Foundation models are pretrained on large-scale corpora to learn generalizable patterns across domains and tasks -- such as contours, textures, and edges in images, or tokens and sentences in text. In contrast, discovering such generalities in graph-structured data, especially across heterogeneous graph tasks, remains an open challenge. To address this, we propose a novel approach to cross-task generalization in graphs via task-trees, which serve as unified learning instances aligning node-, edge-, and graph-level tasks. We theoretically analyze the stability, transferability, and generalization properties of task-trees, showing that pretraining a graph neural network (GNN) on diverse task-trees with a reconstruction objective induces transferable knowledge. This enables efficient adaptation to downstream tasks with minimal fine-tuning. To validate our framework, we introduce Graph Generality Identifier on Task-Trees (GIT), a graph foundation model that demonstrates strong performance on over 30 graphs across five domains via fine-tuning, in-context learning, and zero-shot generalization. Code and data are available at https://github.com/Zehong-Wang/GIT.
Graph neural networks (GNNs) have shown promise in integrating protein-protein interaction (PPI) networks for identifying cancer genes in recent studies. However, due to the insufficient modeling of the biological information in PPI networks, more faithfully depiction of complex protein interaction patterns for cancer genes within the graph structure remains largely unexplored. This study takes a pioneering step toward bridging biological anomalies in protein interactions caused by cancer genes to statistical graph anomaly. We find a unique graph anomaly exhibited by cancer genes, namely weight heterogeneity, which manifests as significantly higher variance in edge weights of cancer gene nodes within the graph. Additionally, from the spectral perspective, we demonstrate that the weight heterogeneity could lead to the "flattening out" of spectral energy, with a concentration towards the extremes of the spectrum. Building on these insights, we propose the HIerarchical-Perspective Graph Neural Network (HIPGNN) that not only determines spectral energy distribution variations on the spectral perspective, but also perceives detailed protein interaction context on the spatial perspective. Extensive experiments are conducted on two reprocessed datasets STRINGdb and CPDB, and the experimental results demonstrate the superiority of HIPGNN.
This paper explores the impact of relational state abstraction on sample efficiency and performance in collaborative Multi-Agent Reinforcement Learning. The proposed abstraction is based on spatial relationships in environments where direct communication between agents is not allowed, leveraging the ubiquity of spatial reasoning in real-world multi-agent scenarios. We introduce MARC (Multi-Agent Relational Critic), a simple yet effective critic architecture incorporating spatial relational inductive biases by transforming the state into a spatial graph and processing it through a relational graph neural network. The performance of MARC is evaluated across six collaborative tasks, including a novel environment with heterogeneous agents. We conduct a comprehensive empirical analysis, comparing MARC against state-of-the-art MARL baselines, demonstrating improvements in both sample efficiency and asymptotic performance, as well as its potential for generalization. Our findings suggest that a minimal integration of spatial relational inductive biases as abstraction can yield substantial benefits without requiring complex designs or task-specific engineering. This work provides insights into the potential of relational state abstraction to address sample efficiency, a key challenge in MARL, offering a promising direction for developing more efficient algorithms in spatially complex environments.
This study aims to build a pre-trained Graph Neural Network (GNN) model on molecules without human annotations or prior knowledge. Although various attempts have been proposed to overcome limitations in acquiring labeled molecules, the previous pre-training methods still rely on semantic subgraphs, i.e., functional groups. Only focusing on the functional groups could overlook the graph-level distinctions. The key challenge to build a pre-trained GNN on molecules is how to (1) generate well-distinguished graph-level representations and (2) automatically discover the functional groups without prior knowledge. To solve it, we propose a novel Subgraph-conditioned Graph Information Bottleneck, named S-CGIB, for pre-training GNNs to recognize core subgraphs (graph cores) and significant subgraphs. The main idea is that the graph cores contain compressed and sufficient information that could generate well-distinguished graph-level representations and reconstruct the input graph conditioned on significant subgraphs across molecules under the S-CGIB principle. To discover significant subgraphs without prior knowledge about functional groups, we propose generating a set of functional group candidates, i.e., ego networks, and using an attention-based interaction between the graph core and the candidates. Despite being identified from self-supervised learning, our learned subgraphs match the real-world functional groups. Extensive experiments on molecule datasets across various domains demonstrate the superiority of S-CGIB.
Nuclear magnetic resonance (NMR) is a powerful spectroscopic technique that is sensitive to the local atomic structure of matter. Computational predictions of NMR parameters can help to interpret experimental data and validate structural models, and machine learning (ML) has emerged as an efficient route to making such predictions. Here, we systematically study graph-neural-network approaches to representing and learning tensor quantities for solid-state NMR -- specifically, the anisotropic magnetic shielding and the electric field gradient. We assess how the numerical accuracy of different ML models translates into prediction quality for experimentally relevant NMR properties: chemical shifts, quadrupolar coupling constants, tensor orientations, and even static 1D spectra. We apply these ML models to a structurally diverse dataset of amorphous SiO$_2$ configurations, spanning a wide range of density and local order, to larger configurations beyond the reach of traditional first-principles methods, and to the dynamics of the $\alpha\unicode{x2013}\beta$ inversion in cristobalite. Our work marks a step toward streamlining ML-driven NMR predictions for both static and dynamic behavior of complex materials, and toward bridging the gap between first-principles modeling and real-world experimental data.
Graph Neural Networks (GNNs) are a highly effective neural network architecture for processing graph -- structured data. Unlike traditional neural networks that rely solely on the features of the data as input, GNNs leverage both the graph structure, which represents the relationships between data points, and the feature matrix of the data to optimize their feature representation. This unique capability enables GNNs to achieve superior performance across various tasks. However, it also makes GNNs more susceptible to noise from both the graph structure and data features, which can significantly increase the training difficulty and degrade their performance. To address this issue, this paper proposes a novel method for selecting noise-sensitive training samples from the original training set to construct a smaller yet more effective training set for model training. These samples are used to help improve the model's ability to correctly process data in noisy environments. We have evaluated our approach on three of the most classical GNN models -- GCN, GAT, and GraphSAGE -- as well as three widely used benchmark datasets: Cora, Citeseer, and PubMed. Our experiments demonstrate that the proposed method can substantially boost the training of Graph Neural Networks compared to using randomly sampled training sets of the same size from the original training set and the larger original full training set.
In recent years, Large Language Models (LLMs) gain considerable attention for their potential to enhance personalized experiences in virtual assistants and chatbots. A key area of interest is the integration of personas into LLMs to improve dialogue naturalness and user engagement. This study addresses the challenge of persona classification, a crucial component in dialogue understanding, by proposing a framework that combines text embeddings with Graph Neural Networks (GNNs) for effective persona classification. Given the absence of dedicated persona classification datasets, we create a manually annotated dataset to facilitate model training and evaluation. Our method involves extracting semantic features from persona statements using text embeddings and constructing a graph where nodes represent personas and edges capture their similarities. The GNN component uses this graph structure to propagate relevant information, thereby improving classification performance. Experimental results show that our approach, in particular the integration of GNNs, significantly improves classification performance, especially with limited data. Our contributions include the development of a persona classification framework and the creation of a dataset.
Graph Neural Networks (GNNs) have demonstrated significant achievements in processing graph data, yet scalability remains a substantial challenge. To address this, numerous graph coarsening methods have been developed. However, most existing coarsening methods are training-dependent, leading to lower efficiency, and they all require a predefined coarsening rate, lacking an adaptive approach. In this paper, we employ granular-ball computing to effectively compress graph data. We construct a coarsened graph network by iteratively splitting the graph into granular-balls based on a purity threshold and using these granular-balls as super vertices. This granulation process significantly reduces the size of the original graph, thereby greatly enhancing the training efficiency and scalability of GNNs. Additionally, our algorithm can adaptively perform splitting without requiring a predefined coarsening rate. Experimental results demonstrate that our method achieves accuracy comparable to training on the original graph. Noise injection experiments further indicate that our method exhibits robust performance. Moreover, our approach can reduce the graph size by up to 20 times without compromising test accuracy, substantially enhancing the scalability of GNNs.
In many problem settings that require spatio-temporal forecasting, the values in the time-series not only exhibit spatio-temporal correlations but are also influenced by spatial diffusion across locations. One such example is forecasting the concentration of fine particulate matter (PM2.5) in the atmosphere which is influenced by many complex factors, the most important ones being diffusion due to meteorological factors as well as transport across vast distances over a period of time. We present a novel Spatio-Temporal Graph Neural Network architecture, that specifically captures these dependencies to forecast the PM2.5 concentration. Our model is based on an encoder-decoder architecture where the encoder and decoder parts leverage gated recurrent units (GRU) augmented with a graph neural network (TransformerConv) to account for spatial diffusion. Our model can also be seen as a generalization of various existing models for time-series or spatio-temporal forecasting. We demonstrate the model's effectiveness on two real-world PM2.5 datasets: (1) data collected by us using a recently deployed network of low-cost PM$_{2.5}$ sensors from 511 locations spanning the entirety of the Indian state of Bihar over a period of one year, and (2) another publicly available dataset that covers severely polluted regions from China for a period of 4 years. Our experimental results show our model's impressive ability to account for both spatial as well as temporal dependencies precisely.
Natural language explanations (NLEs) are commonly used to provide plausible free-text explanations of a model's reasoning about its predictions. However, recent work has questioned the faithfulness of NLEs, as they may not accurately reflect the model's internal reasoning process regarding its predicted answer. In contrast, highlight explanations -- input fragments identified as critical for the model's predictions -- exhibit measurable faithfulness, which has been incrementally improved through existing research. Building on this foundation, we propose G-Tex, a Graph-Guided Textual Explanation Generation framework designed to enhance the faithfulness of NLEs by leveraging highlight explanations. Specifically, highlight explanations are extracted as highly faithful cues representing the model's reasoning and are subsequently encoded through a graph neural network layer, which explicitly guides the NLE generation process. This alignment ensures that the generated explanations closely reflect the model's underlying reasoning. Experiments on T5 and BART using three reasoning datasets show that G-Tex improves NLE faithfulness by up to 17.59% compared to baseline methods. Additionally, G-Tex generates NLEs with greater semantic and lexical similarity to human-written ones. Human evaluations show that G-Tex can decrease redundant content and enhance the overall quality of NLEs. As our work introduces a novel method for explicitly guiding NLE generation to improve faithfulness, we hope it will serve as a stepping stone for addressing additional criteria for NLE and generated text overall.
Accurately modeling and analyzing time series data is crucial for downstream applications across various fields, including healthcare, finance, astronomy, and epidemiology. However, real-world time series often exhibit irregularities such as misaligned timestamps, missing entries, and variable sampling rates, complicating their analysis. Existing approaches often rely on imputation, which can introduce biases. A few approaches that directly model irregularity tend to focus exclusively on either capturing intra-series patterns or inter-series relationships, missing the benefits of integrating both. To this end, we present WaveGNN, a novel framework designed to directly (i.e., no imputation) embed irregularly sampled multivariate time series data for accurate predictions. WaveGNN utilizes a Transformer-based encoder to capture intra-series patterns by directly encoding the temporal dynamics of each time series. To capture inter-series relationships, WaveGNN uses a dynamic graph neural network model, where each node represents a sensor, and the edges capture the long- and short-term relationships between them. Our experimental results on real-world healthcare datasets demonstrate that WaveGNN consistently outperforms existing state-of-the-art methods, with an average relative improvement of 14.7% in F1-score when compared to the second-best baseline in cases with extreme sparsity. Our ablation studies reveal that both intra-series and inter-series modeling significantly contribute to this notable improvement.
The Fussell-Vesely Importance (FV) reflects the potential impact of a basic event on system failure, and is crucial for ensuring system reliability. However, traditional methods for calculating FV importance are complex and time-consuming, requiring the construction of fault trees and the calculation of minimal cut set. To address these limitations, this study proposes a hybrid real-time framework to evaluate the FV importance of basic events. Our framework combines expert knowledge with a data-driven model. First, we use Interpretive Structural Modeling (ISM) to build a virtual fault tree that captures the relationships between basic events. Unlike traditional fault trees, which include intermediate events, our virtual fault tree consists solely of basic events, reducing its complexity and space requirements. Additionally, our virtual fault tree considers the dependencies between basic events rather than assuming their independence, as is typically done in traditional fault trees. We then feed both the event relationships and relevant data into a graph neural network (GNN). This approach enables a rapid, data-driven calculation of FV importance, significantly reducing processing time and quickly identifying critical events, thus providing robust decision support for risk control. Results demonstrate that our model performs well in terms of MSE, RMSE, MAE, and R2, reducing computational energy consumption and offering real-time, risk-informed decision support for complex systems.
We introduce a foundation model for event classification in high-energy physics, built on a Graph Neural Network architecture and trained on 120 million simulated proton-proton collision events spanning 12 distinct physics processes. The model is pretrained to learn a general and robust representation of collision data using challenging multiclass and multilabel classification tasks. Its performance is evaluated across five event classification tasks, which include both physics processes used during pretraining and new processes not encountered during pretraining. Fine-tuning the pretrained model significantly improves classification performance, particularly in scenarios with limited training data, demonstrating gains in both accuracy and computational efficiency. To investigate the underlying mechanisms behind these performance improvements, we employ a representational similarity evaluation framework based on Centered Kernel Alignment. This analysis reveals notable differences in the learned representations of fine-tuned pretrained models compared to baseline models trained from scratch.
Integrating multiple functionalities into a system poses a fascinating challenge to the field of deep learning. While the precise mechanisms by which the brain encodes and decodes information, and learns diverse skills, remain elusive, memorization undoubtedly plays a pivotal role in this process. In this article, we delve into the implementation and application of an autoencoder-inspired hippocampus network in a multi-functional system. We propose an autoencoder-based memorization method for policy function's parameters. Specifically, the encoder of the autoencoder maps policy function's parameters to a skill vector, while the decoder retrieves the parameters via this skill vector. The policy function is dynamically adjusted tailored to corresponding tasks. Henceforth, a skill vectors graph neural network is employed to represent the homeomorphic topological structure of subtasks and manage subtasks execution.
Graph neural networks (GNNs) with unsupervised learning can solve large-scale combinatorial optimization problems (COPs) with efficient time complexity, making them versatile for various applications. However, since this method maps the combinatorial optimization problem to the training process of a graph neural network, and the current mainstream backpropagation-based training algorithms are prone to fall into local minima, the optimization performance is still inferior to the current state-of-the-art (SOTA) COP methods. To address this issue, inspired by possibly chaotic dynamics of real brain learning, we introduce a chaotic training algorithm, i.e. chaotic graph backpropagation (CGBP), which introduces a local loss function in GNN that makes the training process not only chaotic but also highly efficient. Different from existing methods, we show that the global ergodicity and pseudo-randomness of such chaotic dynamics enable CGBP to learn each optimal GNN effectively and globally, thus solving the COP efficiently. We have applied CGBP to solve various COPs, such as the maximum independent set, maximum cut, and graph coloring. Results on several large-scale benchmark datasets showcase that CGBP can outperform not only existing GNN algorithms but also SOTA methods. In addition to solving large-scale COPs, CGBP as a universal learning algorithm for GNNs, i.e. as a plug-in unit, can be easily integrated into any existing method for improving the performance.
Traffic signal control plays a crucial role in urban mobility. However, existing methods often struggle to generalize beyond their training environments to unseen scenarios with varying traffic dynamics. We present TransferLight, a novel framework designed for robust generalization across road-networks, diverse traffic conditions and intersection geometries. At its core, we propose a log-distance reward function, offering spatially-aware signal prioritization while remaining adaptable to varied lane configurations - overcoming the limitations of traditional pressure-based rewards. Our hierarchical, heterogeneous, and directed graph neural network architecture effectively captures granular traffic dynamics, enabling transferability to arbitrary intersection layouts. Using a decentralized multi-agent approach, global rewards, and novel state transition priors, we develop a single, weight-tied policy that scales zero-shot to any road network without re-training. Through domain randomization during training, we additionally enhance generalization capabilities. Experimental results validate TransferLight's superior performance in unseen scenarios, advancing practical, generalizable intelligent transportation systems to meet evolving urban traffic demands.
This paper proposes a graph neural network (GNN)-based space multiple-input multiple-output (MIMO) framework, named GSM, for direct-to-cell communications, aiming to achieve distributed coordinated beamforming for low Earth orbit (LEO) satellites. Firstly, a system model for LEO multi-satellite communications is established, where multiple LEO satellites collaborate to perform distributed beamforming and communicate with terrestrial user terminals coherently. Based on the system model, a weighted sum rate maximization problem is formulated. Secondly, a GNN-based method is developed to address the optimization problem. Particularly, the adopted neural network is composed of multiple identical GNNs, which are trained together and then deployed individually on each LEO satellite. Finally, the trained GNN is quantized and deployed on a field-programmable gate array (FPGA) to accelerate the inference by customizing the microarchitecture. Simulation results demonstrate that the proposed GNN scheme outperforms the benchmark ones including maximum ratio transmission, zero forcing and minimum mean square error. Furthermore, experimental results show that the FPGA-based accelerator achieves remarkably low inference latency, ranging from 3.863 to 5.883 ms under a 10-ns target clock period with 8-bit fixed-point data representation.
Branch-and-Bound (B\&B) is an exact method in integer programming that recursively divides the search space into a tree. During the resolution process, determining the next subproblem to explore within the tree-known as the search strategy-is crucial. Hand-crafted heuristics are commonly used, but none are effective over all problem classes. Recent approaches utilizing neural networks claim to make more intelligent decisions but are computationally expensive. In this paper, we introduce GP2S (Genetic Programming for Search Strategy), a novel machine learning approach that automatically generates a B\&B search strategy heuristic, aiming to make intelligent decisions while being computationally lightweight. We define a policy as a function that evaluates the quality of a B\&B node by combining features from the node and the problem; the search strategy policy is then defined by a best-first search based on this node ranking. The policy space is explored using a genetic programming algorithm, and the policy that achieves the best performance on a training set is selected. We compare our approach with the standard method of the SCIP solver, a recent graph neural network-based method, and handcrafted heuristics. Our first evaluation includes three types of primal hard problems, tested on instances similar to the training set and on larger instances. Our method is at most 2\% slower than the best baseline and consistently outperforms SCIP, achieving an average speedup of 11.3\%. Additionally, GP2S is tested on the MIPLIB 2017 dataset, generating multiple heuristics from different subsets of instances. It exceeds SCIP's average performance in 7 out of 10 cases across 15 times more instances and under a time limit 15 times longer, with some GP2S methods leading on most experiments in terms of the number of feasible solutions or optimality gap.
Nowadays, social media is the ground for political debate and exchange of opinions. There is a significant amount of research that suggests that social media are highly polarized. A phenomenon that is commonly observed is the echo chamber structure, where users are organized in polarized communities and form connections only with similar-minded individuals, limiting themselves to consume specific content. In this paper we explore a way to decrease the polarization of networks with two echo chambers. Particularly, we observe that if some users adopt a moderate opinion about a topic, the polarization of the network decreases. Based on this observation, we propose an efficient algorithm to identify a good set of K users, such that if they adopt a moderate stance around a topic, the polarization is minimized. Our algorithm employs a Graph Neural Network and thus it can handle large graphs more effectively than other approaches
Optimization is crucial for MEC networks to function efficiently and reliably, most of which are NP-hard and lack efficient approximation algorithms. This leads to a paucity of optimal solution, constraining the effectiveness of conventional deep learning approaches. Most existing learning-based methods necessitate extensive optimal data and fail to exploit the potential benefits of suboptimal data that can be obtained with greater efficiency and effectiveness. Taking the multi-server multi-user computation offloading (MSCO) problem, which is widely observed in systems like Internet-of-Vehicles (IoV) and Unmanned Aerial Vehicle (UAV) networks, as a concrete scenario, we present a Graph Diffusion-based Solution Generation (GDSG) method. This approach is designed to work with suboptimal datasets while converging to the optimal solution large probably. We transform the optimization issue into distribution-learning and offer a clear explanation of learning from suboptimal training datasets. We build GDSG as a multi-task diffusion model utilizing a Graph Neural Network (GNN) to acquire the distribution of high-quality solutions. We use a simple and efficient heuristic approach to obtain a sufficient amount of training data composed entirely of suboptimal solutions. In our implementation, we enhance the backbone GNN and achieve improved generalization. GDSG also reaches nearly 100\% task orthogonality, ensuring no interference between the discrete and continuous generation tasks. We further reveal that this orthogonality arises from the diffusion-related training loss, rather than the neural network architecture itself. The experiments demonstrate that GDSG surpasses other benchmark methods on both the optimal and suboptimal training datasets. The MSCO datasets has open-sourced at this http URL, as well as the GDSG algorithm codes at https://github.com/qiyu3816/GDSG.