundling solutions. The predicted probabilities are then converted into restricted candidate bundle families through fixed cutoff pruning and progressive cutoff pruning; the final prices and assignments are obtained by solving the mixed bundling formulation over the retained bundles. We further introduce a GNN-guided local search and an iterative self-improvement procedure for larger instances. The local search refines the retained bundle family by prioritizing high-confidence add/drop moves, while the iterative self-improvement procedure generates high-quality solutions on larger instances for retraining. Theoretically, we show that under mild distinguishability conditions the proposed edge-output GNN class is expressive enough to recover the optimal product-assignment mapping. Experiments show that the proposed policies recover over 98% of the optimal profit on small instances and outperform bundle-size pricing on larger instances with substantial runtime savings.

Graph foundation models face several fundamental challenges including transferability across diverse domains and data scarcity, which calls into question the very feasibility of creating such models. However, despite similar challenges, the tabular domain has recently witnessed the emergence of the first successful foundation models such as TabPFN. These models are based on the prior-data fitted networks (PFN) framework, in which models are pretrained on carefully designed synthetic datasets to make predictions in an in-context learning setting. Recently, G2T-FM, a framework that converts graph node-level tasks into tabular tasks, has made the first step towards adopting PFNs for graphs, yet it is limited to hand-crafted features and was never pretrained on graph data. In this work, we make the next step by proposing GraphPFN, a PFN-based model designed and pretrained specifically for graph node-level tasks. Following the PFN framework, we first design a prior distribution of synthetic attributed graphs by using a novel combination of multi-level stochastic block models and a preferential attachment process for structure generation and graph-aware structured causal models for attribute generation. Then, we augment the tabular foundation model LimiX with attention-based graph neighborhood aggregation layers and train it on millions of synthetic graphs sampled from our prior. On diverse real-world graph datasets with node-level tasks, GraphPFN achieves state-of-the-art results in both in-context learning and finetuning regimes, outperforming G2T-FM, prior GFMs, and task-specific GNNs trained from scratch. More broadly, GraphPFN shows the potential of PFN-based models for building graph foundation models.

We present a learnable physics-based model that predicts motion of the robot end effector and reaction force-torque in contact-rich manipulation. The model represents the end effector and the environment as interacting meshes in a graph structure, and conditions its prediction explicitly on the applied control input. It predicts object-level pose update directly, while the reaction torque emerges from a per-vertex force field. Training is self-supervised using only joint encoder and force-torque data while the robot is randomly touching the environment without task context. In simulation, our model transfers to peg insertion with unseen concave geometry, where an MPC agent using it reaches up to 98% success rate, and after fine-tuning on self-collected data matches an agent planning with the ground truth dynamics at the tightest 1 mm clearance. In the real world, it outperforms the system-identified MuJoCo model by 45% in position and by 74% and 63% in force and torque error.

Generalized extreme value models capture dependence among choice alternatives in discrete choice modeling, but require this dependence to be predefined, symmetric, and shared uniformly across individuals. Recent efforts to synergize discrete choice models with deep neural networks have improved predictive performance but still cannot explicitly represent alternative dependence within neural architectures. To address these gaps, we introduce the alternative graph -- a graph in which nodes represent choice alternatives and edges encode their dependence -- and propose Alternative Graph Neural Networks (Alt-GNNs), a family of GNN-based discrete choice models that embed alternative dependence within a unified framework. Theoretically, Alt-GNNs incorporate multinomial logit, nested logit, and ASU-DNN as special cases and enable innovative model designs, including Nested Alt-GNN, Complete Alt-GNN, and Attention Alt-GNN. Alt-GNNs are consistent with random utility maximization theory, enforce behavioral constraints through alternative graphs, and offer a novel graph-based interpretation of utility functions. Empirically, on two travel mode choice datasets from London and Chicago, Alt-GNNs significantly improve predictive performance over all benchmark models in mode choice modeling because of their flexible alternative graph design and vast hyperparameter space. Even the simplest Alt-GNN variant -- Nested Alt-GNN -- generalizes the nested logit model while preserving its unique two-layer substitution properties, enabling graph-based behavioral constraints over otherwise unconstrained behavioral patterns from deep neural networks.

Accurately predicting the performance of active radio frequency (RF) circuits is essential for modern wireless systems but remains challenging due to highly nonlinear behavior and the high computational cost of traditional simulation tools. Existing machine learning (ML) surrogates often require large datasets to generalize across various topologies or are not accurate on held-out circuits. This work presents a lightweight, data-efficient, and topology-aware graph neural network (GNN) framework for predicting key performance metrics of active RF circuit classes, such as low-noise amplifiers (LNAs), mixers, voltage-controlled oscillators (VCOs), power amplifiers (PAs), and voltage amplifiers (VAs). The proposed framework employs RFIC domain-informed feature indexing to enable cross-topology adaptability by cheap encoding of functional device semantics (e.g., differential pair and varactor transistors) and efficient knowledge transfer. The surrogate model represents circuits using device-terminal graph abstractions to preserve fine-grained connectivity and transistor-level symmetry. The final model is generalized to a wide variety of classes by being trained in parallel. Experimental results demonstrate accurate modeling of multimodal and heavy-tailed RF performance distributions, achieving an average mean relative error (MRE) of 2.71% across nineteen topologies, an improvement of 3.3x and 20x faster in training over prior art, and the generalization to held-out topologies is improved by ~26.2x. Furthermore, this work shows ~36x training data efficiency compared to state-of-the-art, demonstrating its effectiveness for scalable and deployment-ready RF design automation.

Although the Maximum Clique Problem (MCP) has been extensively studied and features a rich ecosystem of exact solvers, empirical evidence shows that solver performance varies substantially across graph families. Consequently, selecting an appropriate algorithm for a given instance remains an open and practically important challenge that has received little systematic attention. We address this gap by developing an instance-aware selection framework that systematically combines global statistical descriptors with learned topological representations. We construct a comprehensive benchmark by evaluating four state-of-the-art exact solvers on a diverse collection of graph instances and deriving both global statistical and local structural features. An evaluation of conventional classifiers establishes Random Forest as a strong baseline and reveals that connectivity and topological features are key predictors of performance. Motivated by these observations, we introduce a dual-channel architecture that jointly leverages a Graph Attention Network for capturing local neighborhood patterns and a Multilayer Perceptron for modeling global statistical features. Extensive experiments show that the proposed dual-channel model consistently surpasses classical baselines and the single-best solver, achieving 90.43% test accuracy. These findings demonstrate the value of integrating local topological encoding with global statistical cues for combinatorial algorithm selection. Code and models are available at: https://anonymous.4open.science/r/GAT-MLP-7E5F.

Explainable artificial intelligence approaches accelerate drug discovery by improving molecular representation learning, identifying key molecular structures, and rationalizing drug property prediction. However, developing end-to-end explainable models for target-specific structure-activity relationship modeling remains challenging because compound-protein interaction data are often limited for individual targets, and small changes in chemical substituents or local structural motifs can cause large differences in molecular properties. Therefore, effectively leveraging structural and property information to identify key moieties associated with compound-protein affinity is essential. We propose a graph neural network (GNN) framework that uses property and structural information from activity-cliff molecule pairs targeting specific proteins to predict compound-protein affinity, measured by half-maximal inhibitory concentration (IC50), and explain property differences. To improve explainability, we trained GNNs with structure-aware loss functions using group lasso and sparse group lasso regularization, which prune and highlight molecular subgraphs relevant to activity differences. We applied this framework to activity-cliff data from molecules targeting six tyrosine-protein kinases across the Src, Abl, and Tec families, as well as anaplastic lymphoma kinase. Integrating common- and uncommon-node information with sparse group lasso improved target-specific molecular property prediction, producing lower root mean square errors and higher Pearson correlation coefficients. Regularization also enhanced GNN feature attribution by improving graph-level global direction scores and atom-level coloring accuracy. These results support more interpretable drug discovery pipelines, particularly for identifying critical molecular substructures during lead optimization.

Prompt tuning has become a key mechanism for adapting pre-trained Graph Neural Networks (GNNs) to new downstream tasks. However, existing approaches are predominantly supervised, relying on labeled data to optimize the prompting parameters and typically fine-tuning a task-specific prediction head -- practices that undermine the promise of parameter-efficient adaptation. We propose Unsupervised Graph Prompting Problem (UGPP), a challenging new setting where the pre-trained GNN is kept entirely frozen, labels on the target domain are unavailable, the source data is inaccessible, and the target distribution exhibits covariate shift. To address this, we propose UGPrompt, the first fully unsupervised GNN prompting framework. UGPrompt leverages consistency regularization and pseudo-labeling to train a prompting function, complemented with diversity and domain regularization to mitigate class imbalance and distribution mismatch. Our extensive experiments demonstrate that UGPrompt consistently outperforms state-of-the-art supervised prompting methods with access to labeled data, demonstrating the viability of unsupervised prompting as a practical adaptation paradigm for GNNs.

We propose a novel benchmarking methodology for graph neural networks (GNNs) based on the graph alignment problem, a combinatorial optimization task that generalizes graph isomorphism by aligning two unlabeled graphs to maximize overlapping edges. We frame this problem as a self-supervised learning task and present several methods to generate graph alignment datasets using synthetic random graphs and real-world graph datasets from multiple domains. For a given graph dataset, we generate a family of graph alignment datasets with increasing difficulty, allowing us to rank the performance of various architectures. Our experiments prove that there is an optimal task difficulty for having a statistically relevant ranking of different models and that, even on a structure-only task, anisotropic models perform better compared to isotropic ones. To further prove that our synthetic task capture meaningful information, we show its effectiveness for self-supervised GNN pre-training: the learned node embeddings can be leveraged as positional encodings by transformers for graph regression or can be used to reconstruct the full structure of the graph with $98\%$ accuracy. To support reproducibility and further research, we provide an open-source Python package to generate graph alignment datasets and benchmark new GNN architectures. The source code is available at https://github.com/adrien-lagesse/graph-alignment-benchmark.

This work presents a comprehensive evaluation of neural network graph compilers across heterogeneous hardware platforms, addressing the critical gap between theoretical optimization techniques and practical deployment scenarios. We demonstrate how vendor-specific optimizations can invalidate relative performance comparisons between architectural archetypes, with performance advantages sometimes completely reversing after compilation. Our systematic analysis reveals that graph compilers exhibit performance patterns highly dependent on both neural architecture and batch sizes. Through fine-grained block-level experimentation, we establish that vendor-specific compilers can leverage repeated patterns in simple architectures, yielding disproportionate throughput gains as model depth increases. We introduce novel metrics to quantify a compiler's ability to mitigate performance friction as batch size increases. Our methodology bridges the gap between academic research and practical deployment by incorporating compiler effects throughout the research process, providing actionable insights for practitioners navigating complex optimization landscapes across heterogeneous hardware environments.

Traffic prediction is difficult due to the complex interplay of temporal evolution, spatial interactions, and delayed spatio-temporal propagation over road networks. Existing methods either model spatial and temporal dependencies separately or employ unified spatio-temporal structures, but they often insufficiently characterize how neighboring sensors at historical timestamps influence a target node, while complex joint models may incur high computation. This paper proposes STEI-PCN, an efficient pure convolutional network based on spatio-temporal encoding and relation inference. It first builds a local causal joint spatio-temporal graph to restrict candidate interactions, then uses absolute position and relative distance encodings to infer dynamic edge weights. A single-layer graph convolution with a position-aware gated activation unit captures local joint dependencies, and temporal dilated causal convolutions complement long-range temporal patterns. A multi-view prediction module fuses raw, local propagation, and long-range temporal representations for direct multi-step forecasting. Experiments on PeMS03, PeMS04, PeMS07, PeMS08, and PeMS-Bay under multiple horizons show that STEI-PCN achieves competitive accuracy with moderate parameters and low training and inference costs. Ablation and fluctuation analyses further verify the contributions of the main components and empirically analyze the effects of the training-stage constraints under sharp speed changes. Our code is available at a GitHub link https://github.com/Jessez2/STEI-PCN.

Traffic Engineering (TE) in large-scale networks like cloud Wide Area Networks (WANs) and Low Earth Orbit (LEO) satellite constellations is a critical challenge. Although learning-based approaches have been proposed to address the scalability of traditional TE algorithms, their practical application is often hindered by a lack of generalization, high training overhead, and a failure to respect link capacities. This paper proposes TELGEN, a novel TE algorithm that learns to solve TE problems efficiently in large-scale network scenarios, while achieving superior generalizability across diverse network conditions. TELGEN is based on the novel idea of transforming the problem of "predicting the optimal TE solution" into "predicting the optimal TE algorithm", which enables TELGEN to learn and efficiently approximate the end-to-end solving process of classical optimal TE algorithms. The learned algorithm is agnostic to the exact underlying network topology or traffic patterns, and is able to very efficiently solve TE problems given arbitrary inputs and generalize well to unseen topologies and demands. We train and evaluate TELGEN with random and real-world topologies, with networks of up to 5000 nodes and 3.6x10^6 links in testing. TELGEN shows less than 3% optimality gap while ensuring feasibility in all testing scenarios, even when the test network has 2-20x more nodes than the largest training network. It also saves up to 84% TE solving time than traditional interior-point method, and reduces up to 79.6% training time per epoch than the state-of-the-art learning-based algorithm.

Proteins move and deform to ensure their biological functions. Despite significant progress in protein structure prediction, approximating conformational ensembles at physiological conditions remains a fundamental open problem. This paper presents a novel perspective on the problem by directly targeting continuous compact representations of protein motions inferred from sparse experimental observations. We develop a task-specific loss function enforcing data symmetries, including scaling and permutation operations. Our method PETIMOT (Protein sEquence and sTructure-based Inference of MOTions) leverages transfer learning from pre-trained protein language models through an SE(3)-equivariant graph neural network. When trained and evaluated on the Protein Data Bank, PETIMOT shows superior performance in time and accuracy, capturing protein dynamics, particularly large/slow conformational changes, compared to state-of-the-art diffusion and flow-matching approaches, as well as traditional physics-based models. Our code and protocols are available at https://github.com/PhyloSofS-Team/PETIMOT.

Rational design of lipid nanoparticles (LNPs) for tissue-specific delivery critically depends on predicting the composition of the protein corona that forms on the lipid surface after intravenous administration. However, conventional characterization of the protein corona relies on costly and time-consuming mass spectrometry experiments, which require physically prepared liposome samples and therefore cannot serve as a pre-synthesis screening strategy for large candidate lipid spaces. The adsorption of plasma proteins onto liposomal surfaces is shaped by lipid chemical structures, protein properties and the biological environment, making this process difficult to simulate directly. In this work, we propose that scoring lipid-plasma protein pairs and ranking the resulting scores can provide a practical signal for revealing the relative composition of the liposomal surface protein corona.Here we introduce GenShin, a geometry-enhanced pose-free graph neural network designed to score lipid-plasma protein pairs. GenShin is pretrained on compound-protein affinity data to initialize a generalizable scoring function and is then fine-tuned on a rank fine-tuning dataset constructed from liposomal protein-corona abundance measurements to adapt the model to lipid-plasma protein pair scoring. Before fine-tuning, GenShin achieves competitive pose-free affinity prediction on the PDBbind v2016 benchmark compared with representative pose-dependent models. CASF-2016 perturbation experiments using the pretrained GenShin model further show that pose-dependent inference substantially degrades when intermolecular poses are unreliable, whereas GenShin remains stable without requiring such poses. This supports the practical advantage of GenShin for large-scale lipid-protein scoring.

Text-Attributed Graphs (TAGs), where each node is associated with text descriptions, are ubiquitous in real-world scenarios. They typically exhibit distinctive structure and domain-specific knowledge, motivating the development of a Graph Foundation Model (GFM) that generalizes across diverse graphs and tasks. Despite large efforts to integrate Large Language Models (LLMs) and Graph Neural Networks (GNNs) for TAGs, existing approaches suffer from decoupled architectures with two-stage alignment, limiting their synergistic potential. Even worse, existing methods assign out-of-vocabulary (OOV) tokens to graph nodes, leading to graph-specific semantics, token explosion, and incompatibility with task-oriented prompt templates, which hinders cross-graph and cross-task transferability. To address these challenges, we propose PromptGFM, a versatile GFM for TAGs grounded in graph vocabulary learning. PromptGFM comprises two key components: (1) Graph Understanding Module, which explicitly prompts LLMs to replicate the finest GNN workflow within the text space, facilitating seamless GNN-LLM integration and elegant graph-text alignment; (2) Graph Inference Module, which establishes a language-based graph vocabulary ensuring expressiveness, transferability, and scalability, enabling readable instructions for LLM fine-tuning. Extensive experiments demonstrate our superiority and transferability across diverse graphs and tasks. The code is available at this: https://github.com/agiresearch/PromptGFM.

Graph neural networks (GNNs) have demonstrated success in modeling relational data primarily under the assumption of homophily. However, many real-world graphs exhibit heterophily, where linked nodes belong to different categories or possess diverse attributes, such as webpages, Wikipedia articles, social networks, and e-commerce platforms. Additionally, nodes in many domains are associated with textual descriptions, forming heterophilic text-attributed graphs (TAGs). Despite their significance, heterophilic TAGs remain underexplored due to the lack of dedicated benchmarks that jointly capture heterophilic structures and rich textual attributes. To address this gap, we introduce the \textbf{He}terophilic \textbf{T}ext-attributed \textbf{G}raph \textbf{B}enchmark (HeTGB), a novel benchmark comprising five real-world heterophilic graph datasets from diverse domains, with nodes enriched by extensive textual descriptions. HeTGB enables systematic evaluation of GNNs, pre-trained language models (PLMs) and co-training methods on the node classification task. Through extensive benchmarking experiments, we showcase the utility of text attributes in heterophilic graphs, analyze the challenges posed by heterophilic TAGs and the limitations of existing models, and provide insights into the interplay between graph structures and textual attributes.

Over the past decade, Graph Neural Networks (GNNs) have achieved great success on machine learning tasks with relational data. However, recent studies have found that heterophily can cause significant performance degradation of GNNs, especially on node-level tasks. Numerous heterophilic benchmark datasets have been put forward to validate the efficacy of heterophily-specific GNNs, and various homophily metrics have been designed to help recognize these challenging datasets. Nevertheless, there still exist multiple pitfalls that severely hinder the proper evaluation of new models and metrics: 1) lack of hyperparameter tuning; 2) insufficient evaluation on the truly challenging heterophilic datasets; 3) missing quantitative evaluation for homophily metrics on synthetic graphs. To overcome these challenges, we first train and fine-tune baseline models on $27$ most widely used benchmark datasets, and categorize them into three distinct groups: malignant, benign and ambiguous heterophilic datasets. We identify malignant and ambiguous heterophily as the truly challenging subsets of tasks, and to our best knowledge, we are the first to propose such taxonomy. Then, we re-evaluate $11$ state-of-the-arts (SOTA) GNNs, covering six popular methods, with fine-tuned hyperparameters on different groups of heterophilic datasets. Based on the model performance, we comprehensively reassess the effectiveness of different methods on heterophily. At last, we evaluate $11$ popular homophily metrics on synthetic graphs with three different graph generation approaches. To overcome the unreliability of observation-based comparison and evaluation, we conduct the first quantitative evaluation and provide detailed analysis.

The rapid adoption, usefulness, and resource-intensive training of Graph Neural Network (GNN) models have made them an invaluable intellectual property in graph-based machine learning. However, their wide-spread adoption also makes them susceptible to stealing, necessitating robust Ownership Demonstration (OD) techniques. Watermarking is a promising OD framework for deep neural networks, but existing methods fail to generalize to GNNs due to the non-Euclidean nature of graph data. Existing works on GNN watermarking primarily focus on node and graph classification, overlooking Link Prediction (LP). In this paper, we propose GENIE (watermarking Graph nEural Networks for lInk prEdiction), the first scheme to watermark GNNs for LP. GENIE creates a novel backdoor for both node-representation and subgraph-based LP methods, utilizing a unique trigger set and a secret watermark vector. Our OD scheme is equipped with Dynamic Watermark Thresholding (DWT), ensuring high verification probability while addressing practical issues in existing OD schemes. We extensively evaluate GENIE across 4 diverse model architectures (i.e., SEAL, GCN, GraphSAGE and NeoGNN), 7 real-world datasets and 21 watermark removal techniques and demonstrate its robustness to watermark removal and ownership piracy attacks. Finally, we discuss adaptive attacks against GENIE and a defense strategy to counter it. The codebase and related artifacts are publicly available at our Project Page.

Unitarity is a useful principle for stabilizing deep neural networks, but in graph neural networks (GNNs) instability is induced not only by learnable parameters but also by the graph propagation operator. Motivated by this distinction, we propose Graph Unitary Message Passing (GUMP), a message-passing framework that uses a unitary propagation operator on a transformed graph to avoid graph-induced exponential decay under repeated propagation. GUMP combines (i) a graph transformation that maps an input graph to an Eulerian line-graph construction admitting unitary adjacency matrices, and (ii) a practical unitary projection procedure based on Newton-Schulz iteration. Theoretical analysis clarifies that, under standard analysis assumptions, unitary propagation keeps the graph-propagation term depth-stable, while vanilla normalized propagation exhibits exponential decay in its non-trivial spectral components. Across synthetic long-range tasks, TUDataset benchmarks, and LRGB datasets, GUMP improves over vanilla message passing and achieves competitive or superior performance against strong baselines. Code is available at https://github.com/ucker/gump_code.

This manuscript provides a comprehensive review of the Maximum Clique Problem, a computational problem that involves finding subsets of vertices in a graph that are all pairwise adjacent to each other. As such, this review is a continuation of the series of previous reviews from 1994, 1999 and 2014. The manuscript covers in a simple way classical algorithms and includes a review of recent developments in graph neural networks and quantum algorithms.

Graph clustering, an important unsupervised problem, has been shown to be more resistant to advances in Graph Neural Networks (GNNs). In addition, almost all clustering methods focus on homophilic graphs and ignore heterophily. This significantly limits their applicability in practice, since real-world graphs exhibit a structural disparity and cannot simply be classified as homophily and heterophily. Thus, a principled way to handle practical graphs is urgently needed. To fill this gap, we provide a novel solution with theoretical support. Interestingly, we find that most homophilic and heterophilic edges can be correctly identified on the basis of neighbor information. Motivated by this finding, we construct two graphs that are highly homophilic and heterophilic, respectively. They are used to build low-pass and high-pass filters to capture holistic information. Important features are further enhanced by the squeeze-and-excitation block. We validate our approach through extensive experiments on both homophilic and heterophilic graphs. Empirical results demonstrate the superiority of our method compared to state-of-the-art clustering methods.