Machine-learning force fields (MLFFs) have emerged as a promising solution for speeding up ab initio molecular dynamics (MD) simulations, where accurate force predictions are critical but often computationally expensive. In this work, we employ GemNet-T, a graph neural network model, as an MLFF and investigate two training strategies: (1) direct training on MD17 (10K samples) without pre-training, and (2) pre-training on the large-scale OC20 dataset followed by fine-tuning on MD17 (10K). While both approaches achieve low force mean absolute errors (MAEs), reaching 5 meV/A per atom, we find that lower force errors do not necessarily guarantee stable MD simulations. Notably, the pre-trained GemNet-T model yields significantly improved simulation stability, sustaining trajectories up to three times longer than the model trained from scratch. These findings underscore the value of pre-training on large, diverse datasets to capture complex molecular interactions and highlight that force MAE alone is not always a sufficient metric of MD simulation stability.
This work presents a novel graph neural network (GNN) architecture, the Feature-specific Interpretable Graph Neural Network (FIGNN), designed to enhance the interpretability of deep learning surrogate models defined on unstructured grids in scientific applications. Traditional GNNs often obscure the distinct spatial influences of different features in multivariate prediction tasks. FIGNN addresses this limitation by introducing a feature-specific pooling strategy, which enables independent attribution of spatial importance for each predicted variable. Additionally, a mask-based regularization term is incorporated into the training objective to explicitly encourage alignment between interpretability and predictive error, promoting localized attribution of model performance. The method is evaluated for surrogate modeling of two physically distinct systems: the SPEEDY atmospheric circulation model and the backward-facing step (BFS) fluid dynamics benchmark. Results demonstrate that FIGNN achieves competitive predictive performance while revealing physically meaningful spatial patterns unique to each feature. Analysis of rollout stability, feature-wise error budgets, and spatial mask overlays confirm the utility of FIGNN as a general-purpose framework for interpretable surrogate modeling in complex physical domains.
In the modern context of power systems, rapid, scalable, and physically plausible power flow predictions are essential for ensuring the grid's safe and efficient operation. While traditional numerical methods have proven robust, they require extensive computation to maintain physical fidelity under dynamic or contingency conditions. In contrast, recent advancements in artificial intelligence (AI) have significantly improved computational speed; however, they often fail to enforce fundamental physical laws during real-world contingencies, resulting in physically implausible predictions. In this work, we introduce KCLNet, a physics-informed graph neural network that incorporates Kirchhoff's Current Law as a hard constraint via hyperplane projections. KCLNet attains competitive prediction accuracy while ensuring zero KCL violations, thereby delivering reliable and physically consistent power flow predictions critical to secure the operation of modern smart grids.
Chip manufacturing is a complex process, and to achieve a faster time to market, an increasing number of untrusted third-party tools and designs from around the world are being utilized. The use of these untrusted third party intellectual properties (IPs) and tools increases the risk of adversaries inserting hardware trojans (HTs). The covert nature of HTs poses significant threats to cyberspace, potentially leading to severe consequences for national security, the economy, and personal privacy. Many graph neural network (GNN)-based HT detection methods have been proposed. However, they perform poorly on larger designs because they rely on training with smaller designs. Additionally, these methods do not explore different GNN models that are well-suited for HT detection or provide efficient training and inference processes. We propose a novel framework that generates graph embeddings for large designs (e.g., RISC-V) and incorporates various GNN models tailored for HT detection. Furthermore, our framework introduces domain-specific techniques for efficient training and inference by implementing model quantization. Model quantization reduces the precision of the weights, lowering the computational requirements, enhancing processing speed without significantly affecting detection accuracy. We evaluate our framework using a custom dataset, and our results demonstrate a precision of 98.66% and a recall (true positive rate) of 92.30%, highlighting the effectiveness and efficiency of our approach in detecting hardware trojans in large-scale chip designs
Combinatorial optimization (CO) problems, central to operation research and theoretical computer science, present significant computational challenges due to their NP-hard nature. While large language models (LLMs) have emerged as promising tools for CO--either by directly generating solutions or synthesizing solver-specific codes--existing approaches often neglect critical structural priors inherent to CO problems, leading to suboptimality and iterative inefficiency. Inspired by human experts' success in leveraging CO structures for algorithm design, we propose STRCMP, a novel structure-aware LLM-based algorithm discovery framework that systematically integrates structure priors to enhance solution quality and solving efficiency. Our framework combines a graph neural network (GNN) for extracting structural embeddings from CO instances with an LLM conditioned on these embeddings to identify high-performing algorithms in the form of solver-specific codes. This composite architecture ensures syntactic correctness, preserves problem topology, and aligns with natural language objectives, while an evolutionary refinement process iteratively optimizes generated algorithm. Extensive evaluations across Mixed Integer Linear Programming and Boolean Satisfiability problems, using nine benchmark datasets, demonstrate that our proposed STRCMP outperforms five strong neural and LLM-based methods by a large margin, in terms of both solution optimality and computational efficiency. The code and learned model will be publicly available upon the acceptance of the paper.
Link prediction is a classical problem in graph analysis with many practical applications. For directed graphs, recently developed deep learning approaches typically analyze node similarities through contrastive learning and aggregate neighborhood information through graph convolutions. In this work, we propose a novel graph neural network (GNN) framework to fuse feature embedding with community information. We theoretically demonstrate that such hybrid features can improve the performance of directed link prediction. To utilize such features efficiently, we also propose an approach to transform input graphs into directed line graphs so that nodes in the transformed graph can aggregate more information during graph convolutions. Experiments on benchmark datasets show that our approach outperforms the state-of-the-art in most cases when 30%, 40%, 50%, and 60% of the connected links are used as training data, respectively.
Operations in disaster response, search \& rescue, and military missions that involve multiple agents demand automated processes to support the planning of the courses of action (COA). Moreover, traverse-affecting changes in the environment (rain, snow, blockades, etc.) may impact the expected performance of a COA, making it desirable to have a pool of COAs that are diverse in task distributions across agents. Further, variations in agent capabilities, which could be human crews and/or autonomous systems, present practical opportunities and computational challenges to the planning process. This paper presents a new theoretical formulation and computational framework to generate such diverse pools of COAs for operations with soft variations in agent-task compatibility. Key to the problem formulation is a graph abstraction of the task space and the pool of COAs itself to quantify its diversity. Formulating the COAs as a centralized multi-robot task allocation problem, a genetic algorithm is used for (order-ignoring) allocations of tasks to each agent that jointly maximize diversity within the COA pool and overall compatibility of the agent-task mappings. A graph neural network is trained using a policy gradient approach to then perform single agent task sequencing in each COA, which maximizes completion rates adaptive to task features. Our tests of the COA generation process in a simulated environment demonstrate significant performance gain over a random walk baseline, small optimality gap in task sequencing, and execution time of about 50 minutes to plan up to 20 COAs for 5 agent/100 task operations.
We present a novel graph-informed transformer operator (GITO) architecture for learning complex partial differential equation systems defined on irregular geometries and non-uniform meshes. GITO consists of two main modules: a hybrid graph transformer (HGT) and a transformer neural operator (TNO). HGT leverages a graph neural network (GNN) to encode local spatial relationships and a transformer to capture long-range dependencies. A self-attention fusion layer integrates the outputs of the GNN and transformer to enable more expressive feature learning on graph-structured data. TNO module employs linear-complexity cross-attention and self-attention layers to map encoded input functions to predictions at arbitrary query locations, ensuring discretization invariance and enabling zero-shot super-resolution across any mesh. Empirical results on benchmark PDE tasks demonstrate that GITO outperforms existing transformer-based neural operators, paving the way for efficient, mesh-agnostic surrogate solvers in engineering applications.
As one of the most detrimental code smells, code clones significantly increase software maintenance costs and heighten vulnerability risks, making their detection a critical challenge in software engineering. Abstract Syntax Trees (ASTs) dominate deep learning-based code clone detection due to their precise syntactic structure representation, but they inherently lack semantic depth. Recent studies address this by enriching AST-based representations with semantic graphs, such as Control Flow Graphs (CFGs) and Data Flow Graphs (DFGs). However, the effectiveness of various enriched AST-based representations and their compatibility with different graph-based machine learning techniques remains an open question, warranting further investigation to unlock their full potential in addressing the complexities of code clone detection. In this paper, we present a comprehensive empirical study to rigorously evaluate the effectiveness of AST-based hybrid graph representations in Graph Neural Network (GNN)-based code clone detection. We systematically compare various hybrid representations ((CFG, DFG, Flow-Augmented ASTs (FA-AST)) across multiple GNN architectures. Our experiments reveal that hybrid representations impact GNNs differently: while AST+CFG+DFG consistently enhances accuracy for convolution- and attention-based models (Graph Convolutional Networks (GCN), Graph Attention Networks (GAT)), FA-AST frequently introduces structural complexity that harms performance. Notably, GMN outperforms others even with standard AST representations, highlighting its superior cross-code similarity detection and reducing the need for enriched structures.
Temporal Betweenness Centrality (TBC) measures how often a node appears on optimal temporal paths, reflecting its importance in temporal networks. However, exact computation is highly expensive, and real-world TBC distributions are extremely imbalanced. The severe imbalance leads learning-based models to overfit to zero-centrality nodes, resulting in inaccurate TBC predictions and failure to identify truly central nodes. Existing graph neural network (GNN) methods either fail to handle such imbalance or ignore temporal dependencies altogether. To address these issues, we propose a scalable and inductive contrastive learning-based GNN (CLGNN) for accurate and efficient TBC prediction. CLGNN builds an instance graph to preserve path validity and temporal order, then encodes structural and temporal features using dual aggregation, i.e., mean and edge-to-node multi-head attention mechanisms, enhanced by temporal path count and time encodings. A stability-based clustering-guided contrastive module (KContrastNet) is introduced to separate high-, median-, and low-centrality nodes in representation space, mitigating class imbalance, while a regression module (ValueNet) estimates TBC values. CLGNN also supports multiple optimal path definitions to accommodate diverse temporal semantics. Extensive experiments demonstrate the effectiveness and efficiency of CLGNN across diverse benchmarks. CLGNN achieves up to a 663.7~$\times$ speedup compared to state-of-the-art exact TBC computation methods. It outperforms leading static GNN baselines with up to 31.4~$\times$ lower MAE and 16.7~$\times$ higher Spearman correlation, and surpasses state-of-the-art temporal GNNs with up to 5.7~$\times$ lower MAE and 3.9~$\times$ higher Spearman correlation.
Automatic sample identification (ASID), the detection and identification of portions of audio recordings that have been reused in new musical works, is an essential but challenging task in the field of audio query-based retrieval. While a related task, audio fingerprinting, has made significant progress in accurately retrieving musical content under "real world" (noisy, reverberant) conditions, ASID systems struggle to identify samples that have undergone musical modifications. Thus, a system robust to common music production transformations such as time-stretching, pitch-shifting, effects processing, and underlying or overlaying music is an important open challenge. In this work, we propose a lightweight and scalable encoding architecture employing a Graph Neural Network within a contrastive learning framework. Our model uses only 9% of the trainable parameters compared to the current state-of-the-art system while achieving comparable performance, reaching a mean average precision (mAP) of 44.2%. To enhance retrieval quality, we introduce a two-stage approach consisting of an initial coarse similarity search for candidate selection, followed by a cross-attention classifier that rejects irrelevant matches and refines the ranking of retrieved candidates - an essential capability absent in prior models. In addition, because queries in real-world applications are often short in duration, we benchmark our system for short queries using new fine-grained annotations for the Sample100 dataset, which we publish as part of this work.
While online advertising is highly dependent on implicit interaction networks of anonymous users for engagement inference, and for the selection and optimization of delivery strategies, existing graph models seldom can capture the multi-scale temporal, semantic and higher-order dependency features of these interaction networks, thus it's hard to describe the complicated patterns of the anonymous behavior. In this paper, we propose Decoupled Temporal-Hierarchical Graph Neural Network (DTH-GNN), which achieves three main contributions. Above all, we introduce temporal edge decomposition, which divides each interaction into three types of channels: short-term burst, diurnal cycle and long-range memory, and conducts feature extraction using the convolution kernel of parallel dilated residuals; Furthermore, our model builds a hierarchical heterogeneous aggregation, where user-user, user-advertisement, advertisement-advertisement subgraphs are combined through the meta-path conditional Transformer encoder, where the noise structure is dynamically tamped down via the synergy of cross-channel self-attention and gating relationship selector. Thirdly, the contrast regularity of feedback perception is formulated, the consistency of various time slices is maximized, the entropy of control exposure information with dual-view target is maximized, the global prototype of dual-momentum queue distillation is presented, and the strategy gradient layer with light weight is combined with delaying transformation signal to fine-tune the node representation for benefit-oriented. The AUC of DTH-GNN improved by 8.2% and the logarithmic loss improved by 5.7% in comparison with the best baseline model.
Graph Neural Networks (GNNs) have recently been found to excel in histopathology. However, an important histopathological task, where GNNs have not been extensively explored, is the classification of glomeruli health as an important indicator in nephropathology. This task presents unique difficulties, particularly for the graph construction, i.e., the identification of nodes, edges, and informative features. In this work, we propose a pipeline composed of different traditional and machine learning-based computer vision techniques to identify nodes, edges, and their corresponding features to form a heterogeneous graph. We then proceed to propose a novel heterogeneous GNN architecture for glomeruli classification, called HIEGNet, that integrates both glomeruli and their surrounding immune cells. Hence, HIEGNet is able to consider the immune environment of each glomerulus in its classification. Our HIEGNet was trained and tested on a dataset of Whole Slide Images from kidney transplant patients. Experimental results demonstrate that HIEGNet outperforms several baseline models and generalises best between patients among all baseline models. Our implementation is publicly available at https://github.com/nklsKrmnn/HIEGNet.git.
In the recent years, branch-and-cut algorithms have been the target of data-driven approaches designed to enhance the decision making in different phases of the algorithm such as branching, or the choice of cutting planes (cuts). In particular, for cutting plane selection two score functions have been proposed in the literature to evaluate the quality of a cut: branch-and-cut tree size and gap closed. In this paper, we present new sample complexity lower bounds, valid for both scores. We show that for a wide family of classes $\mathcal{F}$ that maps an instance to a cut, learning over an unknown distribution of the instances to minimize those scores requires at least (up to multiplicative constants) as many samples as learning from the same class function $\mathcal{F}$ any generic target function (using square loss). Our results also extend to the case of learning from a restricted set of cuts, namely those from the Simplex tableau. To the best of our knowledge, these constitute the first lower bounds for the learning-to-cut framework. We compare our bounds to known upper bounds in the case of neural networks and show they are nearly tight. We illustrate our results with a graph neural network selection evaluated on set covering and facility location integer programming models and we empirically show that the gap closed score is an effective proxy to minimize the branch-and-cut tree size. Although the gap closed score has been extensively used in the integer programming literature, this is the first principled analysis discussing both scores at the same time both theoretically and computationally.
As the number of mobile devices continues to grow, interference has become a major bottleneck in improving data rates in wireless networks. Efficient joint channel and power allocation (JCPA) is crucial for managing interference. In this paper, we first propose an enhanced WMMSE (eWMMSE) algorithm to solve the JCPA problem in multi-channel wireless networks. To reduce the computational complexity of iterative optimization, we further introduce JCPGNN-M, a graph neural network-based solution that enables simultaneous multi-channel allocation for each user. We reformulate the problem as a Lagrangian function, which allows us to enforce the total power constraints systematically. Our solution involves combining this Lagrangian framework with GNNs and iteratively updating the Lagrange multipliers and resource allocation scheme. Unlike existing GNN-based methods that limit each user to a single channel, JCPGNN-M supports efficient spectrum reuse and scales well in dense network scenarios. Simulation results show that JCPGNN-M achieves better data rate compared to eWMMSE. Meanwhile, the inference time of JCPGNN-M is much lower than eWMMS, and it can generalize well to larger networks.
Emerging economies, particularly the MINT countries (Mexico, Indonesia, Nigeria, and T\"urkiye), are gaining influence in global stock markets, although they remain susceptible to the economic conditions of developed countries like the G7 (Canada, France, Germany, Italy, Japan, the United Kingdom, and the United States). This interconnectedness and sensitivity of financial markets make understanding these relationships crucial for investors and policymakers to predict stock price movements accurately. To this end, we examined the main stock market indices of G7 and MINT countries from 2012 to 2024, using a recent graph neural network (GNN) algorithm called multivariate time series forecasting with graph neural network (MTGNN). This method allows for considering complex spatio-temporal connections in multivariate time series. In the implementations, MTGNN revealed that the US and Canada are the most influential G7 countries regarding stock indices in the forecasting process, and Indonesia and T\"urkiye are the most influential MINT countries. Additionally, our results showed that MTGNN outperformed traditional methods in forecasting the prices of stock market indices for MINT and G7 countries. Consequently, the study offers valuable insights into economic blocks' markets and presents a compelling empirical approach to analyzing global stock market dynamics using MTGNN.
Graph-based learned simulators have emerged as a promising approach for simulating physical systems on unstructured meshes, offering speed and generalization across diverse geometries. However, they often struggle with capturing global phenomena, such as bending or long-range correlations, and suffer from error accumulation over long rollouts due to their reliance on local message passing and direct next-step prediction. We address these limitations by introducing the Rolling Diffusion-Batched Inference Network (ROBIN), a novel learned simulator that integrates two key innovations: (i) Rolling Diffusion, a parallelized inference scheme that amortizes the cost of diffusion-based refinement across physical time steps by overlapping denoising steps across a temporal window. (ii) A Hierarchical Graph Neural Network built on algebraic multigrid coarsening, enabling multiscale message passing across different mesh resolutions. This architecture, implemented via Algebraic-hierarchical Message Passing Networks, captures both fine-scale local dynamics and global structural effects critical for phenomena like beam bending or multi-body contact. We validate ROBIN on challenging 2D and 3D solid mechanics benchmarks involving geometric, material, and contact nonlinearities. ROBIN achieves state-of-the-art accuracy on all tasks, substantially outperforming existing next-step learned simulators while reducing inference time by up to an order of magnitude compared to standard diffusion simulators.
Machine learning potentials (MLPs) have advanced rapidly and show great promise to transform molecular dynamics (MD) simulations. However, most existing software tools are tied to specific MLP architectures, lack integration with standard MD packages, or are not parallelizable across GPUs. To address these challenges, we present chemtrain-deploy, a framework that enables model-agnostic deployment of MLPs in LAMMPS. chemtrain-deploy supports any JAX-defined semi-local potential, allowing users to exploit the functionality of LAMMPS and perform large-scale MLP-based MD simulations on multiple GPUs. It achieves state-of-the-art efficiency and scales to systems containing millions of atoms. We validate its performance and scalability using graph neural network architectures, including MACE, Allegro, and PaiNN, applied to a variety of systems, such as liquid-vapor interfaces, crystalline materials, and solvated peptides. Our results highlight the practical utility of chemtrain-deploy for real-world, high-performance simulations and provide guidance for MLP architecture selection and future design.
Nowadays, the issue of information overload is gradually gaining exposure in the Internet of Things (IoT), calling for more research on recommender system in advance for industrial IoT scenarios. With the ever-increasing prevalence of various social networks, social recommendations (SoR) will certainly become an integral application that provides more feasibly personalized information service for future IoT users. However, almost all of the existing research managed to explore and quantify correlations between user preferences and social relationships, while neglecting the correlations among item features which could further influence the topologies of some social groups. To tackle with this challenge, in this article, a deep graph neural network-based social recommendation framework (GNN-SoR) is proposed for future IoTs. First, user and item feature spaces are abstracted as two graph networks and respectively encoded via the graph neural network method. Next, two encoded spaces are embedded into two latent factors of matrix factorization to complete missing rating values in a user-item rating matrix. Finally, a large amount of experiments are conducted on three real-world data sets to verify the efficiency and stability of the proposed GNN-SoR.
Matrix completion is a widely adopted framework in recommender systems, as predicting the missing entries in the user-item rating matrix enables a comprehensive understanding of user preferences. However, current graph neural network (GNN)-based approaches are highly sensitive to noisy or irrelevant edges--due to their inherent message-passing mechanisms--and are prone to overfitting, which limits their generalizability. To overcome these challenges, we propose a novel method called Matrix Completion using Contrastive Learning (MCCL). Our approach begins by extracting local neighborhood subgraphs for each interaction and subsequently generates two distinct graph representations. The first representation emphasizes denoising by integrating GNN layers with an attention mechanism, while the second is obtained via a graph variational autoencoder that aligns the feature distribution with a standard prior. A mutual learning loss function is employed during training to gradually harmonize these representations, enabling the model to capture common patterns and significantly enhance its generalizability. Extensive experiments on several real-world datasets demonstrate that our approach not only improves the numerical accuracy of the predicted scores--achieving up to a 0.8% improvement in RMSE--but also produces superior rankings with improvements of up to 36% in ranking metrics.