Graph Neural Networks (GNNs) address two key challenges in applying deep learning to graph-structured data: they handle varying size input graphs and ensure invariance under graph isomorphism. While GNNs have demonstrated broad applicability, understanding their expressive power remains an important question. In this paper, we show that bounded GNN architectures correspond to specific fragments of first-order logic (FO), including modal logic (ML), graded modal logic (GML), modal logic with the universal modality (ML(A)), the two-variable fragment (FO2) and its extension with counting quantifiers (C2). To establish these results, we apply methods and tools from finite model theory of first-order and modal logics to the domain of graph representation learning. This provides a unifying framework for understanding the logical expressiveness of GNNs within FO.
Existing biomedical benchmarks do not provide end-to-end infrastructure for training, evaluation, and inference of models that integrate multimodal biological data and a broad range of machine learning tasks in therapeutics. We present PyTDC, an open-source machine-learning platform providing streamlined training, evaluation, and inference software for multimodal biological AI models. PyTDC unifies distributed, heterogeneous, continuously updated data sources and model weights and standardizes benchmarking and inference endpoints. This paper discusses the components of PyTDC's architecture and, to our knowledge, the first-of-its-kind case study on the introduced single-cell drug-target nomination ML task. We find state-of-the-art methods in graph representation learning and domain-specific methods from graph theory perform poorly on this task. Though we find a context-aware geometric deep learning method that outperforms the evaluated SoTA and domain-specific baseline methods, the model is unable to generalize to unseen cell types or incorporate additional modalities, highlighting PyTDC's capacity to facilitate an exciting avenue of research developing multimodal, context-aware, foundation models for open problems in biomedical AI.
The comorbidities of hypertension impose a heavy burden on patients and society. Early identification is necessary to prompt intervention, but it remains a challenging task. This study aims to address this challenge by combining joint graph learning with network analysis. Motivated by this discovery, we develop a Conjoint Graph Representation Learning (CGRL) framework that: a) constructs two networks based on disease coding, including the patient network and the disease difference network. Three comorbidity network features were generated based on the basic difference network to capture the potential relationship between comorbidities and risk diseases; b) incorporates computational structure intervention and learning feature representation, CGRL was developed to predict the risks of diabetes and coronary heart disease in patients; and c) analysis the comorbidity patterns and exploring the pathways of disease progression, the pathological pathogenesis of diabetes and coronary heart disease may be revealed. The results show that the network features extracted based on the difference network are important, and the framework we proposed provides more accurate predictions than other strong models in terms of accuracy.
Diffusion probabilistic models (DPMs), widely recognized for their potential to generate high-quality samples, tend to go unnoticed in representation learning. While recent progress has highlighted their potential for capturing visual semantics, adapting DPMs to graph representation learning remains in its infancy. In this paper, we introduce Graffe, a self-supervised diffusion model proposed for graph representation learning. It features a graph encoder that distills a source graph into a compact representation, which, in turn, serves as the condition to guide the denoising process of the diffusion decoder. To evaluate the effectiveness of our model, we first explore the theoretical foundations of applying diffusion models to representation learning, proving that the denoising objective implicitly maximizes the conditional mutual information between data and its representation. Specifically, we prove that the negative logarithm of the denoising score matching loss is a tractable lower bound for the conditional mutual information. Empirically, we conduct a series of case studies to validate our theoretical insights. In addition, Graffe delivers competitive results under the linear probing setting on node and graph classification tasks, achieving state-of-the-art performance on 9 of the 11 real-world datasets. These findings indicate that powerful generative models, especially diffusion models, serve as an effective tool for graph representation learning.
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene regulatory networks (GRN) is essential to understand and predict the effects of genetic perturbations. However, current methods fail to fully leverage gene-related information, and solely rely on simple evaluation metrics to construct coarse-grained GRN. More importantly, they ignore functional differences between biotypes, limiting the ability to capture potential gene interactions. In this work, we leverage pre-trained large language model and DNA sequence model to extract features from gene descriptions and DNA sequence data, respectively, which serve as the initialization for gene representations. Additionally, we introduce gene biotype information for the first time in genetic perturbation, simulating the distinct roles of genes with different biotypes in regulating cellular processes, while capturing implicit gene relationships through graph structure learning (GSL). We propose GRAPE, a heterogeneous graph neural network (HGNN) that leverages gene representations initialized with features from descriptions and sequences, models the distinct roles of genes with different biotypes, and dynamically refines the GRN through GSL. The results on publicly available datasets show that our method achieves state-of-the-art performance.
Temporal interaction graphs (TIGs), defined by sequences of timestamped interaction events, have become ubiquitous in real-world applications due to their capability to model complex dynamic system behaviors. As a result, temporal interaction graph representation learning (TIGRL) has garnered significant attention in recent years. TIGRL aims to embed nodes in TIGs into low-dimensional representations that effectively preserve both structural and temporal information, thereby enhancing the performance of downstream tasks such as classification, prediction, and clustering within constantly evolving data environments. In this paper, we begin by introducing the foundational concepts of TIGs and emphasize the critical role of temporal dependencies. We then propose a comprehensive taxonomy of state-of-the-art TIGRL methods, systematically categorizing them based on the types of information utilized during the learning process to address the unique challenges inherent to TIGs. To facilitate further research and practical applications, we curate the source of datasets and benchmarks, providing valuable resources for empirical investigations. Finally, we examine key open challenges and explore promising research directions in TIGRL, laying the groundwork for future advancements that have the potential to shape the evolution of this field.
Heterogeneous graph neural networks (HeteGNNs) have demonstrated strong abilities to learn node representations by effectively extracting complex structural and semantic information in heterogeneous graphs. Most of the prevailing HeteGNNs follow the neighborhood aggregation paradigm, leveraging meta-path based message passing to learn latent node representations. However, due to the pairwise nature of meta-paths, these models fail to capture high-order relations among nodes, resulting in suboptimal performance. Additionally, the challenge of ``over-squashing'', where long-range message passing in HeteGNNs leads to severe information distortion, further limits the efficacy of these models. To address these limitations, this paper proposes MGA-HHN, a Multi-Granular Attention based Heterogeneous Hypergraph Neural Network for heterogeneous graph representation learning. MGA-HHN introduces two key innovations: (1) a novel approach for constructing meta-path based heterogeneous hypergraphs that explicitly models higher-order semantic information in heterogeneous graphs through multiple views, and (2) a multi-granular attention mechanism that operates at both the node and hyperedge levels. This mechanism enables the model to capture fine-grained interactions among nodes sharing the same semantic context within a hyperedge type, while preserving the diversity of semantics across different hyperedge types. As such, MGA-HHN effectively mitigates long-range message distortion and generates more expressive node representations. Extensive experiments on real-world benchmark datasets demonstrate that MGA-HHN outperforms state-of-the-art models, showcasing its effectiveness in node classification, node clustering and visualization tasks.
Representation learning, a task of learning latent vectors to represent entities, is a key task in improving search and recommender systems in web applications. Various representation learning methods have been developed, including graph-based approaches for relationships among entities, sequence-based methods for capturing the temporal evolution of user activities, and content-based models for leveraging text and visual content. However, the development of a unifying framework that integrates these diverse techniques to support multiple applications remains a significant challenge. This paper presents OmniSage, a large-scale representation framework that learns universal representations for a variety of applications at Pinterest. OmniSage integrates graph neural networks with content-based models and user sequence models by employing multiple contrastive learning tasks to effectively process graph data, user sequence data, and content signals. To support the training and inference of OmniSage, we developed an efficient infrastructure capable of supporting Pinterest graphs with billions of nodes. The universal representations generated by OmniSage have significantly enhanced user experiences on Pinterest, leading to an approximate 2.5% increase in sitewide repins (saves) across five applications. This paper highlights the impact of unifying representation learning methods, and we will open source the OmniSage code by the time of publication.
Effective and efficient graph representation learning is essential for enabling critical downstream tasks, such as node classification, link prediction, and subgraph search. However, existing graph neural network (GNN) architectures often struggle to adapt to diverse and complex graph structures, limiting their ability to produce structure-aware and task-discriminative representations. To address this challenge, we propose ABG-NAS, a novel framework for automated graph neural network architecture search tailored for efficient graph representation learning. ABG-NAS encompasses three key components: a Comprehensive Architecture Search Space (CASS), an Adaptive Genetic Optimization Strategy (AGOS), and a Bayesian-Guided Tuning Module (BGTM). CASS systematically explores diverse propagation (P) and transformation (T) operations, enabling the discovery of GNN architectures capable of capturing intricate graph characteristics. AGOS dynamically balances exploration and exploitation, ensuring search efficiency and preserving solution diversity. BGTM further optimizes hyperparameters periodically, enhancing the scalability and robustness of the resulting architectures. Empirical evaluations on benchmark datasets (Cora, PubMed, Citeseer, and CoraFull) demonstrate that ABG-NAS consistently outperforms both manually designed GNNs and state-of-the-art neural architecture search (NAS) methods. These results highlight the potential of ABG-NAS to advance graph representation learning by providing scalable and adaptive solutions for diverse graph structures. Our code is publicly available at https://github.com/sserranw/ABG-NAS.
Surgical workflow recognition is vital for automating tasks, supporting decision-making, and training novice surgeons, ultimately improving patient safety and standardizing procedures. However, data corruption can lead to performance degradation due to issues like occlusion from bleeding or smoke in surgical scenes and problems with data storage and transmission. In this case, we explore a robust graph-based multimodal approach to integrating vision and kinematic data to enhance accuracy and reliability. Vision data captures dynamic surgical scenes, while kinematic data provides precise movement information, overcoming limitations of visual recognition under adverse conditions. We propose a multimodal Graph Representation network with Adversarial feature Disentanglement (GRAD) for robust surgical workflow recognition in challenging scenarios with domain shifts or corrupted data. Specifically, we introduce a Multimodal Disentanglement Graph Network that captures fine-grained visual information while explicitly modeling the complex relationships between vision and kinematic embeddings through graph-based message modeling. To align feature spaces across modalities, we propose a Vision-Kinematic Adversarial framework that leverages adversarial training to reduce modality gaps and improve feature consistency. Furthermore, we design a Contextual Calibrated Decoder, incorporating temporal and contextual priors to enhance robustness against domain shifts and corrupted data. Extensive comparative and ablation experiments demonstrate the effectiveness of our model and proposed modules. Moreover, our robustness experiments show that our method effectively handles data corruption during storage and transmission, exhibiting excellent stability and robustness. Our approach aims to advance automated surgical workflow recognition, addressing the complexities and dynamism inherent in surgical procedures.
Graph auto-encoder is considered a framework for unsupervised learning on graph-structured data by representing graphs in a low dimensional space. It has been proved very powerful for graph analytics. In the real world, complex relationships in various entities can be represented by heterogeneous graphs that contain more abundant semantic information than homogeneous graphs. In general, graph auto-encoders based on homogeneous graphs are not applicable to heterogeneous graphs. In addition, little work has been done to evaluate the effect of different semantics on node embedding in heterogeneous graphs for unsupervised graph representation learning. In this work, we propose a novel Heterogeneous Graph Attention Auto-Encoders (HGATE) for unsupervised representation learning on heterogeneous graph-structured data. Based on the consideration of semantic information, our architecture of HGATE reconstructs not only the edges of the heterogeneous graph but also node attributes, through stacked encoder/decoder layers. Hierarchical attention is used to learn the relevance between a node and its meta-path based neighbors, and the relevance among different meta-paths. HGATE is applicable to transductive learning as well as inductive learning. Node classification and link prediction experiments on real-world heterogeneous graph datasets demonstrate the effectiveness of HGATE for both transductive and inductive tasks.
Graph Neural Networks (GNNs) update node representations through message passing, which is primarily based on the homophily principle, assuming that adjacent nodes share similar features. However, in real-world graphs with long-tailed degree distributions, high-degree nodes dominate message passing, causing a degree bias where low-degree nodes remain under-represented due to inadequate messages. The main challenge in addressing degree bias is how to discover non-adjacent nodes to provide additional messages to low-degree nodes while reducing excessive messages for high-degree nodes. Nevertheless, exploiting non-adjacent nodes to provide valuable messages is challenging, as it could generate noisy information and disrupt the original graph structures. To solve it, we propose a novel Degree Fairness Graph Transformer, named DegFairGT, to mitigate degree bias by discovering structural similarities between non-adjacent nodes through learnable structural augmentation and structural self-attention. Our key idea is to exploit non-adjacent nodes with similar roles in the same community to generate informative edges under our augmentation, which could provide informative messages between nodes with similar roles while ensuring that the homophily principle is maintained within the community. To enable DegFairGT to learn such structural similarities, we then propose a structural self-attention to capture the similarities between node pairs. To preserve global graph structures and prevent graph augmentation from hindering graph structure, we propose a Self-Supervised Learning task to preserve p-step transition probability and regularize graph augmentation. Extensive experiments on six datasets showed that DegFairGT outperformed state-of-the-art baselines in degree fairness analysis, node classification, and node clustering tasks.
Graph Transformers (GTs), which simultaneously integrate message-passing and self-attention mechanisms, have achieved promising empirical results in some graph prediction tasks. Although these approaches show the potential of Transformers in capturing long-range graph topology information, issues concerning the quadratic complexity and high computing energy consumption severely limit the scalability of GTs on large-scale graphs. Recently, as brain-inspired neural networks, Spiking Neural Networks (SNNs), facilitate the development of graph representation learning methods with lower computational and storage overhead through the unique event-driven spiking neurons. Inspired by these characteristics, we propose a linear-time Graph Transformer using Spiking Vector Quantization (GT-SVQ) for node classification. GT-SVQ reconstructs codebooks based on rate coding outputs from spiking neurons, and injects the codebooks into self-attention blocks to aggregate global information in linear complexity. Besides, spiking vector quantization effectively alleviates codebook collapse and the reliance on complex machinery (distance measure, auxiliary loss, etc.) present in previous vector quantization-based graph learning methods. In experiments, we compare GT-SVQ with other state-of-the-art baselines on node classification datasets ranging from small to large. Experimental results show that GT-SVQ has achieved competitive performances on most datasets while maintaining up to 130x faster inference speed compared to other GTs.
RGB-Thermal Video Object Detection (RGBT VOD) can address the limitation of traditional RGB-based VOD in challenging lighting conditions, making it more practical and effective in many applications. However, similar to most RGBT fusion tasks, it still mainly relies on manually aligned multimodal image pairs. In this paper, we propose a novel Multimodal Spatio-temporal Graph learning Network (MSGNet) for alignment-free RGBT VOD problem by leveraging the robust graph representation learning model. Specifically, we first design an Adaptive Partitioning Layer (APL) to estimate the corresponding regions of the Thermal image within the RGB image (high-resolution), achieving a preliminary inexact alignment. Then, we introduce the Spatial Sparse Graph Learning Module (S-SGLM) which employs a sparse information passing mechanism on the estimated inexact alignment to achieve reliable information interaction between different modalities. Moreover, to fully exploit the temporal cues for RGBT VOD problem, we introduce Hybrid Structured Temporal Modeling (HSTM), which involves a Temporal Sparse Graph Learning Module (T-SGLM) and Temporal Star Block (TSB). T-SGLM aims to filter out some redundant information between adjacent frames by employing the sparse aggregation mechanism on the temporal graph. Meanwhile, TSB is dedicated to achieving the complementary learning of local spatial relationships. Extensive comparative experiments conducted on both the aligned dataset VT-VOD50 and the unaligned dataset UVT-VOD2024 demonstrate the effectiveness and superiority of our proposed method. Our project will be made available on our website for free public access.
This paper introduces a cutting-edge method for enhancing recommender systems through the integration of generative self-supervised learning (SSL) with a Residual Graph Transformer. Our approach emphasizes the importance of superior data enhancement through the use of pertinent pretext tasks, automated through rationale-aware SSL to distill clear ways of how users and items interact. The Residual Graph Transformer incorporates a topology-aware transformer for global context and employs residual connections to improve graph representation learning. Additionally, an auto-distillation process refines self-supervised signals to uncover consistent collaborative rationales. Experimental evaluations on multiple datasets demonstrate that our approach consistently outperforms baseline methods.
Learning node representations is a fundamental problem in graph machine learning. While existing embedding methods effectively preserve local similarity measures, they often fail to capture global functions like graph distances. Inspired by Bourgain's seminal work on Hilbert space embeddings of metric spaces (1985), we study the performance of local distance-preserving node embeddings. Known as landmark-based algorithms, these embeddings approximate pairwise distances by computing shortest paths from a small subset of reference nodes (i.e., landmarks). Our main theoretical contribution shows that random graphs, such as Erd\H{o}s-R\'enyi random graphs, require lower dimensions in landmark-based embeddings compared to worst-case graphs. Empirically, we demonstrate that the GNN-based approximations for the distances to landmarks generalize well to larger networks, offering a scalable alternative for graph representation learning.
Fleets of robo-taxis offering on-demand transportation services, commonly known as Autonomous Mobility-on-Demand (AMoD) systems, hold significant promise for societal benefits, such as reducing pollution, energy consumption, and urban congestion. However, orchestrating these systems at scale remains a critical challenge, with existing coordination algorithms often failing to exploit the systems' full potential. This work introduces a novel decision-making framework that unites mathematical modeling with data-driven techniques. In particular, we present the AMoD coordination problem through the lens of reinforcement learning and propose a graph network-based framework that exploits the main strengths of graph representation learning, reinforcement learning, and classical operations research tools. Extensive evaluations across diverse simulation fidelities and scenarios demonstrate the flexibility of our approach, achieving superior system performance, computational efficiency, and generalizability compared to prior methods. Finally, motivated by the need to democratize research efforts in this area, we release publicly available benchmarks, datasets, and simulators for network-level coordination alongside an open-source codebase designed to provide accessible simulation platforms and establish a standardized validation process for comparing methodologies. Code available at: https://github.com/StanfordASL/RL4AMOD
While graph neural networks (GNNs) operating in hyperbolic spaces have shown promise for modeling hierarchical and complex relational data, a critical limitation often overlooked is their potentially limited discriminative power compared to their Euclidean counterparts or fundamental graph isomorphism tests like the Weisfeiler-Lehman (WL) hierarchy. Existing hyperbolic aggregation schemes, while curvature-aware, may not sufficiently capture the intricate structural differences required to robustly distinguish non-isomorphic graphs owing to non-injective aggregation functions. To address this expressiveness gap in hyperbolic graph learning, we introduce the Lorentzian Graph Isomorphic Network (LGIN), a novel GNN designed to achieve enhanced discriminative capabilities within the Lorentzian model of hyperbolic space. LGIN proposes a new update rule that effectively combines local neighborhood information with a richer representation of graph structure designed to preserve the Lorentzian metric tensor. This represents a significant step towards building more expressive GNNs in non-Euclidean geometries, overcoming a common bottleneck in current hyperbolic methods. We conduct extensive evaluations across nine diverse benchmark datasets, including molecular and protein structures. LGIN consistently outperforms or matches state-of-the-art hyperbolic and Euclidean GNNs, showcasing its practical efficacy and validating its superior ability to capture complex graph structures and distinguish between different graphs. To the best of our knowledge, LGIN is the first work to study the framework behind a powerful GNN on the hyperbolic space. The code for our paper can be found at https://github.com/Deceptrax123/LGIN
Quantum Graph Neural Networks (QGNNs) present a promising approach for combining quantum computing with graph-structured data processing. While classical Graph Neural Networks (GNNs) are renowned for their scalability and robustness, existing QGNNs often lack flexibility due to graph-specific quantum circuit designs, limiting their applicability to a narrower range of graph-structured problems, falling short of real-world scenarios. To address these limitations, we propose a versatile QGNN framework inspired by the classical GraphSAGE approach, utilizing quantum models as aggregators. In this work, we integrate established techniques for inductive representation learning on graphs with parametrized quantum convolutional and pooling layers, effectively bridging classical and quantum paradigms. The convolutional layer is flexible, enabling tailored designs for specific problems. Benchmarked on a node regression task with the QM9 dataset, we demonstrate that our framework successfully models a non-trivial molecular dataset, achieving performance comparable to classical GNNs. In particular, we show that our quantum approach exhibits robust generalization across molecules with varying numbers of atoms without requiring circuit modifications, slightly outperforming classical GNNs. Furthermore, we numerically investigate the scalability of the QGNN framework. Specifically, we demonstrate the absence of barren plateaus in our architecture as the number of qubits increases, suggesting that the proposed quantum model can be extended to handle larger and more complex graph-based problems effectively.
Graph layouts and node embeddings are two distinct paradigms for non-parametric graph representation learning. In the former, nodes are embedded into 2D space for visualization purposes. In the latter, nodes are embedded into a high-dimensional vector space for downstream processing. State-of-the-art algorithms for these two paradigms, force-directed layouts and random-walk-based contrastive learning (such as DeepWalk and node2vec), have little in common. In this work, we show that both paradigms can be approached with a single coherent framework based on established neighbor embedding methods. Specifically, we introduce graph t-SNE, a neighbor embedding method for two-dimensional graph layouts, and graph CNE, a contrastive neighbor embedding method that produces high-dimensional node representations by optimizing the InfoNCE objective. We show that both graph t-SNE and graph CNE strongly outperform state-of-the-art algorithms in terms of local structure preservation, while being conceptually simpler.