A Survey of Graph Transformers: Architectures, Theories and Applications

Graph Transformers (GTs) have demonstrated a strong capability in modeling graph structures by addressing the intrinsic limitations of graph neural networks (GNNs), such as over-smoothing and over-squashing. Recent studies have proposed diverse architectures, enhanced explainability, and practical applications for Graph Transformers. In light of these rapid developments, we conduct a comprehensive review of Graph Transformers, covering aspects such as their architectures, theoretical foundations, and applications within this survey. We categorize the architecture of Graph Transformers according to their strategies for processing structural information, including graph tokenization, positional encoding, structure-aware attention and model ensemble. Furthermore, from the theoretical perspective, we examine the expressivity of Graph Transformers in various discussed architectures and contrast them with other advanced graph learning algorithms to discover the connections. Furthermore, we provide a summary of the practical applications where Graph Transformers have been utilized, such as molecule, protein, language, vision traffic, brain and material data. At the end of this survey, we will discuss the current challenges and prospective directions in Graph Transformers for potential future research.

Uncertainty Quantification With Noise Injection in Neural Networks: A Bayesian Perspective

Model uncertainty quantification involves measuring and evaluating the uncertainty linked to a model's predictions, helping assess their reliability and confidence. Noise injection is a technique used to enhance the robustness of neural networks by introducing randomness. In this paper, we establish a connection between noise injection and uncertainty quantification from a Bayesian standpoint. We theoretically demonstrate that injecting noise into the weights of a neural network is equivalent to Bayesian inference on a deep Gaussian process. Consequently, we introduce a Monte Carlo Noise Injection (MCNI) method, which involves injecting noise into the parameters during training and performing multiple forward propagations during inference to estimate the uncertainty of the prediction. Through simulation and experiments on regression and classification tasks, our method demonstrates superior performance compared to the baseline model.

Signal Processing over Time-Varying Graphs: A Systematic Review

As irregularly structured data representations, graphs have received a large amount of attention in recent years and have been widely applied to various real-world scenarios such as social, traffic, and energy settings. Compared to non-graph algorithms, numerous graph-based methodologies benefited from the strong power of graphs for representing high-dimensional and non-Euclidean data. In the field of Graph Signal Processing (GSP), analogies of classical signal processing concepts, such as shifting, convolution, filtering, and transformations are developed. However, many GSP techniques usually postulate the graph is static in both signal and typology. This assumption hinders the effectiveness of GSP methodologies as the assumption ignores the time-varying properties in numerous real-world systems. For example, in the traffic network, the signal on each node varies over time and contains underlying temporal correlation and patterns worthy of analysis. To tackle this challenge, more and more work are being done recently to investigate the processing of time-varying graph signals. They cope with time-varying challenges from three main directions: 1) graph time-spectral filtering, 2) multi-variate time-series forecasting, and 3) spatiotemporal graph data mining by neural networks, where non-negligible progress has been achieved. Despite the success of signal processing and learning over time-varying graphs, there is no survey to compare and conclude the current methodology for GSP and graph learning. To compensate for this, in this paper, we aim to review the development and recent progress on signal processing and learning over time-varying graphs, and compare their advantages and disadvantages from both the methodological and experimental side, to outline the challenges and potential research directions for future research.

LLM Online Spatial-temporal Signal Reconstruction Under Noise

This work introduces the LLM Online Spatial-temporal Reconstruction (LLM-OSR) framework, which integrates Graph Signal Processing (GSP) and Large Language Models (LLMs) for online spatial-temporal signal reconstruction. The LLM-OSR utilizes a GSP-based spatial-temporal signal handler to enhance graph signals and employs LLMs to predict missing values based on spatiotemporal patterns. The performance of LLM-OSR is evaluated on traffic and meteorological datasets under varying Gaussian noise levels. Experimental results demonstrate that utilizing GPT-4-o mini within the LLM-OSR is accurate and robust under Gaussian noise conditions. The limitations are discussed along with future research insights, emphasizing the potential of combining GSP techniques with LLMs for solving spatiotemporal prediction tasks.

LLM-based Online Prediction of Time-varying Graph Signals

In this paper, we propose a novel framework that leverages large language models (LLMs) for predicting missing values in time-varying graph signals by exploiting spatial and temporal smoothness. We leverage the power of LLM to achieve a message-passing scheme. For each missing node, its neighbors and previous estimates are fed into and processed by LLM to infer the missing observations. Tested on the task of the online prediction of wind-speed graph signals, our model outperforms online graph filtering algorithms in terms of accuracy, demonstrating the potential of LLMs in effectively addressing partially observed signals in graphs.

Time-varying Graph Signal Estimation via Dynamic Multi-hop Topologies

The assumption of using a static graph to represent multivariate time-varying signals oversimplifies the complexity of modeling their interactions over time. We propose a Dynamic Multi-hop model that captures dynamic interactions among time-varying node signals, while also accounting for time-varying edge signals, by extracting latent edges through topological diffusion and edge pruning. The resulting graphs are time-varying and sparse, capturing key dynamic node interactions and representing signal diffusion to both near and distant neighbors over time. The Dynamic Multi-hop Estimation algorithm is further proposed, accurately representing the interaction dynamics among node signals while enabling adaptive estimation of time-varying multivariate signals spatially and temporally. The Dynamic Multi-hop Estimation is evaluated under two real-world datasets of brain network and stock market for the online estimation of partially observed time-varying signals corrupted by noise.

Graph Signal Adaptive Message Passing

This paper proposes Graph Signal Adaptive Message Passing (GSAMP), a novel message passing method that simultaneously conducts online prediction, missing data imputation, and noise removal on time-varying graph signals. Unlike conventional Graph Signal Processing methods that apply the same filter to the entire graph, the spatiotemporal updates of GSAMP employ a distinct approach that utilizes localized computations at each node. This update is based on an adaptive solution obtained from an optimization problem designed to minimize the discrepancy between observed and estimated values. GSAMP effectively processes real-world, time-varying graph signals under Gaussian and impulsive noise conditions.

Bayesian Neural Network For Personalized Federated Learning Parameter Selection

Federated learning's poor performance in the presence of heterogeneous data remains one of the most pressing issues in the field. Personalized federated learning departs from the conventional paradigm in which all clients employ the same model, instead striving to discover an individualized model for each client to address the heterogeneity in the data. One of such approach involves personalizing specific layers of neural networks. However, prior endeavors have not provided a dependable rationale, and some have selected personalized layers that are entirely distinct and conflicting. In this work, we take a step further by proposing personalization at the elemental level, rather than the traditional layer-level personalization. To select personalized parameters, we introduce Bayesian neural networks and rely on the uncertainty they offer to guide our selection of personalized parameters. Finally, we validate our algorithm's efficacy on several real-world datasets, demonstrating that our proposed approach outperforms existing baselines.

Trustworthy Personalized Bayesian Federated Learning via Posterior Fine-Tune

Performance degradation owing to data heterogeneity and low output interpretability are the most significant challenges faced by federated learning in practical applications. Personalized federated learning diverges from traditional approaches, as it no longer seeks to train a single model, but instead tailors a unique personalized model for each client. However, previous work focused only on personalization from the perspective of neural network parameters and lack of robustness and interpretability. In this work, we establish a novel framework for personalized federated learning, incorporating Bayesian methodology which enhances the algorithm's ability to quantify uncertainty. Furthermore, we introduce normalizing flow to achieve personalization from the parameter posterior perspective and theoretically analyze the impact of normalizing flow on out-of-distribution (OOD) detection for Bayesian neural networks. Finally, we evaluated our approach on heterogeneous datasets, and the experimental results indicate that the new algorithm not only improves accuracy but also outperforms the baseline significantly in OOD detection due to the reliable output of the Bayesian approach.

Adaptive Least Mean Squares Graph Neural Networks and Online Graph Signal Estimation

The online prediction of multivariate signals, existing simultaneously in space and time, from noisy partial observations is a fundamental task in numerous applications. We propose an efficient Neural Network architecture for the online estimation of time-varying graph signals named the Adaptive Least Mean Squares Graph Neural Networks (LMS-GNN). LMS-GNN aims to capture the time variation and bridge the cross-space-time interactions under the condition that signals are corrupted by noise and missing values. The LMS-GNN is a combination of adaptive graph filters and Graph Neural Networks (GNN). At each time step, the forward propagation of LMS-GNN is similar to adaptive graph filters where the output is based on the error between the observation and the prediction similar to GNN. The filter coefficients are updated via backpropagation as in GNN. Experimenting on real-world temperature data reveals that our LMS-GNN achieves more accurate online predictions compared to graph-based methods like adaptive graph filters and graph convolutional neural networks.