Daily Papers

Videos of robots interacting with objects encode rich information about the objects' dynamics. However, existing video prediction approaches typically do not explicitly account for the 3D information from videos, such as robot actions and objects' 3D states, limiting their use in real-world robotic applications. In this work, we introduce a framework to learn object dynamics directly from multi-view RGB videos by explicitly considering the robot's action trajectories and their effects on scene dynamics. We utilize the 3D Gaussian representation of 3D Gaussian Splatting (3DGS) to train a particle-based dynamics model using Graph Neural Networks. This model operates on sparse control particles downsampled from the densely tracked 3D Gaussian reconstructions. By learning the neural dynamics model on offline robot interaction data, our method can predict object motions under varying initial configurations and unseen robot actions. The 3D transformations of Gaussians can be interpolated from the motions of control particles, enabling the rendering of predicted future object states and achieving action-conditioned video prediction. The dynamics model can also be applied to model-based planning frameworks for object manipulation tasks. We conduct experiments on various kinds of deformable materials, including ropes, clothes, and stuffed animals, demonstrating our framework's ability to model complex shapes and dynamics. Our project page is available at https://gs-dynamics.github.io.

Recent advances in representation learning on graphs, mainly leveraging graph convolutional networks, have brought a substantial improvement on many graph-based benchmark tasks. While novel approaches to learning node embeddings are highly suitable for node classification and link prediction, their application to graph classification (predicting a single label for the entire graph) remains mostly rudimentary, typically using a single global pooling step to aggregate node features or a hand-designed, fixed heuristic for hierarchical coarsening of the graph structure. An important step towards ameliorating this is differentiable graph coarsening---the ability to reduce the size of the graph in an adaptive, data-dependent manner within a graph neural network pipeline, analogous to image downsampling within CNNs. However, the previous prominent approach to pooling has quadratic memory requirements during training and is therefore not scalable to large graphs. Here we combine several recent advances in graph neural network design to demonstrate that competitive hierarchical graph classification results are possible without sacrificing sparsity. Our results are verified on several established graph classification benchmarks, and highlight an important direction for future research in graph-based neural networks.

Chronic Low Back Pain (CLBP) afflicts millions globally, significantly impacting individuals' well-being and imposing economic burdens on healthcare systems. While artificial intelligence (AI) and deep learning offer promising avenues for analyzing pain-related behaviors to improve rehabilitation strategies, current models, including convolutional neural networks (CNNs), recurrent neural networks, and graph-based neural networks, have limitations. These approaches often focus singularly on the temporal dimension or require complex architectures to exploit spatial interrelationships within multivariate time series data. To address these limitations, we introduce L-SFAN, a lightweight CNN architecture incorporating 2D filters designed to meticulously capture the spatial-temporal interplay of data from motion capture and surface electromyography sensors. Our proposed model, enhanced with an oriented global pooling layer and multi-head self-attention mechanism, prioritizes critical features to better understand CLBP and achieves competitive classification accuracy. Experimental results on the EmoPain database demonstrate that our approach not only enhances performance metrics with significantly fewer parameters but also promotes model interpretability, offering valuable insights for clinicians in managing CLBP. This advancement underscores the potential of AI in transforming healthcare practices for chronic conditions like CLBP, providing a sophisticated framework for the nuanced analysis of complex biomedical data.

Graph-based learning has emerged as a transformative approach for modeling complex relationships across diverse domains, yet its potential in wireless security remains largely unexplored. In this work, we introduce the first application of graph-based learning for jamming source localization, addressing the imminent threat of jamming attacks in wireless networks. Unlike geometric optimization techniques that struggle under environmental uncertainties and dense interference, we reformulate localization as an inductive graph regression task. Our approach integrates structured node representations that encode local and global signal aggregation, ensuring spatial coherence and adaptive signal fusion. To enhance robustness, we incorporate an attention-based graph neural network that adaptively refines neighborhood influence and introduces a confidence-guided estimation mechanism that dynamically balances learned predictions with domain-informed priors. We evaluate our approach under complex radio frequency environments with varying sampling densities and signal propagation conditions, conducting comprehensive ablation studies on graph construction, feature selection, and pooling strategies. Results demonstrate that our novel graph-based learning framework significantly outperforms established localization baselines, particularly in challenging scenarios with sparse and obfuscated signal information. Code is available at [https://github.com/daniaherzalla/gnn-jamming-source-localization](https://github.com/daniaherzalla/gnn-jamming-source-localization).

There is a recent surge in the development of spatio-temporal forecasting models in the transportation domain. Long-range traffic forecasting, however, remains a challenging task due to the intricate and extensive spatio-temporal correlations observed in traffic networks. Current works primarily rely on road networks with graph structures and learn representations using graph neural networks (GNNs), but this approach suffers from over-smoothing problem in deep architectures. To tackle this problem, recent methods introduced the combination of GNNs with residual connections or neural ordinary differential equations (ODE). However, current graph ODE models face two key limitations in feature extraction: (1) they lean towards global temporal patterns, overlooking local patterns that are important for unexpected events; and (2) they lack dynamic semantic edges in their architectural design. In this paper, we propose a novel architecture called Graph-based Multi-ODE Neural Networks (GRAM-ODE) which is designed with multiple connective ODE-GNN modules to learn better representations by capturing different views of complex local and global dynamic spatio-temporal dependencies. We also add some techniques like shared weights and divergence constraints into the intermediate layers of distinct ODE-GNN modules to further improve their communication towards the forecasting task. Our extensive set of experiments conducted on six real-world datasets demonstrate the superior performance of GRAM-ODE compared with state-of-the-art baselines as well as the contribution of different components to the overall performance. The code is available at https://github.com/zbliu98/GRAM-ODE

Neural networks adapt very well to distributed and continuous representations, but struggle to generalize from small amounts of data. Symbolic systems commonly achieve data efficient generalization by exploiting modularity to benefit from local and discrete features of a representation. These features allow symbolic programs to be improved one module at a time and to experience combinatorial growth in the values they can successfully process. However, it is difficult to design a component that can be used to form symbolic abstractions and which is adequately overparametrized to learn arbitrary high-dimensional transformations. I present Graph-based Symbolically Synthesized Neural Networks (G-SSNNs), a class of neural modules that operate on representations modified with synthesized symbolic programs to include a fixed set of local and discrete features. I demonstrate that the choice of injected features within a G-SSNN module modulates the data efficiency and generalization of baseline neural models, creating predictable patterns of both heightened and curtailed generalization. By training G-SSNNs, we also derive information about desirable semantics of symbolic programs without manual engineering. This information is compact and amenable to abstraction, but can also be flexibly recontextualized for other high-dimensional settings. In future work, I will investigate data efficient generalization and the transferability of learned symbolic representations in more complex G-SSNN designs based on more complex classes of symbolic programs. Experimental code and data are available at https://github.com/shlomenu/symbolically_synthesized_networks .

We present graph attention networks (GATs), novel neural network architectures that operate on graph-structured data, leveraging masked self-attentional layers to address the shortcomings of prior methods based on graph convolutions or their approximations. By stacking layers in which nodes are able to attend over their neighborhoods' features, we enable (implicitly) specifying different weights to different nodes in a neighborhood, without requiring any kind of costly matrix operation (such as inversion) or depending on knowing the graph structure upfront. In this way, we address several key challenges of spectral-based graph neural networks simultaneously, and make our model readily applicable to inductive as well as transductive problems. Our GAT models have achieved or matched state-of-the-art results across four established transductive and inductive graph benchmarks: the Cora, Citeseer and Pubmed citation network datasets, as well as a protein-protein interaction dataset (wherein test graphs remain unseen during training).

Retrieval Augmented Generation (RAG) has greatly improved the performance of Large Language Model (LLM) responses by grounding generation with context from existing documents. These systems work well when documents are clearly relevant to a question context. But what about when a document has partial information, or less obvious connections to the context? And how should we reason about connections between documents? In this work, we seek to answer these two core questions about RAG generation. We introduce G-RAG, a reranker based on graph neural networks (GNNs) between the retriever and reader in RAG. Our method combines both connections between documents and semantic information (via Abstract Meaning Representation graphs) to provide a context-informed ranker for RAG. G-RAG outperforms state-of-the-art approaches while having smaller computational footprint. Additionally, we assess the performance of PaLM 2 as a reranker and find it to significantly underperform G-RAG. This result emphasizes the importance of reranking for RAG even when using Large Language Models.

Attention-based graph neural networks (GNNs), such as graph attention networks (GATs), have become popular neural architectures for processing graph-structured data and learning node embeddings. Despite their empirical success, these models rely on labeled data and the theoretical properties of these models have yet to be fully understood. In this work, we propose a novel attention-based node embedding framework for graphs. Our framework builds upon a hierarchical kernel for multisets of subgraphs around nodes (e.g. neighborhoods) and each kernel leverages the geometry of a smooth statistical manifold to compare pairs of multisets, by "projecting" the multisets onto the manifold. By explicitly computing node embeddings with a manifold of Gaussian mixtures, our method leads to a new attention mechanism for neighborhood aggregation. We provide theoretical insights into generalizability and expressivity of our embeddings, contributing to a deeper understanding of attention-based GNNs. We propose both efficient unsupervised and supervised methods for learning the embeddings. Through experiments on several node classification benchmarks, we demonstrate that our proposed method outperforms existing attention-based graph models like GATs. Our code is available at https://github.com/BorgwardtLab/fisher_information_embedding.

Recent progress in Graph Neural Networks has resulted in wide adoption by many applications, including recommendation systems. The reason for Graph Neural Networks' superiority over other approaches is that many problems in recommendation systems can be naturally modeled as graphs, where nodes can be either users or items and edges represent preference relationships. In current Graph Neural Network approaches, nodes are represented with a static vector learned at training time. This static vector might only be suitable to capture some of the nuances of users or items they define. To overcome this limitation, we propose using a recently proposed model inspired by category theory: Sheaf Neural Networks. Sheaf Neural Networks, and its connected Laplacian, can address the previous problem by associating every node (and edge) with a vector space instead than a single vector. The vector space representation is richer and allows picking the proper representation at inference time. This approach can be generalized for different related tasks on graphs and achieves state-of-the-art performance in terms of F1-Score@N in collaborative filtering and Hits@20 in link prediction. For collaborative filtering, the approach is evaluated on the MovieLens 100K with a 5.1% improvement, on MovieLens 1M with a 5.4% improvement and on Book-Crossing with a 2.8% improvement, while for link prediction on the ogbl-ddi dataset with a 1.6% refinement with respect to the respective baselines.

Accurately predicting the criticalness of ICU patients (such as in-ICU mortality risk) is vital for early intervention in critical care. However, conventional models often treat each patient in isolation and struggle to exploit the relational structure in Electronic Health Records (EHR). We propose a Similarity-Based Self-Construct Graph Model (SBSCGM) that dynamically builds a patient similarity graph from multi-modal EHR data, and a HybridGraphMedGNN architecture that operates on this graph to predict patient mortality and a continuous criticalness score. SBSCGM uses a hybrid similarity measure (combining feature-based and structural similarities) to connect patients with analogous clinical profiles in real-time. The HybridGraphMedGNN integrates Graph Convolutional Network (GCN), GraphSAGE, and Graph Attention Network (GAT) layers to learn robust patient representations, leveraging both local and global graph patterns. In experiments on 6,000 ICU stays from the MIMIC-III dataset, our model achieves state-of-the-art performance (AUC-ROC 0.94) outperforming baseline classifiers and single-type GNN models. We also demonstrate improved precision/recall and show that the attention mechanism provides interpretable insights into model predictions. Our framework offers a scalable and interpretable solution for critical care risk prediction, with potential to support clinicians in real-world ICU deployment.

Causal structures for observational survival data provide crucial information regarding the relationships between covariates and time-to-event. We derive motivation from the information theoretic source coding argument, and show that incorporating the knowledge of the directed acyclic graph (DAG) can be beneficial if suitable source encoders are employed. As a possible source encoder in this context, we derive a variational inference based conditional variational autoencoder for causal structured survival prediction, which we refer to as DAGSurv. We illustrate the performance of DAGSurv on low and high-dimensional synthetic datasets, and real-world datasets such as METABRIC and GBSG. We demonstrate that the proposed method outperforms other survival analysis baselines such as Cox Proportional Hazards, DeepSurv and Deephit, which are oblivious to the underlying causal relationship between data entities.

Document AI aims to automatically analyze documents by leveraging natural language processing and computer vision techniques. One of the major tasks of Document AI is document layout analysis, which structures document pages by interpreting the content and spatial relationships of layout, image, and text. This task can be image-centric, wherein the aim is to identify and label various regions such as authors and paragraphs, or text-centric, where the focus is on classifying individual words in a document. Although there are increasingly sophisticated methods for improving layout analysis, doubts remain about the extent to which their findings can be generalized to a broader context. Specifically, prior work developed systems based on very different architectures, such as transformer-based, graph-based, and CNNs. However, no work has mentioned the effectiveness of these models in a comparative analysis. Moreover, while language-independent Document AI models capable of knowledge transfer have been developed, it remains to be investigated to what degree they can effectively transfer knowledge. In this study, we aim to fill these gaps by conducting a comparative evaluation of state-of-the-art models in document layout analysis and investigating the potential of cross-lingual layout analysis by utilizing machine translation techniques.

Graph-based collaborative filtering methods have prevailing performance for recommender systems since they can capture high-order information between users and items, in which the graphs are constructed from the observed user-item interactions that might miss links or contain spurious positive interactions in industrial scenarios. The Bayesian Graph Neural Network framework approaches this issue with generative models for the interaction graphs. The critical problem is to devise a proper family of graph generative models tailored to recommender systems. We propose an efficient generative model that jointly considers the preferences of users, the concurrence of items and some important graph structure information. Experiments on four popular benchmark datasets demonstrate the effectiveness of our proposed graph generative methods for recommender systems.

Graph Neural Networks (GNNs) have achieved remarkable performance on graph-based tasks. The key idea for GNNs is to obtain informative representation through aggregating information from local neighborhoods. However, it remains an open question whether the neighborhood information is adequately aggregated for learning representations of nodes with few neighbors. To address this, we propose a simple and efficient data augmentation strategy, local augmentation, to learn the distribution of the node features of the neighbors conditioned on the central node's feature and enhance GNN's expressive power with generated features. Local augmentation is a general framework that can be applied to any GNN model in a plug-and-play manner. It samples feature vectors associated with each node from the learned conditional distribution as additional input for the backbone model at each training iteration. Extensive experiments and analyses show that local augmentation consistently yields performance improvement when applied to various GNN architectures across a diverse set of benchmarks. For example, experiments show that plugging in local augmentation to GCN and GAT improves by an average of 3.4\% and 1.6\% in terms of test accuracy on Cora, Citeseer, and Pubmed. Besides, our experimental results on large graphs (OGB) show that our model consistently improves performance over backbones. Code is available at https://github.com/SongtaoLiu0823/LAGNN.

Graph neural networks (GNNs) have shown great prowess in learning representations suitable for numerous graph-based machine learning tasks. When applied to semi-supervised node classification, GNNs are widely believed to work well due to the homophily assumption ("like attracts like"), and fail to generalize to heterophilous graphs where dissimilar nodes connect. Recent works design new architectures to overcome such heterophily-related limitations, citing poor baseline performance and new architecture improvements on a few heterophilous graph benchmark datasets as evidence for this notion. In our experiments, we empirically find that standard graph convolutional networks (GCNs) can actually achieve better performance than such carefully designed methods on some commonly used heterophilous graphs. This motivates us to reconsider whether homophily is truly necessary for good GNN performance. We find that this claim is not quite true, and in fact, GCNs can achieve strong performance on heterophilous graphs under certain conditions. Our work carefully characterizes these conditions, and provides supporting theoretical understanding and empirical observations. Finally, we examine existing heterophilous graphs benchmarks and reconcile how the GCN (under)performs on them based on this understanding.

Recent advancements in deep neural networks for graph-structured data have led to state-of-the-art performance on recommender system benchmarks. However, making these methods practical and scalable to web-scale recommendation tasks with billions of items and hundreds of millions of users remains a challenge. Here we describe a large-scale deep recommendation engine that we developed and deployed at Pinterest. We develop a data-efficient Graph Convolutional Network (GCN) algorithm PinSage, which combines efficient random walks and graph convolutions to generate embeddings of nodes (i.e., items) that incorporate both graph structure as well as node feature information. Compared to prior GCN approaches, we develop a novel method based on highly efficient random walks to structure the convolutions and design a novel training strategy that relies on harder-and-harder training examples to improve robustness and convergence of the model. We also develop an efficient MapReduce model inference algorithm to generate embeddings using a trained model. We deploy PinSage at Pinterest and train it on 7.5 billion examples on a graph with 3 billion nodes representing pins and boards, and 18 billion edges. According to offline metrics, user studies and A/B tests, PinSage generates higher-quality recommendations than comparable deep learning and graph-based alternatives. To our knowledge, this is the largest application of deep graph embeddings to date and paves the way for a new generation of web-scale recommender systems based on graph convolutional architectures.

In this paper, we present LiGNN, a deployed large-scale Graph Neural Networks (GNNs) Framework. We share our insight on developing and deployment of GNNs at large scale at LinkedIn. We present a set of algorithmic improvements to the quality of GNN representation learning including temporal graph architectures with long term losses, effective cold start solutions via graph densification, ID embeddings and multi-hop neighbor sampling. We explain how we built and sped up by 7x our large-scale training on LinkedIn graphs with adaptive sampling of neighbors, grouping and slicing of training data batches, specialized shared-memory queue and local gradient optimization. We summarize our deployment lessons and learnings gathered from A/B test experiments. The techniques presented in this work have contributed to an approximate relative improvements of 1% of Job application hearing back rate, 2% Ads CTR lift, 0.5% of Feed engaged daily active users, 0.2% session lift and 0.1% weekly active user lift from people recommendation. We believe that this work can provide practical solutions and insights for engineers who are interested in applying Graph neural networks at large scale.

Fairness-aware graph neural networks (GNNs) have gained a surge of attention as they can reduce the bias of predictions on any demographic group (e.g., female) in graph-based applications. Although these methods greatly improve the algorithmic fairness of GNNs, the fairness can be easily corrupted by carefully designed adversarial attacks. In this paper, we investigate the problem of adversarial attacks on fairness of GNNs and propose G-FairAttack, a general framework for attacking various types of fairness-aware GNNs in terms of fairness with an unnoticeable effect on prediction utility. In addition, we propose a fast computation technique to reduce the time complexity of G-FairAttack. The experimental study demonstrates that G-FairAttack successfully corrupts the fairness of different types of GNNs while keeping the attack unnoticeable. Our study on fairness attacks sheds light on potential vulnerabilities in fairness-aware GNNs and guides further research on the robustness of GNNs in terms of fairness.

Medical image classification requires not only high predictive performance but also interpretability to ensure clinical trust and adoption. Graph Neural Networks (GNNs) offer a powerful framework for modeling relational structures within datasets; however, standard GNNs often operate as black boxes, limiting transparency and usability, particularly in clinical settings. In this work, we present an interpretable graph-based learning framework named FireGNN that integrates trainable fuzzy rules into GNNs for medical image classification. These rules embed topological descriptors - node degree, clustering coefficient, and label agreement - using learnable thresholds and sharpness parameters to enable intrinsic symbolic reasoning. Additionally, we explore auxiliary self-supervised tasks (e.g., homophily prediction, similarity entropy) as a benchmark to evaluate the contribution of topological learning. Our fuzzy-rule-enhanced model achieves strong performance across five MedMNIST benchmarks and the synthetic dataset MorphoMNIST, while also generating interpretable rule-based explanations. To our knowledge, this is the first integration of trainable fuzzy rules within a GNN. Source Code: https://github.com/basiralab/FireGNN

Transformer-based models dominate NLP tasks like sentiment analysis, machine translation, and claim verification. However, their massive computational demands and lack of interpretability pose challenges for real-world applications requiring efficiency and transparency. In this work, we explore Graph Neural Networks (GNNs) and Hyperbolic Graph Neural Networks (HGNNs) as lightweight yet effective alternatives for Environmental Claim Detection, reframing it as a graph classification problem. We construct dependency parsing graphs to explicitly model syntactic structures, using simple word embeddings (word2vec) for node features with dependency relations encoded as edge features. Our results demonstrate that these graph-based models achieve comparable or superior performance to state-of-the-art transformers while using 30x fewer parameters. This efficiency highlights the potential of structured, interpretable, and computationally efficient graph-based approaches.

Equivariant Graph Neural Networks (EGNNs) have emerged as a promising approach in Multi-Agent Reinforcement Learning (MARL), leveraging symmetry guarantees to greatly improve sample efficiency and generalization. However, real-world environments often exhibit inherent asymmetries arising from factors such as external forces, measurement inaccuracies, or intrinsic system biases. This paper introduces Partially Equivariant Graph NeUral Networks (PEnGUiN), a novel architecture specifically designed to address these challenges. We formally identify and categorize various types of partial equivariance relevant to MARL, including subgroup equivariance, feature-wise equivariance, regional equivariance, and approximate equivariance. We theoretically demonstrate that PEnGUiN is capable of learning both fully equivariant (EGNN) and non-equivariant (GNN) representations within a unified framework. Through extensive experiments on a range of MARL problems incorporating various asymmetries, we empirically validate the efficacy of PEnGUiN. Our results consistently demonstrate that PEnGUiN outperforms both EGNNs and standard GNNs in asymmetric environments, highlighting their potential to improve the robustness and applicability of graph-based MARL algorithms in real-world scenarios.

Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs.GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating both graph structure and feature information leads to complex models, and explaining predictions made by GNNs remains unsolved. Here we propose GNNExplainer, the first general, model-agnostic approach for providing interpretable explanations for predictions of any GNN-based model on any graph-based machine learning task. Given an instance, GNNExplainer identifies a compact subgraph structure and a small subset of node features that have a crucial role in GNN's prediction. Further, GNNExplainer can generate consistent and concise explanations for an entire class of instances. We formulate GNNExplainer as an optimization task that maximizes the mutual information between a GNN's prediction and distribution of possible subgraph structures. Experiments on synthetic and real-world graphs show that our approach can identify important graph structures as well as node features, and outperforms baselines by 17.1% on average. GNNExplainer provides a variety of benefits, from the ability to visualize semantically relevant structures to interpretability, to giving insights into errors of faulty GNNs.

Many real-world data come in the form of graphs. Graph neural networks (GNNs), a new family of machine learning (ML) models, have been proposed to fully leverage graph data to build powerful applications. In particular, the inductive GNNs, which can generalize to unseen data, become mainstream in this direction. Machine learning models have shown great potential in various tasks and have been deployed in many real-world scenarios. To train a good model, a large amount of data as well as computational resources are needed, leading to valuable intellectual property. Previous research has shown that ML models are prone to model stealing attacks, which aim to steal the functionality of the target models. However, most of them focus on the models trained with images and texts. On the other hand, little attention has been paid to models trained with graph data, i.e., GNNs. In this paper, we fill the gap by proposing the first model stealing attacks against inductive GNNs. We systematically define the threat model and propose six attacks based on the adversary's background knowledge and the responses of the target models. Our evaluation on six benchmark datasets shows that the proposed model stealing attacks against GNNs achieve promising performance.

Understanding pain-related facial behaviors is essential for digital healthcare in terms of effective monitoring, assisted diagnostics, and treatment planning, particularly for patients unable to communicate verbally. Existing data-driven methods of detecting pain from facial expressions are limited due to interpretability and severity quantification. To this end, we propose GraphAU-Pain, leveraging a graph-based framework to model facial Action Units (AUs) and their interrelationships for pain intensity estimation. AUs are represented as graph nodes, with co-occurrence relationships as edges, enabling a more expressive depiction of pain-related facial behaviors. By utilizing a relational graph neural network, our framework offers improved interpretability and significant performance gains. Experiments conducted on the publicly available UNBC dataset demonstrate the effectiveness of the GraphAU-Pain, achieving an F1-score of 66.21% and accuracy of 87.61% in pain intensity estimation.

The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the molecule structures. However, automatically parsing the exact chemical structure is a formidable challenge, due to the amount of detailed information, the diversity of drawing styles, and the need for training data. In this work, we introduce MolGrapher to recognize chemical structures visually. First, a deep keypoint detector detects the atoms. Second, we treat all candidate atoms and bonds as nodes and put them in a graph. This construct allows a natural graph representation of the molecule. Last, we classify atom and bond nodes in the graph with a Graph Neural Network. To address the lack of real training data, we propose a synthetic data generation pipeline producing diverse and realistic results. In addition, we introduce a large-scale benchmark of annotated real molecule images, USPTO-30K, to spur research on this critical topic. Extensive experiments on five datasets show that our approach significantly outperforms classical and learning-based methods in most settings. Code, models, and datasets are available.

Traditionally, convolutional neural networks (CNN) and vision transformers (ViT) have dominated computer vision. However, recently proposed vision graph neural networks (ViG) provide a new avenue for exploration. Unfortunately, for mobile applications, ViGs are computationally expensive due to the overhead of representing images as graph structures. In this work, we propose a new graph-based sparse attention mechanism, Sparse Vision Graph Attention (SVGA), that is designed for ViGs running on mobile devices. Additionally, we propose the first hybrid CNN-GNN architecture for vision tasks on mobile devices, MobileViG, which uses SVGA. Extensive experiments show that MobileViG beats existing ViG models and existing mobile CNN and ViT architectures in terms of accuracy and/or speed on image classification, object detection, and instance segmentation tasks. Our fastest model, MobileViG-Ti, achieves 75.7% top-1 accuracy on ImageNet-1K with 0.78 ms inference latency on iPhone 13 Mini NPU (compiled with CoreML), which is faster than MobileNetV2x1.4 (1.02 ms, 74.7% top-1) and MobileNetV2x1.0 (0.81 ms, 71.8% top-1). Our largest model, MobileViG-B obtains 82.6% top-1 accuracy with only 2.30 ms latency, which is faster and more accurate than the similarly sized EfficientFormer-L3 model (2.77 ms, 82.4%). Our work proves that well designed hybrid CNN-GNN architectures can be a new avenue of exploration for designing models that are extremely fast and accurate on mobile devices. Our code is publicly available at https://github.com/SLDGroup/MobileViG.

Part-of-Speech (POS) tagging is an important component of the NLP pipeline, but many low-resource languages lack labeled data for training. An established method for training a POS tagger in such a scenario is to create a labeled training set by transferring from high-resource languages. In this paper, we propose a novel method for transferring labels from multiple high-resource source to low-resource target languages. We formalize POS tag projection as graph-based label propagation. Given translations of a sentence in multiple languages, we create a graph with words as nodes and alignment links as edges by aligning words for all language pairs. We then propagate node labels from source to target using a Graph Neural Network augmented with transformer layers. We show that our propagation creates training sets that allow us to train POS taggers for a diverse set of languages. When combined with enhanced contextualized embeddings, our method achieves a new state-of-the-art for unsupervised POS tagging of low-resource languages.

Electronic Health Records (EHR) are high-dimensional data with implicit connections among thousands of medical concepts. These connections, for instance, the co-occurrence of diseases and lab-disease correlations can be informative when only a subset of these variables is documented by the clinician. A feasible approach to improving the representation learning of EHR data is to associate relevant medical concepts and utilize these connections. Existing medical ontologies can be the reference for EHR structures, but they place numerous constraints on the data source. Recent progress on graph neural networks (GNN) enables end-to-end learning of topological structures for non-grid or non-sequential data. However, there are problems to be addressed on how to learn the medical graph adaptively and how to understand the effect of the medical graph on representation learning. In this paper, we propose a variationally regularized encoder-decoder graph network that achieves more robustness in graph structure learning by regularizing node representations. Our model outperforms the existing graph and non-graph based methods in various EHR predictive tasks based on both public data and real-world clinical data. Besides the improvements in empirical experiment performances, we provide an interpretation of the effect of variational regularization compared to standard graph neural network, using singular value analysis.

Molecular interactions often involve high-order relationships that cannot be fully captured by traditional graph-based models limited to pairwise connections. Hypergraphs naturally extend graphs by enabling multi-way interactions, making them well-suited for modeling complex molecular systems. In this work, we introduce EquiHGNN, an Equivariant HyperGraph Neural Network framework that integrates symmetry-aware representations to improve molecular modeling. By enforcing the equivariance under relevant transformation groups, our approach preserves geometric and topological properties, leading to more robust and physically meaningful representations. We examine a range of equivariant architectures and demonstrate that integrating symmetry constraints leads to notable performance gains on large-scale molecular datasets. Experiments on both small and large molecules show that high-order interactions offer limited benefits for small molecules but consistently outperform 2D graphs on larger ones. Adding geometric features to these high-order structures further improves the performance, emphasizing the value of spatial information in molecular learning. Our source code is available at https://github.com/HySonLab/EquiHGNN/

In community-based question answering (CQA) platforms, automatic answer ranking for a given question is critical for finding potentially popular answers in early times. The mainstream approaches learn to generate answer ranking scores based on the matching degree between question and answer representations as well as the influence of respondents. However, they encounter two main limitations: (1) Correlations between answers in the same question are often overlooked. (2) Question and respondent representations are built independently of specific answers before affecting answer representations. To address the limitations, we devise a novel graph-based tri-attention network, namely GTAN, which has two innovations. First, GTAN proposes to construct a graph for each question and learn answer correlations from each graph through graph neural networks (GNNs). Second, based on the representations learned from GNNs, an alternating tri-attention method is developed to alternatively build target-aware respondent representations, answer-specific question representations, and context-aware answer representations by attention computation. GTAN finally integrates the above representations to generate answer ranking scores. Experiments on three real-world CQA datasets demonstrate GTAN significantly outperforms state-of-the-art answer ranking methods, validating the rationality of the network architecture.

The robustness of a model for real-world deployment is decided by how well it performs on unseen data and distinguishes between in-domain and out-of-domain samples. Visual document classifiers have shown impressive performance on in-distribution test sets. However, they tend to have a hard time correctly classifying and differentiating out-of-distribution examples. Image-based classifiers lack the text component, whereas multi-modality transformer-based models face the token serialization problem in visual documents due to their diverse layouts. They also require a lot of computing power during inference, making them impractical for many real-world applications. We propose, GVdoc, a graph-based document classification model that addresses both of these challenges. Our approach generates a document graph based on its layout, and then trains a graph neural network to learn node and graph embeddings. Through experiments, we show that our model, even with fewer parameters, outperforms state-of-the-art models on out-of-distribution data while retaining comparable performance on the in-distribution test set.

In the hospitality industry, understanding the factors that drive customer review ratings is critical for improving guest satisfaction and business performance. This work proposes ReviewGraph for Review Rating Prediction (RRP), a novel framework that transforms textual customer reviews into knowledge graphs by extracting (subject, predicate, object) triples and associating sentiment scores. Using graph embeddings (Node2Vec) and sentiment features, the framework predicts review rating scores through machine learning classifiers. We compare ReviewGraph performance with traditional NLP baselines (such as Bag of Words, TF-IDF, and Word2Vec) and large language models (LLMs), evaluating them in the HotelRec dataset. In comparison to the state of the art literature, our proposed model performs similar to their best performing model but with lower computational cost (without ensemble). While ReviewGraph achieves comparable predictive performance to LLMs and outperforms baselines on agreement-based metrics such as Cohen's Kappa, it offers additional advantages in interpretability, visual exploration, and potential integration into Retrieval-Augmented Generation (RAG) systems. This work highlights the potential of graph-based representations for enhancing review analytics and lays the groundwork for future research integrating advanced graph neural networks and fine-tuned LLM-based extraction methods. We will share ReviewGraph output and platform open-sourced on our GitHub page https://github.com/aaronlifenghan/ReviewGraph

This paper presents a novel hybrid model that integrates long-short-term memory (LSTM) networks and Graph Neural Networks (GNNs) to significantly enhance the accuracy of stock market predictions. The LSTM component adeptly captures temporal patterns in stock price data, effectively modeling the time series dynamics of financial markets. Concurrently, the GNN component leverages Pearson correlation and association analysis to model inter-stock relational data, capturing complex nonlinear polyadic dependencies influencing stock prices. The model is trained and evaluated using an expanding window validation approach, enabling continuous learning from increasing amounts of data and adaptation to evolving market conditions. Extensive experiments conducted on historical stock data demonstrate that our hybrid LSTM-GNN model achieves a mean square error (MSE) of 0.00144, representing a substantial reduction of 10.6% compared to the MSE of the standalone LSTM model of 0.00161. Furthermore, the hybrid model outperforms traditional and advanced benchmarks, including linear regression, convolutional neural networks (CNN), and dense networks. These compelling results underscore the significant potential of combining temporal and relational data through a hybrid approach, offering a powerful tool for real-time trading and financial analysis.

In this paper, we present an Adaptive Ensemble Learning framework that aims to boost the performance of deep neural networks by intelligently fusing features through ensemble learning techniques. The proposed framework integrates ensemble learning strategies with deep learning architectures to create a more robust and adaptable model capable of handling complex tasks across various domains. By leveraging intelligent feature fusion methods, the Adaptive Ensemble Learning framework generates more discriminative and effective feature representations, leading to improved model performance and generalization capabilities. We conducted extensive experiments and evaluations on several benchmark datasets, including image classification, object detection, natural language processing, and graph-based learning tasks. The results demonstrate that the proposed framework consistently outperforms baseline models and traditional feature fusion techniques, highlighting its effectiveness in enhancing deep learning models' performance. Furthermore, we provide insights into the impact of intelligent feature fusion on model performance and discuss the potential applications of the Adaptive Ensemble Learning framework in real-world scenarios. The paper also explores the design and implementation of adaptive ensemble models, ensemble training strategies, and meta-learning techniques, which contribute to the framework's versatility and adaptability. In conclusion, the Adaptive Ensemble Learning framework represents a significant advancement in the field of feature fusion and ensemble learning for deep neural networks, with the potential to transform a wide range of applications across multiple domains.

Graph-structured data plays a vital role in numerous domains, such as social networks, citation networks, commonsense reasoning graphs and knowledge graphs. While graph neural networks have been employed for graph processing, recent advancements have explored integrating large language models for graph-based tasks. In this paper, we propose a novel approach named Learnable Graph Pooling Token (LGPT), which addresses the limitations of the scalability issues in node-level projection and information loss in graph-level projection. LGPT enables flexible and efficient graph representation by introducing learnable parameters that act as tokens in large language models, balancing fine-grained and global graph information. Additionally, we investigate an Early Query Fusion technique, which fuses query context before constructing the graph representation, leading to more effective graph embeddings. Our method achieves a 4.13\% performance improvement on the GraphQA benchmark without training the large language model, demonstrating significant gains in handling complex textual-attributed graph data.

Retrieval-augmented generation (RAG) has revitalized Large Language Models (LLMs) by injecting non-parametric factual knowledge. Compared with long-context LLMs, RAG is considered an effective summarization tool in a more concise and lightweight manner, which can interact with LLMs multiple times using diverse queries to get comprehensive responses. However, the LLM-generated historical responses, which contain potentially insightful information, are largely neglected and discarded by existing approaches, leading to suboptimal results. In this paper, we propose graph of records (GoR), which leverages historical responses generated by LLMs to enhance RAG for long-context global summarization. Inspired by the retrieve-then-generate paradigm of RAG, we construct a graph by establishing an edge between the retrieved text chunks and the corresponding LLM-generated response. To further uncover the intricate correlations between them, GoR further features a graph neural network and an elaborately designed BERTScore-based objective for self-supervised model training, enabling seamless supervision signal backpropagation between reference summaries and node embeddings. We comprehensively compare GoR with 12 baselines across four long-context summarization datasets, and the results indicate that our proposed method reaches the best performance e.g., 15\%, 8\%, and 19\% improvement over retrievers w.r.t. Rouge-L, Rouge-1, and Rouge-2 on the WCEP dataset). Extensive experiments further demonstrate the effectiveness of GoR. Code is available at https://github.com/ulab-uiuc/GoR

Which transformer scaling regimes are able to perfectly solve different classes of algorithmic problems? While tremendous empirical advances have been attained by transformer-based neural networks, a theoretical understanding of their algorithmic reasoning capabilities in realistic parameter regimes is lacking. We investigate this question in terms of the network's depth, width, and number of extra tokens for algorithm execution. Our novel representational hierarchy separates 9 algorithmic reasoning problems into classes solvable by transformers in different realistic parameter scaling regimes. We prove that logarithmic depth is necessary and sufficient for tasks like graph connectivity, while single-layer transformers with small embedding dimensions can solve contextual retrieval tasks. We also support our theoretical analysis with ample empirical evidence using the GraphQA benchmark. These results show that transformers excel at many graph reasoning tasks, even outperforming specialized graph neural networks.

Information sharing is critical in time-sensitive and realistic multi-robot exploration, especially for smaller robotic teams in large-scale environments where connectivity may be sparse and intermittent. Existing methods often overlook such communication constraints by assuming unrealistic global connectivity. Other works account for communication constraints (by maintaining close proximity or line of sight during information exchange), but are often inefficient. For instance, preplanned rendezvous approaches typically involve unnecessary detours resulting from poorly timed rendezvous, while pursuit-based approaches often result in short-sighted decisions due to their greedy nature. We present IR2, a deep reinforcement learning approach to information sharing for multi-robot exploration. Leveraging attention-based neural networks trained via reinforcement and curriculum learning, IR2 allows robots to effectively reason about the longer-term trade-offs between disconnecting for solo exploration and reconnecting for information sharing. In addition, we propose a hierarchical graph formulation to maintain a sparse yet informative graph, enabling our approach to scale to large-scale environments. We present simulation results in three large-scale Gazebo environments, which show that our approach yields 6.6-34.1% shorter exploration paths when compared to state-of-the-art baselines, and lastly deploy our learned policy on hardware. Our simulation training and testing code is available at https://ir2-explore.github.io.

Sparse matrices, more specifically SpGEMM kernels, are commonly found in a wide range of applications, spanning graph-based path-finding to machine learning algorithms (e.g., neural networks). A particular challenge in implementing SpGEMM kernels has been the pressure placed on DRAM memory. One approach to tackle this problem is to use an inner product method for the SpGEMM kernel implementation. While the inner product produces fewer intermediate results, it can end up saturating the memory bandwidth, given the high number of redundant fetches of the input matrix elements. Using an outer product-based SpGEMM kernel can reduce redundant fetches, but at the cost of increased overhead due to extra computation and memory accesses for producing/managing partial products. In this thesis, we introduce a novel SpGEMM kernel implementation based on the row-wise product approach. We leverage atomic instructions to merge intermediate partial products as they are generated. The use of atomic instructions eliminates the need to create partial product matrices. To evaluate our row-wise product approach, we map an optimized SpGEMM kernel to a custom accelerator designed to accelerate graph-based applications. The targeted accelerator is an experimental system named PIUMA, being developed by Intel. PIUMA provides several attractive features, including fast context switching, user-configurable caches, globally addressable memory, non-coherent caches, and asynchronous pipelines. We tailor our SpGEMM kernel to exploit many of the features of the PIUMA fabric. This thesis compares our SpGEMM implementation against prior solutions, all mapped to the PIUMA framework. We briefly describe some of the PIUMA architecture features and then delve into the details of our optimized SpGEMM kernel. Our SpGEMM kernel can achieve 9.4x speedup as compared to competing approaches.

Memory-based Dynamic Graph Neural Networks (MDGNNs) are a family of dynamic graph neural networks that leverage a memory module to extract, distill, and memorize long-term temporal dependencies, leading to superior performance compared to memory-less counterparts. However, training MDGNNs faces the challenge of handling entangled temporal and structural dependencies, requiring sequential and chronological processing of data sequences to capture accurate temporal patterns. During the batch training, the temporal data points within the same batch will be processed in parallel, while their temporal dependencies are neglected. This issue is referred to as temporal discontinuity and restricts the effective temporal batch size, limiting data parallelism and reducing MDGNNs' flexibility in industrial applications. This paper studies the efficient training of MDGNNs at scale, focusing on the temporal discontinuity in training MDGNNs with large temporal batch sizes. We first conduct a theoretical study on the impact of temporal batch size on the convergence of MDGNN training. Based on the analysis, we propose PRES, an iterative prediction-correction scheme combined with a memory coherence learning objective to mitigate the effect of temporal discontinuity, enabling MDGNNs to be trained with significantly larger temporal batches without sacrificing generalization performance. Experimental results demonstrate that our approach enables up to a 4x larger temporal batch (3.4x speed-up) during MDGNN training.

Geometric Deep Learning has recently attracted significant interest in a wide range of machine learning fields, including document analysis. The application of Graph Neural Networks (GNNs) has become crucial in various document-related tasks since they can unravel important structural patterns, fundamental in key information extraction processes. Previous works in the literature propose task-driven models and do not take into account the full power of graphs. We propose Doc2Graph, a task-agnostic document understanding framework based on a GNN model, to solve different tasks given different types of documents. We evaluated our approach on two challenging datasets for key information extraction in form understanding, invoice layout analysis and table detection. Our code is freely accessible on https://github.com/andreagemelli/doc2graph.

AutoML systems build machine learning models automatically by performing a search over valid data transformations and learners, along with hyper-parameter optimization for each learner. Many AutoML systems use meta-learning to guide search for optimal pipelines. In this work, we present a novel meta-learning system called KGpip which, (1) builds a database of datasets and corresponding pipelines by mining thousands of scripts with program analysis, (2) uses dataset embeddings to find similar datasets in the database based on its content instead of metadata-based features, (3) models AutoML pipeline creation as a graph generation problem, to succinctly characterize the diverse pipelines seen for a single dataset. KGpip's meta-learning is a sub-component for AutoML systems. We demonstrate this by integrating KGpip with two AutoML systems. Our comprehensive evaluation using 126 datasets, including those used by the state-of-the-art systems, shows that KGpip significantly outperforms these systems.

Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments (reads) of the individual microbes can be obtained, which through assembly graphs can be combined into long contiguous DNA sequences (contigs). Given the complexity of microbial communities, single contig microbial genomes are rarely obtained. Instead, contigs are eventually clustered into bins, with each bin ideally making up a full genome. This process is referred to as metagenomic binning. Current state-of-the-art techniques for metagenomic binning rely only on the local features for the individual contigs. These techniques therefore fail to exploit the similarities between contigs as encoded by the assembly graph, in which the contigs are organized. In this paper, we propose to use Graph Neural Networks (GNNs) to leverage the assembly graph when learning contig representations for metagenomic binning. Our method, VaeG-Bin, combines variational autoencoders for learning latent representations of the individual contigs, with GNNs for refining these representations by taking into account the neighborhood structure of the contigs in the assembly graph. We explore several types of GNNs and demonstrate that VaeG-Bin recovers more high-quality genomes than other state-of-the-art binners on both simulated and real-world datasets.

Deep neural networks (DNN) can approximate value functions or policies for reinforcement learning, which makes the reinforcement learning algorithms more powerful. However, some DNNs, such as convolutional neural networks (CNN), cannot extract enough information or take too long to obtain enough features from the inputs under specific circumstances of reinforcement learning. For example, the input data of Google Research Football, a reinforcement learning environment which trains agents to play football, is the small map of players' locations. The information is contained not only in the coordinates of players, but also in the relationships between different players. CNNs can neither extract enough information nor take too long to train. To address this issue, this paper proposes a deep q-learning network (DQN) with a graph neural network (GNN) as its model. The GNN transforms the input data into a graph which better represents the football players' locations so that it extracts more information of the interactions between different players. With two GNNs to approximate its local and target value functions, this DQN allows players to learn from their experience by using value functions to see the prospective value of each intended action. The proposed model demonstrated the power of GNN in the football game by outperforming other DRL models with significantly fewer steps.

Roman Numeral analysis is the important task of identifying chords and their functional context in pieces of tonal music. This paper presents a new approach to automatic Roman Numeral analysis in symbolic music. While existing techniques rely on an intermediate lossy representation of the score, we propose a new method based on Graph Neural Networks (GNNs) that enable the direct description and processing of each individual note in the score. The proposed architecture can leverage notewise features and interdependencies between notes but yield onset-wise representation by virtue of our novel edge contraction algorithm. Our results demonstrate that ChordGNN outperforms existing state-of-the-art models, achieving higher accuracy in Roman Numeral analysis on the reference datasets. In addition, we investigate variants of our model using proposed techniques such as NADE, and post-processing of the chord predictions. The full source code for this work is available at https://github.com/manoskary/chordgnn

Social recommender systems (SocialRS) simultaneously leverage user-to-item interactions as well as user-to-user social relations for the task of generating item recommendations to users. Additionally exploiting social relations is clearly effective in understanding users' tastes due to the effects of homophily and social influence. For this reason, SocialRS has increasingly attracted attention. In particular, with the advance of Graph Neural Networks (GNN), many GNN-based SocialRS methods have been developed recently. Therefore, we conduct a comprehensive and systematic review of the literature on GNN-based SocialRS. In this survey, we first identify 80 papers on GNN-based SocialRS after annotating 2151 papers by following the PRISMA framework (Preferred Reporting Items for Systematic Reviews and Meta-Analysis). Then, we comprehensively review them in terms of their inputs and architectures to propose a novel taxonomy: (1) input taxonomy includes 5 groups of input type notations and 7 groups of input representation notations; (2) architecture taxonomy includes 8 groups of GNN encoder, 2 groups of decoder, and 12 groups of loss function notations. We classify the GNN-based SocialRS methods into several categories as per the taxonomy and describe their details. Furthermore, we summarize the benchmark datasets and metrics widely used to evaluate the GNN-based SocialRS methods. Finally, we conclude this survey by presenting some future research directions.

The angular synchronization problem aims to accurately estimate (up to a constant additive phase) a set of unknown angles theta_1, dots, theta_nin[0, 2pi) from m noisy measurements of their offsets theta_i-theta_j ;mod ; 2pi. Applications include, for example, sensor network localization, phase retrieval, and distributed clock synchronization. An extension of the problem to the heterogeneous setting (dubbed k-synchronization) is to estimate k groups of angles simultaneously, given noisy observations (with unknown group assignment) from each group. Existing methods for angular synchronization usually perform poorly in high-noise regimes, which are common in applications. In this paper, we leverage neural networks for the angular synchronization problem, and its heterogeneous extension, by proposing GNNSync, a theoretically-grounded end-to-end trainable framework using directed graph neural networks. In addition, new loss functions are devised to encode synchronization objectives. Experimental results on extensive data sets demonstrate that GNNSync attains competitive, and often superior, performance against a comprehensive set of baselines for the angular synchronization problem and its extension, validating the robustness of GNNSync even at high noise levels.

In recent years, graph representation learning has undergone a paradigm shift, driven by the emergence and proliferation of graph neural networks (GNNs) and their heterogeneous counterparts. Heterogeneous GNNs have shown remarkable success in extracting low-dimensional embeddings from complex graphs that encompass diverse entity types and relationships. While meta-path-based techniques have long been recognized for their ability to capture semantic affinities among nodes, their dependence on manual specification poses a significant limitation. In contrast, matrix-focused methods accelerate processing by utilizing structural cues but often overlook contextual richness. In this paper, we challenge the current paradigm by introducing ontology as a fundamental semantic primitive within complex graphs. Our goal is to integrate the strengths of both matrix-centric and meta-path-based approaches into a unified framework. We propose perturbation Ontology-based Graph Attention Networks (POGAT), a novel methodology that combines ontology subgraphs with an advanced self-supervised learning paradigm to achieve a deep contextual understanding. The core innovation of POGAT lies in our enhanced homogeneous perturbing scheme designed to generate rigorous negative samples, encouraging the model to explore minimal contextual features more thoroughly. Through extensive empirical evaluations, we demonstrate that POGAT significantly outperforms state-of-the-art baselines, achieving a groundbreaking improvement of up to 10.78\% in F1-score for the critical task of link prediction and 12.01\% in Micro-F1 for the critical task of node classification.

Recent advances in text-to-speech, particularly those based on Graph Neural Networks (GNNs), have significantly improved the expressiveness of short-form synthetic speech. However, generating human-parity long-form speech with high dynamic prosodic variations is still challenging. To address this problem, we expand the capabilities of GNNs with a hierarchical prosody modeling approach, named HiGNN-TTS. Specifically, we add a virtual global node in the graph to strengthen the interconnection of word nodes and introduce a contextual attention mechanism to broaden the prosody modeling scope of GNNs from intra-sentence to inter-sentence. Additionally, we perform hierarchical supervision from acoustic prosody on each node of the graph to capture the prosodic variations with a high dynamic range. Ablation studies show the effectiveness of HiGNN-TTS in learning hierarchical prosody. Both objective and subjective evaluations demonstrate that HiGNN-TTS significantly improves the naturalness and expressiveness of long-form synthetic speech.

Deceptive path planning (DPP) is the problem of designing a path that hides its true goal from an outside observer. Existing methods for DPP rely on unrealistic assumptions, such as global state observability and perfect model knowledge, and are typically problem-specific, meaning that even minor changes to a previously solved problem can force expensive computation of an entirely new solution. Given these drawbacks, such methods do not generalize to unseen problem instances, lack scalability to realistic problem sizes, and preclude both on-the-fly tunability of deception levels and real-time adaptivity to changing environments. In this paper, we propose a reinforcement learning (RL)-based scheme for training policies to perform DPP over arbitrary weighted graphs that overcomes these issues. The core of our approach is the introduction of a local perception model for the agent, a new state space representation distilling the key components of the DPP problem, the use of graph neural network-based policies to facilitate generalization and scaling, and the introduction of new deception bonuses that translate the deception objectives of classical methods to the RL setting. Through extensive experimentation we show that, without additional fine-tuning, at test time the resulting policies successfully generalize, scale, enjoy tunable levels of deception, and adapt in real-time to changes in the environment.

Recently, data-driven simulators based on graph neural networks have gained attention in modeling physical systems on unstructured meshes. However, they struggle with long-range dependencies in fluid flows, particularly in refined mesh regions. This challenge, known as the 'over-squashing' problem, hinders information propagation. While existing graph rewiring methods address this issue to some extent, they only consider graph topology, overlooking the underlying physical phenomena. We propose Physics-Informed Ollivier-Ricci Flow (PIORF), a novel rewiring method that combines physical correlations with graph topology. PIORF uses Ollivier-Ricci curvature (ORC) to identify bottleneck regions and connects these areas with nodes in high-velocity gradient nodes, enabling long-range interactions and mitigating over-squashing. Our approach is computationally efficient in rewiring edges and can scale to larger simulations. Experimental results on 3 fluid dynamics benchmark datasets show that PIORF consistently outperforms baseline models and existing rewiring methods, achieving up to 26.2 improvement.

Vulnerability identification is crucial to protect the software systems from attacks for cyber security. It is especially important to localize the vulnerable functions among the source code to facilitate the fix. However, it is a challenging and tedious process, and also requires specialized security expertise. Inspired by the work on manually-defined patterns of vulnerabilities from various code representation graphs and the recent advance on graph neural networks, we propose Devign, a general graph neural network based model for graph-level classification through learning on a rich set of code semantic representations. It includes a novel Conv module to efficiently extract useful features in the learned rich node representations for graph-level classification. The model is trained over manually labeled datasets built on 4 diversified large-scale open-source C projects that incorporate high complexity and variety of real source code instead of synthesis code used in previous works. The results of the extensive evaluation on the datasets demonstrate that Devign outperforms the state of the arts significantly with an average of 10.51% higher accuracy and 8.68\% F1 score, increases averagely 4.66% accuracy and 6.37% F1 by the Conv module.

Graphs are widely used for modeling relational data in real-world scenarios, such as social networks and urban computing. Existing LLM-based graph analysis approaches either integrate graph neural networks (GNNs) for specific machine learning tasks, limiting their transferability, or rely solely on LLMs' internal reasoning ability, resulting in suboptimal performance. To address these limitations, we take advantage of recent advances in LLM-based agents, which have shown capabilities of utilizing external knowledge or tools for problem solving. By simulating human problem-solving strategies such as analogy and collaboration, we propose a multi-agent system based on LLMs named GraphTeam, for graph analysis. GraphTeam consists of five LLM-based agents from three modules, and the agents with different specialities can collaborate with each other to address complex problems. Specifically, (1) input-output normalization module: the question agent extracts and refines four key arguments from the original question, facilitating the problem understanding, and the answer agent organizes the results to meet the output requirement; (2) external knowledge retrieval module: we first build a knowledge base consisting of relevant documentation and experience information, and then the search agent retrieves the most relevant entries for each question. (3) problem-solving module: given the retrieved information from search agent, the coding agent uses established algorithms via programming to generate solutions, and in case the coding agent does not work, the reasoning agent will directly compute the results without programming. Extensive experiments on six graph analysis benchmarks demonstrate that GraphTeam achieves state-of-the-art performance with an average 25.85% improvement over the best baseline in terms of accuracy. The code and data are available at https://github.com/BUPT-GAMMA/GraphTeam.

Although Answer Set Programming (ASP) allows constraining neural-symbolic (NeSy) systems, its employment is hindered by the prohibitive costs of computing stable models and the CPU-bound nature of state-of-the-art solvers. To this end, we propose Answer Set Networks (ASN), a NeSy solver. Based on Graph Neural Networks (GNN), ASNs are a scalable approach to ASP-based Deep Probabilistic Logic Programming (DPPL). Specifically, we show how to translate ASPs into ASNs and demonstrate how ASNs can efficiently solve the encoded problem by leveraging GPU's batching and parallelization capabilities. Our experimental evaluations demonstrate that ASNs outperform state-of-the-art CPU-bound NeSy systems on multiple tasks. Simultaneously, we make the following two contributions based on the strengths of ASNs. Namely, we are the first to show the finetuning of Large Language Models (LLM) with DPPLs, employing ASNs to guide the training with logic. Further, we show the "constitutional navigation" of drones, i.e., encoding public aviation laws in an ASN for routing Unmanned Aerial Vehicles in uncertain environments.

We present a neural operator architecture to simulate Lagrangian dynamics, such as fluid flow, granular flows, and elastoplasticity. Traditional numerical methods, such as the finite element method (FEM), suffer from long run times and large memory consumption. On the other hand, approaches based on graph neural networks are faster but still suffer from long computation times on dense graphs, which are often required for high-fidelity simulations. Our model, GIOROM or Graph Interaction Operator for Reduced-Order Modeling, learns temporal dynamics within a reduced-order setting, capturing spatial features from a highly sparse graph representation of the input and generalizing to arbitrary spatial locations during inference. The model is geometry-aware and discretization-agnostic and can generalize to different initial conditions, velocities, and geometries after training. We show that point clouds of the order of 100,000 points can be inferred from sparse graphs with sim1000 points, with negligible change in computation time. We empirically evaluate our model on elastic solids, Newtonian fluids, Non-Newtonian fluids, Drucker-Prager granular flows, and von Mises elastoplasticity. On these benchmarks, our approach results in a 25times speedup compared to other neural network-based physics simulators while delivering high-fidelity predictions of complex physical systems and showing better performance on most benchmarks. The code and the demos are provided at https://github.com/HrishikeshVish/GIOROM.

Much progress has been made recently on text classification with methods based on neural networks. In particular, models using attention mechanism such as BERT have shown to have the capability of capturing the contextual information within a sentence or document. However, their ability of capturing the global information about the vocabulary of a language is more limited. This latter is the strength of Graph Convolutional Networks (GCN). In this paper, we propose VGCN-BERT model which combines the capability of BERT with a Vocabulary Graph Convolutional Network (VGCN). Local information and global information interact through different layers of BERT, allowing them to influence mutually and to build together a final representation for classification. In our experiments on several text classification datasets, our approach outperforms BERT and GCN alone, and achieve higher effectiveness than that reported in previous studies.

A data-driven model (DDM) suitable for regional weather forecasting applications is presented. The model extends the Artificial Intelligence Forecasting System by introducing a stretched-grid architecture that dedicates higher resolution over a regional area of interest and maintains a lower resolution elsewhere on the globe. The model is based on graph neural networks, which naturally affords arbitrary multi-resolution grid configurations. The model is applied to short-range weather prediction for the Nordics, producing forecasts at 2.5 km spatial and 6 h temporal resolution. The model is pre-trained on 43 years of global ERA5 data at 31 km resolution and is further refined using 3.3 years of 2.5 km resolution operational analyses from the MetCoOp Ensemble Prediction System (MEPS). The performance of the model is evaluated using surface observations from measurement stations across Norway and is compared to short-range weather forecasts from MEPS. The DDM outperforms both the control run and the ensemble mean of MEPS for 2 m temperature. The model also produces competitive precipitation and wind speed forecasts, but is shown to underestimate extreme events.

Point defects play a central role in driving the properties of materials. First-principles methods are widely used to compute defect energetics and structures, including at scale for high-throughput defect databases. However, these methods are computationally expensive, making machine-learning force fields (MLFFs) an attractive alternative for accelerating structural relaxations. Most existing MLFFs are based on graph neural networks (GNNs), which can suffer from oversmoothing and poor representation of long-range interactions. Both of these issues are especially of concern when modeling point defects. To address these challenges, we introduce the Accelerated Deep Atomic Potential Transformer (ADAPT), an MLFF that replaces graph representations with a direct coordinates-in-space formulation and explicitly considers all pairwise atomic interactions. Atoms are treated as tokens, with a Transformer encoder modeling their interactions. Applied to a dataset of silicon point defects, ADAPT achieves a roughly 33 percent reduction in both force and energy prediction errors relative to a state-of-the-art GNN-based model, while requiring only a fraction of the computational cost.

Recent work has shown promising results in causal discovery by leveraging interventional data with gradient-based methods, even when the intervened variables are unknown. However, previous work assumes that the correspondence between samples and interventions is known, which is often unrealistic. We envision a scenario with an extensive dataset sampled from multiple intervention distributions and one observation distribution, but where we do not know which distribution originated each sample and how the intervention affected the system, i.e., interventions are entirely latent. We propose a method based on neural networks and variational inference that addresses this scenario by framing it as learning a shared causal graph among an infinite mixture (under a Dirichlet process prior) of intervention structural causal models. Experiments with synthetic and real data show that our approach and its semi-supervised variant are able to discover causal relations in this challenging scenario.

The Machine Learning for Combinatorial Optimization (ML4CO) NeurIPS 2021 competition aims to improve state-of-the-art combinatorial optimization solvers by replacing key heuristic components with machine learning models. On the dual task, we design models to make branching decisions to promote the dual bound increase faster. We propose a knowledge inheritance method to generalize knowledge of different models from the dataset aggregation process, named KIDA. Our improvement overcomes some defects of the baseline graph-neural-networks-based methods. Further, we won the 1st Place on the dual task. We hope this report can provide useful experience for developers and researchers. The code is available at https://github.com/megvii-research/NeurIPS2021-ML4CO-KIDA.

This paper approaches the problem of separating the notes from a quantized symbolic music piece (e.g., a MIDI file) into multiple voices and staves. This is a fundamental part of the larger task of music score engraving (or score typesetting), which aims to produce readable musical scores for human performers. We focus on piano music and support homophonic voices, i.e., voices that can contain chords, and cross-staff voices, which are notably difficult tasks that have often been overlooked in previous research. We propose an end-to-end system based on graph neural networks that clusters notes that belong to the same chord and connects them with edges if they are part of a voice. Our results show clear and consistent improvements over a previous approach on two datasets of different styles. To aid the qualitative analysis of our results, we support the export in symbolic music formats and provide a direct visualization of our outputs graph over the musical score. All code and pre-trained models are available at https://github.com/CPJKU/piano_svsep

Accurate weather forecasts are important for disaster prevention, agricultural planning, etc. Traditional numerical weather prediction (NWP) methods offer physically interpretable high-accuracy predictions but are computationally expensive and fail to fully leverage rapidly growing historical data. In recent years, deep learning models have made significant progress in weather forecasting, but challenges remain, such as balancing global and regional high-resolution forecasts, excessive smoothing in extreme event predictions, and insufficient dynamic system modeling. To address these issues, this paper proposes a global-regional nested weather forecasting framework (OneForecast) based on graph neural networks. By combining a dynamic system perspective with multi-grid theory, we construct a multi-scale graph structure and densify the target region to capture local high-frequency features. We introduce an adaptive messaging mechanism, using dynamic gating units to deeply integrate node and edge features for more accurate extreme event forecasting. For high-resolution regional forecasts, we propose a neural nested grid method to mitigate boundary information loss. Experimental results show that OneForecast performs excellently across global to regional scales and short-term to long-term forecasts, especially in extreme event predictions. Codes link https://github.com/YuanGao-YG/OneForecast.

Graph generation with Machine Learning is an open problem with applications in various research fields. In this work, we propose to cast the generative process of a graph into a sequential one, relying on a node ordering procedure. We use this sequential process to design a novel generative model composed of two recurrent neural networks that learn to predict the edges of graphs: the first network generates one endpoint of each edge, while the second network generates the other endpoint conditioned on the state of the first. We test our approach extensively on five different datasets, comparing with two well-known baselines coming from graph literature, and two recurrent approaches, one of which holds state of the art performances. Evaluation is conducted considering quantitative and qualitative characteristics of the generated samples. Results show that our approach is able to yield novel, and unique graphs originating from very different distributions, while retaining structural properties very similar to those in the training sample. Under the proposed evaluation framework, our approach is able to reach performances comparable to the current state of the art on the graph generation task.

Graph neural networks are popular architectures for graph machine learning, based on iterative computation of node representations of an input graph through a series of invariant transformations. A large class of graph neural networks follow a standard message-passing paradigm: at every layer, each node state is updated based on an aggregate of messages from its neighborhood. In this work, we propose a novel framework for training graph neural networks, where every node is viewed as a player that can choose to either 'listen', 'broadcast', 'listen and broadcast', or to 'isolate'. The standard message propagation scheme can then be viewed as a special case of this framework where every node 'listens and broadcasts' to all neighbors. Our approach offers a more flexible and dynamic message-passing paradigm, where each node can determine its own strategy based on their state, effectively exploring the graph topology while learning. We provide a theoretical analysis of the new message-passing scheme which is further supported by an extensive empirical analysis on a synthetic dataset and on real-world datasets.

Recently proposed Graph Neural Networks (GNNs) for vertex clustering are trained with an unsupervised minimum cut objective, approximated by a Spectral Clustering (SC) relaxation. However, the SC relaxation is loose and, while it offers a closed-form solution, it also yields overly smooth cluster assignments that poorly separate the vertices. In this paper, we propose a GNN model that computes cluster assignments by optimizing a tighter relaxation of the minimum cut based on graph total variation (GTV). The cluster assignments can be used directly to perform vertex clustering or to implement graph pooling in a graph classification framework. Our model consists of two core components: i) a message-passing layer that minimizes the ell_1 distance in the features of adjacent vertices, which is key to achieving sharp transitions between clusters; ii) an unsupervised loss function that minimizes the GTV of the cluster assignments while ensuring balanced partitions. Experimental results show that our model outperforms other GNNs for vertex clustering and graph classification.

Breaking domain names such as openresearch into component words open and research is important for applications like Text-to-Speech synthesis and web search. We link this problem to the classic problem of Chinese word segmentation and show the effectiveness of a tagging model based on Recurrent Neural Networks (RNNs) using characters as input. To compensate for the lack of training data, we propose a pre-training method on concatenated entity names in a large knowledge database. Pre-training improves the model by 33% and brings the sequence accuracy to 85%.

Time series are the primary data type used to record dynamic system measurements and generated in great volume by both physical sensors and online processes (virtual sensors). Time series analytics is therefore crucial to unlocking the wealth of information implicit in available data. With the recent advancements in graph neural networks (GNNs), there has been a surge in GNN-based approaches for time series analysis. These approaches can explicitly model inter-temporal and inter-variable relationships, which traditional and other deep neural network-based methods struggle to do. In this survey, we provide a comprehensive review of graph neural networks for time series analysis (GNN4TS), encompassing four fundamental dimensions: forecasting, classification, anomaly detection, and imputation. Our aim is to guide designers and practitioners to understand, build applications, and advance research of GNN4TS. At first, we provide a comprehensive task-oriented taxonomy of GNN4TS. Then, we present and discuss representative research works and introduce mainstream applications of GNN4TS. A comprehensive discussion of potential future research directions completes the survey. This survey, for the first time, brings together a vast array of knowledge on GNN-based time series research, highlighting foundations, practical applications, and opportunities of graph neural networks for time series analysis.

Graph Neural Networks (GNNs) have been widely applied to different tasks such as bioinformatics, drug design, and social networks. However, recent studies have shown that GNNs are vulnerable to adversarial attacks which aim to mislead the node or subgraph classification prediction by adding subtle perturbations. Detecting these attacks is challenging due to the small magnitude of perturbation and the discrete nature of graph data. In this paper, we propose a general adversarial edge detection pipeline EDoG without requiring knowledge of the attack strategies based on graph generation. Specifically, we propose a novel graph generation approach combined with link prediction to detect suspicious adversarial edges. To effectively train the graph generative model, we sample several sub-graphs from the given graph data. We show that since the number of adversarial edges is usually low in practice, with low probability the sampled sub-graphs will contain adversarial edges based on the union bound. In addition, considering the strong attacks which perturb a large number of edges, we propose a set of novel features to perform outlier detection as the preprocessing for our detection. Extensive experimental results on three real-world graph datasets including a private transaction rule dataset from a major company and two types of synthetic graphs with controlled properties show that EDoG can achieve above 0.8 AUC against four state-of-the-art unseen attack strategies without requiring any knowledge about the attack type; and around 0.85 with knowledge of the attack type. EDoG significantly outperforms traditional malicious edge detection baselines. We also show that an adaptive attack with full knowledge of our detection pipeline is difficult to bypass it.

Extensive knowledge graphs (KGs) have been constructed to facilitate knowledge-driven tasks across various scenarios. However, existing work usually develops separate reasoning models for different KGs, lacking the ability to generalize and transfer knowledge across diverse KGs and reasoning settings. In this paper, we propose a prompt-based KG foundation model via in-context learning, namely KG-ICL, to achieve a universal reasoning ability. Specifically, we introduce a prompt graph centered with a query-related example fact as context to understand the query relation. To encode prompt graphs with the generalization ability to unseen entities and relations in queries, we first propose a unified tokenizer that maps entities and relations in prompt graphs to predefined tokens. Then, we propose two message passing neural networks to perform prompt encoding and KG reasoning, respectively. We conduct evaluation on 43 different KGs in both transductive and inductive settings. Results indicate that the proposed KG-ICL outperforms baselines on most datasets, showcasing its outstanding generalization and universal reasoning capabilities. The source code is accessible on GitHub: https://github.com/nju-websoft/KG-ICL.

We study a class of optimization problems motivated by automating the design and update of AI systems like coding assistants, robots, and copilots. We propose an end-to-end optimization framework, Trace, which treats the computational workflow of an AI system as a graph akin to neural networks, based on a generalization of back-propagation. Optimization of computational workflows often involves rich feedback (e.g. console output or user's responses), heterogeneous parameters (e.g. prompts, hyper-parameters, codes), and intricate objectives (beyond maximizing a score). Moreover, its computation graph can change dynamically with the inputs and parameters. We frame a new mathematical setup of iterative optimization, Optimization with Trace Oracle (OPTO), to capture and abstract these properties so as to design optimizers that work across many domains. In OPTO, an optimizer receives an execution trace along with feedback on the computed output and updates parameters iteratively. Trace is the tool to implement OPTO in practice. Trace has a Python interface that efficiently converts a computational workflow into an OPTO instance using a PyTorch-like interface. Using Trace, we develop a general-purpose LLM-based optimizer called OptoPrime that can effectively solve OPTO problems. In empirical studies, we find that OptoPrime is capable of first-order numerical optimization, prompt optimization, hyper-parameter tuning, robot controller design, code debugging, etc., and is often competitive with specialized optimizers for each domain. We believe that Trace, OptoPrime and the OPTO framework will enable the next generation of interactive agents that automatically adapt using various kinds of feedback. Website: https://microsoft.github.io/Trace

Compared to other modalities, EEG-based emotion recognition can intuitively respond to the emotional patterns in the human brain and, therefore, has become one of the most concerning tasks in the brain-computer interfaces field. Since dependencies within brain regions are closely related to emotion, a significant trend is to develop Graph Neural Networks (GNNs) for EEG-based emotion recognition. However, brain region dependencies in emotional EEG have physiological bases that distinguish GNNs in this field from those in other time series fields. Besides, there is neither a comprehensive review nor guidance for constructing GNNs in EEG-based emotion recognition. In the survey, our categorization reveals the commonalities and differences of existing approaches under a unified framework of graph construction. We analyze and categorize methods from three stages in the framework to provide clear guidance on constructing GNNs in EEG-based emotion recognition. In addition, we discuss several open challenges and future directions, such as Temporal full-connected graph and Graph condensation.

Generating explanations for graph neural networks (GNNs) has been studied to understand their behavior in analytical tasks such as graph classification. Existing approaches aim to understand the overall results of GNNs rather than providing explanations for specific class labels of interest, and may return explanation structures that are hard to access, nor directly queryable.We propose GVEX, a novel paradigm that generates Graph Views for EXplanation. (1) We design a two-tier explanation structure called explanation views. An explanation view consists of a set of graph patterns and a set of induced explanation subgraphs. Given a database G of multiple graphs and a specific class label l assigned by a GNN-based classifier M, it concisely describes the fraction of G that best explains why l is assigned by M. (2) We propose quality measures and formulate an optimization problem to compute optimal explanation views for GNN explanation. We show that the problem is Σ^2_P-hard. (3) We present two algorithms. The first one follows an explain-and-summarize strategy that first generates high-quality explanation subgraphs which best explain GNNs in terms of feature influence maximization, and then performs a summarization step to generate patterns. We show that this strategy provides an approximation ratio of 1/2. Our second algorithm performs a single-pass to an input node stream in batches to incrementally maintain explanation views, having an anytime quality guarantee of 1/4 approximation. Using real-world benchmark data, we experimentally demonstrate the effectiveness, efficiency, and scalability of GVEX. Through case studies, we showcase the practical applications of GVEX.

In this work we address the problem of landmark-based segmentation for anatomical structures. We propose HybridGNet, an encoder-decoder neural architecture which combines standard convolutions for image feature encoding, with graph convolutional neural networks to decode plausible representations of anatomical structures. We benchmark the proposed architecture considering other standard landmark and pixel-based models for anatomical segmentation in chest x-ray images, and found that HybridGNet is more robust to image occlusions. We also show that it can be used to construct landmark-based segmentations from pixel level annotations. Our experimental results suggest that HybridGNet produces accurate and anatomically plausible landmark-based segmentations, by naturally incorporating shape constraints within the decoding process via spectral convolutions.

We introduce a novel masked pre-training technique for graph neural networks (GNNs) applied to computational fluid dynamics (CFD) problems. By randomly masking up to 40\% of input mesh nodes during pre-training, we force the model to learn robust representations of complex fluid dynamics. We pair this masking strategy with an asymmetric encoder-decoder architecture and gated multi-layer perceptrons to further enhance performance. The proposed method achieves state-of-the-art results on seven CFD datasets, including a new challenging dataset of 3D intracranial aneurysm simulations with over 250,000 nodes per mesh. Moreover, it significantly improves model performance and training efficiency across such diverse range of fluid simulation tasks. We demonstrate improvements of up to 60\% in long-term prediction accuracy compared to previous best models, while maintaining similar computational costs. Notably, our approach enables effective pre-training on multiple datasets simultaneously, significantly reducing the time and data required to achieve high performance on new tasks. Through extensive ablation studies, we provide insights into the optimal masking ratio, architectural choices, and training strategies.

In this paper, we propose REASON, a novel framework that enables the automatic discovery of both intra-level (i.e., within-network) and inter-level (i.e., across-network) causal relationships for root cause localization. REASON consists of Topological Causal Discovery and Individual Causal Discovery. The Topological Causal Discovery component aims to model the fault propagation in order to trace back to the root causes. To achieve this, we propose novel hierarchical graph neural networks to construct interdependent causal networks by modeling both intra-level and inter-level non-linear causal relations. Based on the learned interdependent causal networks, we then leverage random walks with restarts to model the network propagation of a system fault. The Individual Causal Discovery component focuses on capturing abrupt change patterns of a single system entity. This component examines the temporal patterns of each entity's metric data (i.e., time series), and estimates its likelihood of being a root cause based on the Extreme Value theory. Combining the topological and individual causal scores, the top K system entities are identified as root causes. Extensive experiments on three real-world datasets with case studies demonstrate the effectiveness and superiority of the proposed framework.

Robotic odour source localization (OSL) is a critical capability for autonomous systems operating in complex environments. However, current OSL methods often suffer from ambiguities, particularly when robots misattribute odours to incorrect objects due to limitations in olfactory datasets and sensor resolutions. To address this challenge, we introduce a novel machine learning method using diffusion-based molecular generation to enhance odour localization accuracy that can be used by itself or with automated olfactory dataset construction pipelines with vision-language models (VLMs) This generative process of our diffusion model expands the chemical space beyond the limitations of both current olfactory datasets and the training data of VLMs, enabling the identification of potential odourant molecules not previously documented. The generated molecules can then be more accurately validated using advanced olfactory sensors which emulate human olfactory recognition through electronic sensor arrays. By integrating visual analysis, language processing, and molecular generation, our framework enhances the ability of olfaction-vision models on robots to accurately associate odours with their correct sources, thereby improving navigation and decision-making through better sensor selection for a target compound. Our methodology represents a foundational advancement in the field of artificial olfaction, offering a scalable solution to the challenges posed by limited olfactory data and sensor ambiguities.

Volatility forecasting is essential for risk management and decision-making in financial markets. Traditional models like Generalized Autoregressive Conditional Heteroskedasticity (GARCH) effectively capture volatility clustering but often fail to model complex, non-linear interdependencies between multiple indices. This paper proposes a novel approach using Graph Neural Networks (GNNs) to represent global financial markets as dynamic graphs. The Temporal Graph Attention Network (Temporal GAT) combines Graph Convolutional Networks (GCNs) and Graph Attention Networks (GATs) to capture the temporal and structural dynamics of volatility spillovers. By utilizing correlation-based and volatility spillover indices, the Temporal GAT constructs directed graphs that enhance the accuracy of volatility predictions. Empirical results from a 15-year study of eight major global indices show that the Temporal GAT outperforms traditional GARCH models and other machine learning methods, particularly in short- to mid-term forecasts. The sensitivity and scenario-based analysis over a range of parameters and hyperparameters further demonstrate the significance of the proposed technique. Hence, this work highlights the potential of GNNs in modeling complex market behaviors, providing valuable insights for financial analysts and investors.

In an era of information explosion, recommender systems are vital tools to deliver personalized recommendations for users. The key of recommender systems is to forecast users' future behaviors based on previous user-item interactions. Due to their strong expressive power of capturing high-order connectivities in user-item interaction data, recent years have witnessed a rising interest in leveraging Graph Neural Networks (GNNs) to boost the prediction performance of recommender systems. Nonetheless, classic Matrix Factorization (MF) and Deep Neural Network (DNN) approaches still play an important role in real-world large-scale recommender systems due to their scalability advantages. Despite the existence of GNN-acceleration solutions, it remains an open question whether GNN-based recommender systems can scale as efficiently as classic MF and DNN methods. In this paper, we propose a Linear-Time Graph Neural Network (LTGNN) to scale up GNN-based recommender systems to achieve comparable scalability as classic MF approaches while maintaining GNNs' powerful expressiveness for superior prediction accuracy. Extensive experiments and ablation studies are presented to validate the effectiveness and scalability of the proposed algorithm. Our implementation based on PyTorch is available.

Graph Neural Networks (GNNs) have already been widely applied in various graph mining tasks. However, they suffer from the shallow architecture issue, which is the key impediment that hinders the model performance improvement. Although several relevant approaches have been proposed, none of the existing studies provides an in-depth understanding of the root causes of performance degradation in deep GNNs. In this paper, we conduct the first systematic experimental evaluation to present the fundamental limitations of shallow architectures. Based on the experimental results, we answer the following two essential questions: (1) what actually leads to the compromised performance of deep GNNs; (2) when we need and how to build deep GNNs. The answers to the above questions provide empirical insights and guidelines for researchers to design deep and well-performed GNNs. To show the effectiveness of our proposed guidelines, we present Deep Graph Multi-Layer Perceptron (DGMLP), a powerful approach (a paradigm in its own right) that helps guide deep GNN designs. Experimental results demonstrate three advantages of DGMLP: 1) high accuracy -- it achieves state-of-the-art node classification performance on various datasets; 2) high flexibility -- it can flexibly choose different propagation and transformation depths according to graph size and sparsity; 3) high scalability and efficiency -- it supports fast training on large-scale graphs. Our code is available in https://github.com/zwt233/DGMLP.

Graph neural networks have shown significant success in the field of graph representation learning. Graph convolutions perform neighborhood aggregation and represent one of the most important graph operations. Nevertheless, one layer of these neighborhood aggregation methods only consider immediate neighbors, and the performance decreases when going deeper to enable larger receptive fields. Several recent studies attribute this performance deterioration to the over-smoothing issue, which states that repeated propagation makes node representations of different classes indistinguishable. In this work, we study this observation systematically and develop new insights towards deeper graph neural networks. First, we provide a systematical analysis on this issue and argue that the key factor compromising the performance significantly is the entanglement of representation transformation and propagation in current graph convolution operations. After decoupling these two operations, deeper graph neural networks can be used to learn graph node representations from larger receptive fields. We further provide a theoretical analysis of the above observation when building very deep models, which can serve as a rigorous and gentle description of the over-smoothing issue. Based on our theoretical and empirical analysis, we propose Deep Adaptive Graph Neural Network (DAGNN) to adaptively incorporate information from large receptive fields. A set of experiments on citation, co-authorship, and co-purchase datasets have confirmed our analysis and insights and demonstrated the superiority of our proposed methods.

Graph neural networks (GNNs) learn the representation of graph-structured data, and their expressiveness can be further enhanced by inferring node relations for propagation. Attention-based GNNs infer neighbor importance to manipulate the weight of its propagation. Despite their popularity, the discussion on deep graph attention and its unique challenges has been limited. In this work, we investigate some problematic phenomena related to deep graph attention, including vulnerability to over-smoothed features and smooth cumulative attention. Through theoretical and empirical analyses, we show that various attention-based GNNs suffer from these problems. Motivated by our findings, we propose AEROGNN, a novel GNN architecture designed for deep graph attention. AERO-GNN provably mitigates the proposed problems of deep graph attention, which is further empirically demonstrated with (a) its adaptive and less smooth attention functions and (b) higher performance at deep layers (up to 64). On 9 out of 12 node classification benchmarks, AERO-GNN outperforms the baseline GNNs, highlighting the advantages of deep graph attention. Our code is available at https://github.com/syleeheal/AERO-GNN.

Emotion Recognition in Conversation (ERC) is a practical and challenging task. This paper proposes a novel multimodal approach, the Long-Short Distance Graph Neural Network (LSDGNN). Based on the Directed Acyclic Graph (DAG), it constructs a long-distance graph neural network and a short-distance graph neural network to obtain multimodal features of distant and nearby utterances, respectively. To ensure that long- and short-distance features are as distinct as possible in representation while enabling mutual influence between the two modules, we employ a Differential Regularizer and incorporate a BiAffine Module to facilitate feature interaction. In addition, we propose an Improved Curriculum Learning (ICL) to address the challenge of data imbalance. By computing the similarity between different emotions to emphasize the shifts in similar emotions, we design a "weighted emotional shift" metric and develop a difficulty measurer, enabling a training process that prioritizes learning easy samples before harder ones. Experimental results on the IEMOCAP and MELD datasets demonstrate that our model outperforms existing benchmarks.

Graph neural networks (GNNs) have been shown to be highly sensitive to the choice of aggregation function. While summing over a node's neighbours can approximate any permutation-invariant function over discrete inputs, Cohen-Karlik et al. [2020] proved there are set-aggregation problems for which summing cannot generalise to unbounded inputs, proposing recurrent neural networks regularised towards permutation-invariance as a more expressive aggregator. We show that these results carry over to the graph domain: GNNs equipped with recurrent aggregators are competitive with state-of-the-art permutation-invariant aggregators, on both synthetic benchmarks and real-world problems. However, despite the benefits of recurrent aggregators, their O(V) depth makes them both difficult to parallelise and harder to train on large graphs. Inspired by the observation that a well-behaved aggregator for a GNN is a commutative monoid over its latent space, we propose a framework for constructing learnable, commutative, associative binary operators. And with this, we construct an aggregator of O(log V) depth, yielding exponential improvements for both parallelism and dependency length while achieving performance competitive with recurrent aggregators. Based on our empirical observations, our proposed learnable commutative monoid (LCM) aggregator represents a favourable tradeoff between efficient and expressive aggregators.

Given the importance of getting calibrated predictions and reliable uncertainty estimations, various post-hoc calibration methods have been developed for neural networks on standard multi-class classification tasks. However, these methods are not well suited for calibrating graph neural networks (GNNs), which presents unique challenges such as accounting for the graph structure and the graph-induced correlations between the nodes. In this work, we conduct a systematic study on the calibration qualities of GNN node predictions. In particular, we identify five factors which influence the calibration of GNNs: general under-confident tendency, diversity of nodewise predictive distributions, distance to training nodes, relative confidence level, and neighborhood similarity. Furthermore, based on the insights from this study, we design a novel calibration method named Graph Attention Temperature Scaling (GATS), which is tailored for calibrating graph neural networks. GATS incorporates designs that address all the identified influential factors and produces nodewise temperature scaling using an attention-based architecture. GATS is accuracy-preserving, data-efficient, and expressive at the same time. Our experiments empirically verify the effectiveness of GATS, demonstrating that it can consistently achieve state-of-the-art calibration results on various graph datasets for different GNN backbones.

Graph Neural Architecture Search (GNAS) facilitates the automatic design of Graph Neural Networks (GNNs) tailored to specific downstream graph learning tasks. However, existing GNAS approaches often require manual adaptation to new graph search spaces, necessitating substantial code optimization and domain-specific knowledge. To address this challenge, we present LLM4GNAS, a toolkit for GNAS that leverages the generative capabilities of Large Language Models (LLMs). LLM4GNAS includes an algorithm library for graph neural architecture search algorithms based on LLMs, enabling the adaptation of GNAS methods to new search spaces through the modification of LLM prompts. This approach reduces the need for manual intervention in algorithm adaptation and code modification. The LLM4GNAS toolkit is extensible and robust, incorporating LLM-enhanced graph feature engineering, LLM-enhanced graph neural architecture search, and LLM-enhanced hyperparameter optimization. Experimental results indicate that LLM4GNAS outperforms existing GNAS methods on tasks involving both homogeneous and heterogeneous graphs.

Parsing sentences into syntax trees can benefit downstream applications in NLP. Transition-based parsers build trees by executing actions in a state transition system. They are computationally efficient, and can leverage machine learning to predict actions based on partial trees. However, existing transition-based parsers are predominantly based on the shift-reduce transition system, which does not align with how humans are known to parse sentences. Psycholinguistic research suggests that human parsing is strongly incremental: humans grow a single parse tree by adding exactly one token at each step. In this paper, we propose a novel transition system called attach-juxtapose. It is strongly incremental; it represents a partial sentence using a single tree; each action adds exactly one token into the partial tree. Based on our transition system, we develop a strongly incremental parser. At each step, it encodes the partial tree using a graph neural network and predicts an action. We evaluate our parser on Penn Treebank (PTB) and Chinese Treebank (CTB). On PTB, it outperforms existing parsers trained with only constituency trees; and it performs on par with state-of-the-art parsers that use dependency trees as additional training data. On CTB, our parser establishes a new state of the art. Code is available at https://github.com/princeton-vl/attach-juxtapose-parser.

Node centralities play a pivotal role in network science, social network analysis, and recommender systems. In temporal data, static path-based centralities like closeness or betweenness can give misleading results about the true importance of nodes in a temporal graph. To address this issue, temporal generalizations of betweenness and closeness have been defined that are based on the shortest time-respecting paths between pairs of nodes. However, a major issue of those generalizations is that the calculation of such paths is computationally expensive. Addressing this issue, we study the application of De Bruijn Graph Neural Networks (DBGNN), a causality-aware graph neural network architecture, to predict temporal path-based centralities in time series data. We experimentally evaluate our approach in 13 temporal graphs from biological and social systems and show that it considerably improves the prediction of both betweenness and closeness centrality compared to a static Graph Convolutional Neural Network.

Graph Neural Networks have gained huge interest in the past few years. These powerful algorithms expanded deep learning models to non-Euclidean space and were able to achieve state of art performance in various applications including recommender systems and social networks. However, this performance is based on static graph structures assumption which limits the Graph Neural Networks performance when the data varies with time. Spatiotemporal Graph Neural Networks are extension of Graph Neural Networks that takes the time factor into account. Recently, various Spatiotemporal Graph Neural Network algorithms were proposed and achieved superior performance compared to other deep learning algorithms in several time dependent applications. This survey discusses interesting topics related to Spatiotemporal Graph Neural Networks, including algorithms, applications, and open challenges.

Graph neural networks (GNN) has been successfully applied to operate on the graph-structured data. Given a specific scenario, rich human expertise and tremendous laborious trials are usually required to identify a suitable GNN architecture. It is because the performance of a GNN architecture is significantly affected by the choice of graph convolution components, such as aggregate function and hidden dimension. Neural architecture search (NAS) has shown its potential in discovering effective deep architectures for learning tasks in image and language modeling. However, existing NAS algorithms cannot be directly applied to the GNN search problem. First, the search space of GNN is different from the ones in existing NAS work. Second, the representation learning capacity of GNN architecture changes obviously with slight architecture modifications. It affects the search efficiency of traditional search methods. Third, widely used techniques in NAS such as parameter sharing might become unstable in GNN. To bridge the gap, we propose the automated graph neural networks (AGNN) framework, which aims to find an optimal GNN architecture within a predefined search space. A reinforcement learning based controller is designed to greedily validate architectures via small steps. AGNN has a novel parameter sharing strategy that enables homogeneous architectures to share parameters, based on a carefully-designed homogeneity definition. Experiments on real-world benchmark datasets demonstrate that the GNN architecture identified by AGNN achieves the best performance, comparing with existing handcrafted models and tradistional search methods.

Graph Neural Networks (GNN) are inherently limited in their expressive power. Recent seminal works (Xu et al., 2019; Morris et al., 2019b) introduced the Weisfeiler-Lehman (WL) hierarchy as a measure of expressive power. Although this hierarchy has propelled significant advances in GNN analysis and architecture developments, it suffers from several significant limitations. These include a complex definition that lacks direct guidance for model improvement and a WL hierarchy that is too coarse to study current GNNs. This paper introduces an alternative expressive power hierarchy based on the ability of GNNs to calculate equivariant polynomials of a certain degree. As a first step, we provide a full characterization of all equivariant graph polynomials by introducing a concrete basis, significantly generalizing previous results. Each basis element corresponds to a specific multi-graph, and its computation over some graph data input corresponds to a tensor contraction problem. Second, we propose algorithmic tools for evaluating the expressiveness of GNNs using tensor contraction sequences, and calculate the expressive power of popular GNNs. Finally, we enhance the expressivity of common GNN architectures by adding polynomial features or additional operations / aggregations inspired by our theory. These enhanced GNNs demonstrate state-of-the-art results in experiments across multiple graph learning benchmarks.

The recovery of time-varying graph signals is a fundamental problem with numerous applications in sensor networks and forecasting in time series. Effectively capturing the spatio-temporal information in these signals is essential for the downstream tasks. Previous studies have used the smoothness of the temporal differences of such graph signals as an initial assumption. Nevertheless, this smoothness assumption could result in a degradation of performance in the corresponding application when the prior does not hold. In this work, we relax the requirement of this hypothesis by including a learning module. We propose a Time Graph Neural Network (TimeGNN) for the recovery of time-varying graph signals. Our algorithm uses an encoder-decoder architecture with a specialized loss composed of a mean squared error function and a Sobolev smoothness operator.TimeGNN shows competitive performance against previous methods in real datasets.

Graph Neural Networks (GNNs) are popular models for graph learning problems. GNNs show strong empirical performance in many practical tasks. However, the theoretical properties have not been completely elucidated. In this paper, we investigate whether GNNs can exploit the graph structure from the perspective of the expressive power of GNNs. In our analysis, we consider graph generation processes that are controlled by hidden (or latent) node features, which contain all information about the graph structure. A typical example of this framework is kNN graphs constructed from the hidden features. In our main results, we show that GNNs can recover the hidden node features from the input graph alone, even when all node features, including the hidden features themselves and any indirect hints, are unavailable. GNNs can further use the recovered node features for downstream tasks. These results show that GNNs can fully exploit the graph structure by themselves, and in effect, GNNs can use both the hidden and explicit node features for downstream tasks. In the experiments, we confirm the validity of our results by showing that GNNs can accurately recover the hidden features using a GNN architecture built based on our theoretical analysis.

Advancement in finite element methods have become essential in various disciplines, and in particular for Computational Fluid Dynamics (CFD), driving research efforts for improved precision and efficiency. While Convolutional Neural Networks (CNNs) have found success in CFD by mapping meshes into images, recent attention has turned to leveraging Graph Neural Networks (GNNs) for direct mesh processing. This paper introduces a novel model merging Self-Attention with Message Passing in GNNs, achieving a 15\% reduction in RMSE on the well known flow past a cylinder benchmark. Furthermore, a dynamic mesh pruning technique based on Self-Attention is proposed, that leads to a robust GNN-based multigrid approach, also reducing RMSE by 15\%. Additionally, a new self-supervised training method based on BERT is presented, resulting in a 25\% RMSE reduction. The paper includes an ablation study and outperforms state-of-the-art models on several challenging datasets, promising advancements similar to those recently achieved in natural language and image processing. Finally, the paper introduces a dataset with meshes larger than existing ones by at least an order of magnitude. Code and Datasets will be released at https://github.com/DonsetPG/multigrid-gnn.

Real-time assessment of near-term Air Traffic Controller (ATCO) task demand is a critical challenge in an increasingly crowded airspace, as existing complexity metrics often fail to capture nuanced operational drivers beyond simple aircraft counts. This work introduces an interpretable Graph Neural Network (GNN) framework to address this gap. Our attention-based model predicts the number of upcoming clearances, the instructions issued to aircraft by ATCOs, from interactions within static traffic scenarios. Crucially, we derive an interpretable, per-aircraft task demand score by systematically ablating aircraft and measuring the impact on the model's predictions. Our framework significantly outperforms an ATCO-inspired heuristic and is a more reliable estimator of scenario complexity than established baselines. The resulting tool can attribute task demand to specific aircraft, offering a new way to analyse and understand the drivers of complexity for applications in controller training and airspace redesign.

Reasoning system dynamics is one of the most important analytical approaches for many scientific studies. With the initial state of a system as input, the recent graph neural networks (GNNs)-based methods are capable of predicting the future state distant in time with high accuracy. Although these methods have diverse designs in modeling the coordinates and interacting forces of the system, we show that they actually share a common paradigm that learns the integration of the velocity over the interval between the initial and terminal coordinates. However, their integrand is constant w.r.t. time. Inspired by this observation, we propose a new approach to predict the integration based on several velocity estimations with Newton-Cotes formulas and prove its effectiveness theoretically. Extensive experiments on several benchmarks empirically demonstrate consistent and significant improvement compared with the state-of-the-art methods.

Recent years have seen the advent of molecular simulation datasets that are orders of magnitude larger and more diverse. These new datasets differ substantially in four aspects of complexity: 1. Chemical diversity (number of different elements), 2. system size (number of atoms per sample), 3. dataset size (number of data samples), and 4. domain shift (similarity of the training and test set). Despite these large differences, benchmarks on small and narrow datasets remain the predominant method of demonstrating progress in graph neural networks (GNNs) for molecular simulation, likely due to cheaper training compute requirements. This raises the question -- does GNN progress on small and narrow datasets translate to these more complex datasets? This work investigates this question by first developing the GemNet-OC model based on the large Open Catalyst 2020 (OC20) dataset. GemNet-OC outperforms the previous state-of-the-art on OC20 by 16% while reducing training time by a factor of 10. We then compare the impact of 18 model components and hyperparameter choices on performance in multiple datasets. We find that the resulting model would be drastically different depending on the dataset used for making model choices. To isolate the source of this discrepancy we study six subsets of the OC20 dataset that individually test each of the above-mentioned four dataset aspects. We find that results on the OC-2M subset correlate well with the full OC20 dataset while being substantially cheaper to train on. Our findings challenge the common practice of developing GNNs solely on small datasets, but highlight ways of achieving fast development cycles and generalizable results via moderately-sized, representative datasets such as OC-2M and efficient models such as GemNet-OC. Our code and pretrained model weights are open-sourced.

This paper introduces SuperGlue, a neural network that matches two sets of local features by jointly finding correspondences and rejecting non-matchable points. Assignments are estimated by solving a differentiable optimal transport problem, whose costs are predicted by a graph neural network. We introduce a flexible context aggregation mechanism based on attention, enabling SuperGlue to reason about the underlying 3D scene and feature assignments jointly. Compared to traditional, hand-designed heuristics, our technique learns priors over geometric transformations and regularities of the 3D world through end-to-end training from image pairs. SuperGlue outperforms other learned approaches and achieves state-of-the-art results on the task of pose estimation in challenging real-world indoor and outdoor environments. The proposed method performs matching in real-time on a modern GPU and can be readily integrated into modern SfM or SLAM systems. The code and trained weights are publicly available at https://github.com/magicleap/SuperGluePretrainedNetwork.

AutoML has demonstrated remarkable success in finding an effective neural architecture for a given machine learning task defined by a specific dataset and an evaluation metric. However, most present AutoML techniques consider each task independently from scratch, which requires exploring many architectures, leading to high computational cost. Here we propose AutoTransfer, an AutoML solution that improves search efficiency by transferring the prior architectural design knowledge to the novel task of interest. Our key innovation includes a task-model bank that captures the model performance over a diverse set of GNN architectures and tasks, and a computationally efficient task embedding that can accurately measure the similarity among different tasks. Based on the task-model bank and the task embeddings, we estimate the design priors of desirable models of the novel task, by aggregating a similarity-weighted sum of the top-K design distributions on tasks that are similar to the task of interest. The computed design priors can be used with any AutoML search algorithm. We evaluate AutoTransfer on six datasets in the graph machine learning domain. Experiments demonstrate that (i) our proposed task embedding can be computed efficiently, and that tasks with similar embeddings have similar best-performing architectures; (ii) AutoTransfer significantly improves search efficiency with the transferred design priors, reducing the number of explored architectures by an order of magnitude. Finally, we release GNN-Bank-101, a large-scale dataset of detailed GNN training information of 120,000 task-model combinations to facilitate and inspire future research.

Propositional satisfiability (SAT) is an NP-complete problem that impacts many research fields, such as planning, verification, and security. Mainstream modern SAT solvers are based on the Conflict-Driven Clause Learning (CDCL) algorithm. Recent work aimed to enhance CDCL SAT solvers using Graph Neural Networks (GNNs). However, so far this approach either has not made solving more effective, or required substantial GPU resources for frequent online model inferences. Aiming to make GNN improvements practical, this paper proposes an approach called NeuroBack, which builds on two insights: (1) predicting phases (i.e., values) of variables appearing in the majority (or even all) of the satisfying assignments are essential for CDCL SAT solving, and (2) it is sufficient to query the neural model only once for the predictions before the SAT solving starts. Once trained, the offline model inference allows NeuroBack to execute exclusively on the CPU, removing its reliance on GPU resources. To train NeuroBack, a new dataset called DataBack containing 120,286 data samples is created. Finally, NeuroBack is implemented as an enhancement to a state-of-the-art SAT solver called Kissat. As a result, it allowed Kissat to solve 5.2% more problems on the recent SAT competition problem set, SATCOMP-2022. NeuroBack therefore shows how machine learning can be harnessed to improve SAT solving in an effective and practical manner.

Understanding where people go after visiting one business is crucial for urban planning, retail analytics, and location-based services. However, predicting these co-visitation patterns across millions of venues remains challenging due to extreme data sparsity and the complex interplay between spatial proximity and business relationships. Traditional approaches using only geographic distance fail to capture why coffee shops attract different customer flows than fine dining restaurants, even when co-located. We introduce NAICS-aware GraphSAGE, a novel graph neural network that integrates business taxonomy knowledge through learnable embeddings to predict population-scale co-visitation patterns. Our key insight is that business semantics, captured through detailed industry codes, provide crucial signals that pure spatial models cannot explain. The approach scales to massive datasets (4.2 billion potential venue pairs) through efficient state-wise decomposition while combining spatial, temporal, and socioeconomic features in an end-to-end framework. Evaluated on our POI-Graph dataset comprising 94.9 million co-visitation records across 92,486 brands and 48 US states, our method achieves significant improvements over state-of-the-art baselines: the R-squared value increases from 0.243 to 0.625 (a 157 percent improvement), with strong gains in ranking quality (32 percent improvement in NDCG at 10).

This paper analyses a set of simple adaptations that transform standard message-passing Graph Neural Networks (GNN) into provably powerful directed multigraph neural networks. The adaptations include multigraph port numbering, ego IDs, and reverse message passing. We prove that the combination of these theoretically enables the detection of any directed subgraph pattern. To validate the effectiveness of our proposed adaptations in practice, we conduct experiments on synthetic subgraph detection tasks, which demonstrate outstanding performance with almost perfect results. Moreover, we apply our proposed adaptations to two financial crime analysis tasks. We observe dramatic improvements in detecting money laundering transactions, improving the minority-class F1 score of a standard message-passing GNN by up to 30%, and closely matching or outperforming tree-based and GNN baselines. Similarly impressive results are observed on a real-world phishing detection dataset, boosting three standard GNNs' F1 scores by around 15% and outperforming all baselines.

Graph neural networks (GNNs) are effective models for representation learning on relational data. However, standard GNNs are limited in their expressive power, as they cannot distinguish graphs beyond the capability of the Weisfeiler-Leman graph isomorphism heuristic. In order to break this expressiveness barrier, GNNs have been enhanced with random node initialization (RNI), where the idea is to train and run the models with randomized initial node features. In this work, we analyze the expressive power of GNNs with RNI, and prove that these models are universal, a first such result for GNNs not relying on computationally demanding higher-order properties. This universality result holds even with partially randomized initial node features, and preserves the invariance properties of GNNs in expectation. We then empirically analyze the effect of RNI on GNNs, based on carefully constructed datasets. Our empirical findings support the superior performance of GNNs with RNI over standard GNNs.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Mesh-based simulations are central to modeling complex physical systems in many disciplines across science and engineering. Mesh representations support powerful numerical integration methods and their resolution can be adapted to strike favorable trade-offs between accuracy and efficiency. However, high-dimensional scientific simulations are very expensive to run, and solvers and parameters must often be tuned individually to each system studied. Here we introduce MeshGraphNets, a framework for learning mesh-based simulations using graph neural networks. Our model can be trained to pass messages on a mesh graph and to adapt the mesh discretization during forward simulation. Our results show it can accurately predict the dynamics of a wide range of physical systems, including aerodynamics, structural mechanics, and cloth. The model's adaptivity supports learning resolution-independent dynamics and can scale to more complex state spaces at test time. Our method is also highly efficient, running 1-2 orders of magnitude faster than the simulation on which it is trained. Our approach broadens the range of problems on which neural network simulators can operate and promises to improve the efficiency of complex, scientific modeling tasks.

Recent advancements in large language model (LLM)-based agents have demonstrated that collective intelligence can significantly surpass the capabilities of individual agents, primarily due to well-crafted inter-agent communication topologies. Despite the diverse and high-performing designs available, practitioners often face confusion when selecting the most effective pipeline for their specific task: Which topology is the best choice for my task, avoiding unnecessary communication token overhead while ensuring high-quality solution? In response to this dilemma, we introduce G-Designer, an adaptive, efficient, and robust solution for multi-agent deployment, which dynamically designs task-aware, customized communication topologies. Specifically, G-Designer models the multi-agent system as a multi-agent network, leveraging a variational graph auto-encoder to encode both the nodes (agents) and a task-specific virtual node, and decodes a task-adaptive and high-performing communication topology. Extensive experiments on six benchmarks showcase that G-Designer is: (1) high-performing, achieving superior results on MMLU with accuracy at 84.50% and on HumanEval with pass@1 at 89.90%; (2) task-adaptive, architecting communication protocols tailored to task difficulty, reducing token consumption by up to 95.33% on HumanEval; and (3) adversarially robust, defending against agent adversarial attacks with merely 0.3% accuracy drop.

With the increase of data in day-to-day life, businesses and different stakeholders need to analyze the data for better predictions. Traditionally, relational data has been a source of various insights, but with the increase in computational power and the need to understand deeper relationships between entities, the need to design new techniques has arisen. For this graph data analysis has become an extraordinary tool for understanding the data, which reveals more realistic and flexible modelling of complex relationships. Recently, Graph Neural Networks (GNNs) have shown great promise in various applications, such as social network analysis, recommendation systems, drug discovery, and more. However, many adversarial attacks can happen over the data, whether during training (poisoning attack) or during testing (evasion attack), which can adversely manipulate the desired outcome from the GNN model. Therefore, it is crucial to make the GNNs robust to such attacks. The existing robustness methods are computationally demanding and perform poorly when the intensity of attack increases. This paper presents a computationally efficient framework, namely, pLapGNN, based on weighted p-Laplacian for making GNNs robust. Empirical evaluation on real datasets establishes the efficacy and efficiency of the proposed method.

In node classification using graph neural networks (GNNs), a typical model generates logits for different class labels at each node. A softmax layer often outputs a label prediction based on the largest logit. We demonstrate that it is possible to infer hidden graph structural information from the dataset using these logits. We introduce the key notion of label non-uniformity, which is derived from the Wasserstein distance between the softmax distribution of the logits and the uniform distribution. We demonstrate that nodes with small label non-uniformity are harder to classify correctly. We theoretically analyze how the label non-uniformity varies across the graph, which provides insights into boosting the model performance: increasing training samples with high non-uniformity or dropping edges to reduce the maximal cut size of the node set of small non-uniformity. These mechanisms can be easily added to a base GNN model. Experimental results demonstrate that our approach improves the performance of many benchmark base models.

Feature-based image matching has extensive applications in computer vision. Keypoints detected in images can be naturally represented as graph structures, and Graph Neural Networks (GNNs) have been shown to outperform traditional deep learning techniques. Consequently, the paradigm of image matching via GNNs has gained significant prominence in recent academic research. In this paper, we first introduce an innovative adaptive graph construction method that utilizes a filtering mechanism based on distance and dynamic threshold similarity. This method dynamically adjusts the criteria for incorporating new vertices based on the characteristics of existing vertices, allowing for the construction of more precise and robust graph structures while avoiding redundancy. We further combine the vertex processing capabilities of GNNs with the global awareness capabilities of Transformers to enhance the model's representation of spatial and feature information within graph structures. This hybrid model provides a deeper understanding of the interrelationships between vertices and their contributions to the matching process. Additionally, we employ the Sinkhorn algorithm to iteratively solve for optimal matching results. Finally, we validate our system using extensive image datasets and conduct comprehensive comparative experiments. Experimental results demonstrate that our system achieves an average improvement of 3.8x-40.3x in overall matching performance. Additionally, the number of vertices and edges significantly impacts training efficiency and memory usage; therefore, we employ multi-GPU technology to accelerate the training process. Our code is available at https://github.com/songxf1024/GIMS.

Anatomical segmentation is a fundamental task in medical image computing, generally tackled with fully convolutional neural networks which produce dense segmentation masks. These models are often trained with loss functions such as cross-entropy or Dice, which assume pixels to be independent of each other, thus ignoring topological errors and anatomical inconsistencies. We address this limitation by moving from pixel-level to graph representations, which allow to naturally incorporate anatomical constraints by construction. To this end, we introduce HybridGNet, an encoder-decoder neural architecture that leverages standard convolutions for image feature encoding and graph convolutional neural networks (GCNNs) to decode plausible representations of anatomical structures. We also propose a novel image-to-graph skip connection layer which allows localized features to flow from standard convolutional blocks to GCNN blocks, and show that it improves segmentation accuracy. The proposed architecture is extensively evaluated in a variety of domain shift and image occlusion scenarios, and audited considering different types of demographic domain shift. Our comprehensive experimental setup compares HybridGNet with other landmark and pixel-based models for anatomical segmentation in chest x-ray images, and shows that it produces anatomically plausible results in challenging scenarios where other models tend to fail.

The expressive power of Graph Neural Networks (GNNs) has been studied extensively through the Weisfeiler-Leman (WL) graph isomorphism test. However, standard GNNs and the WL framework are inapplicable for geometric graphs embedded in Euclidean space, such as biomolecules, materials, and other physical systems. In this work, we propose a geometric version of the WL test (GWL) for discriminating geometric graphs while respecting the underlying physical symmetries: permutations, rotation, reflection, and translation. We use GWL to characterise the expressive power of geometric GNNs that are invariant or equivariant to physical symmetries in terms of distinguishing geometric graphs. GWL unpacks how key design choices influence geometric GNN expressivity: (1) Invariant layers have limited expressivity as they cannot distinguish one-hop identical geometric graphs; (2) Equivariant layers distinguish a larger class of graphs by propagating geometric information beyond local neighbourhoods; (3) Higher order tensors and scalarisation enable maximally powerful geometric GNNs; and (4) GWL's discrimination-based perspective is equivalent to universal approximation. Synthetic experiments supplementing our results are available at https://github.com/chaitjo/geometric-gnn-dojo

In this study, we propose a novel graph neural network called propagate-selector (PS), which propagates information over sentences to understand information that cannot be inferred when considering sentences in isolation. First, we design a graph structure in which each node represents an individual sentence, and some pairs of nodes are selectively connected based on the text structure. Then, we develop an iterative attentive aggregation and a skip-combine method in which a node interacts with its neighborhood nodes to accumulate the necessary information. To evaluate the performance of the proposed approaches, we conduct experiments with the standard HotpotQA dataset. The empirical results demonstrate the superiority of our proposed approach, which obtains the best performances, compared to the widely used answer-selection models that do not consider the intersentential relationship.

Detecting anomalies is important for identifying inefficiencies, errors, or fraud in business processes. Traditional process mining approaches focus on analyzing 'flattened', sequential, event logs based on a single case notion. However, many real-world process executions exhibit a graph-like structure, where events can be associated with multiple cases. Flattening event logs requires selecting a single case identifier which creates a gap with the real event data and artificially introduces anomalies in the event logs. Object-centric process mining avoids these limitations by allowing events to be related to different cases. This study proposes a novel framework for anomaly detection in business processes that exploits graph neural networks and the enhanced information offered by object-centric process mining. We first reconstruct and represent the process dependencies of the object-centric event logs as attributed graphs and then employ a graph convolutional autoencoder architecture to detect anomalous events. Our results show that our approach provides promising performance in detecting anomalies at the activity type and attributes level, although it struggles to detect anomalies in the temporal order of events.

Task planning in language agents is emerging as an important research topic alongside the development of large language models (LLMs). It aims to break down complex user requests in natural language into solvable sub-tasks, thereby fulfilling the original requests. In this context, the sub-tasks can be naturally viewed as a graph, where the nodes represent the sub-tasks, and the edges denote the dependencies among them. Consequently, task planning is a decision-making problem that involves selecting a connected path or subgraph within the corresponding graph and invoking it. In this paper, we explore graph learning-based methods for task planning, a direction that is orthogonal to the prevalent focus on prompt design. Our interest in graph learning stems from a theoretical discovery: the biases of attention and auto-regressive loss impede LLMs' ability to effectively navigate decision-making on graphs, which is adeptly addressed by graph neural networks (GNNs). This theoretical insight led us to integrate GNNs with LLMs to enhance overall performance. Extensive experiments demonstrate that GNN-based methods surpass existing solutions even without training, and minimal training can further enhance their performance. The performance gain increases with a larger task graph size.

Rationale is defined as a subset of input features that best explains or supports the prediction by machine learning models. Rationale identification has improved the generalizability and interpretability of neural networks on vision and language data. In graph applications such as molecule and polymer property prediction, identifying representative subgraph structures named as graph rationales plays an essential role in the performance of graph neural networks. Existing graph pooling and/or distribution intervention methods suffer from lack of examples to learn to identify optimal graph rationales. In this work, we introduce a new augmentation operation called environment replacement that automatically creates virtual data examples to improve rationale identification. We propose an efficient framework that performs rationale-environment separation and representation learning on the real and augmented examples in latent spaces to avoid the high complexity of explicit graph decoding and encoding. Comparing against recent techniques, experiments on seven molecular and four polymer real datasets demonstrate the effectiveness and efficiency of the proposed augmentation-based graph rationalization framework.

Online social media works as a source of various valuable and actionable information during disasters. These information might be available in multiple languages due to the nature of user generated content. An effective system to automatically identify and categorize these actionable information should be capable to handle multiple languages and under limited supervision. However, existing works mostly focus on English language only with the assumption that sufficient labeled data is available. To overcome these challenges, we propose a multilingual disaster related text classification system which is capable to work under \{mono, cross and multi\} lingual scenarios and under limited supervision. Our end-to-end trainable framework combines the versatility of graph neural networks, by applying over the corpus, with the power of transformer based large language models, over examples, with the help of cross-attention between the two. We evaluate our framework over total nine English, Non-English and monolingual datasets in \{mono, cross and multi\} lingual classification scenarios. Our framework outperforms state-of-the-art models in disaster domain and multilingual BERT baseline in terms of Weighted F_1 score. We also show the generalizability of the proposed model under limited supervision.

We present a generalization of graph convolutional networks by generalizing the diffusion operation underlying this class of graph neural networks. These sheaf neural networks are based on the sheaf Laplacian, a generalization of the graph Laplacian that encodes additional relational structure parameterized by the underlying graph. The sheaf Laplacian and associated matrices provide an extended version of the diffusion operation in graph convolutional networks, providing a proper generalization for domains where relations between nodes are non-constant, asymmetric, and varying in dimension. We show that the resulting sheaf neural networks can outperform graph convolutional networks in domains where relations between nodes are asymmetric and signed.

This work introduces a novel graph neural networks (GNNs)-based method to predict stream water temperature and reduce model bias across locations of different income and education levels. Traditional physics-based models often have limited accuracy because they are necessarily approximations of reality. Recently, there has been an increasing interest of using GNNs in modeling complex water dynamics in stream networks. Despite their promise in improving the accuracy, GNNs can bring additional model bias through the aggregation process, where node features are updated by aggregating neighboring nodes. The bias can be especially pronounced when nodes with similar sensitive attributes are frequently connected. We introduce a new method that leverages physical knowledge to represent the node influence in GNNs, and then utilizes physics-based influence to refine the selection and weights over the neighbors. The objective is to facilitate equitable treatment over different sensitive groups in the graph aggregation, which helps reduce spatial bias over locations, especially for those in underprivileged groups. The results on the Delaware River Basin demonstrate the effectiveness of the proposed method in preserving equitable performance across locations in different sensitive groups.

Top-performing landmark estimation algorithms are based on exploiting the excellent ability of large convolutional neural networks (CNNs) to represent local appearance. However, it is well known that they can only learn weak spatial relationships. To address this problem, we propose a model based on the combination of a CNN with a cascade of Graph Attention Network regressors. To this end, we introduce an encoding that jointly represents the appearance and location of facial landmarks and an attention mechanism to weigh the information according to its reliability. This is combined with a multi-task approach to initialize the location of graph nodes and a coarse-to-fine landmark description scheme. Our experiments confirm that the proposed model learns a global representation of the structure of the face, achieving top performance in popular benchmarks on head pose and landmark estimation. The improvement provided by our model is most significant in situations involving large changes in the local appearance of landmarks.

We propose a framework to learn to schedule a job-shop problem (JSSP) using a graph neural network (GNN) and reinforcement learning (RL). We formulate the scheduling process of JSSP as a sequential decision-making problem with graph representation of the state to consider the structure of JSSP. In solving the formulated problem, the proposed framework employs a GNN to learn that node features that embed the spatial structure of the JSSP represented as a graph (representation learning) and derive the optimum scheduling policy that maps the embedded node features to the best scheduling action (policy learning). We employ Proximal Policy Optimization (PPO) based RL strategy to train these two modules in an end-to-end fashion. We empirically demonstrate that the GNN scheduler, due to its superb generalization capability, outperforms practically favored dispatching rules and RL-based schedulers on various benchmark JSSP. We also confirmed that the proposed framework learns a transferable scheduling policy that can be employed to schedule a completely new JSSP (in terms of size and parameters) without further training.