When Graph Neural Networks Meet Dynamic Mode Decomposition

Graph Neural Networks (GNNs) have emerged as fundamental tools for a wide range of prediction tasks on graph-structured data. Recent studies have drawn analogies between GNN feature propagation and diffusion processes, which can be interpreted as dynamical systems. In this paper, we delve deeper into this perspective by connecting the dynamics in GNNs to modern Koopman theory and its numerical method, Dynamic Mode Decomposition (DMD). We illustrate how DMD can estimate a low-rank, finite-dimensional linear operator based on multiple states of the system, effectively approximating potential nonlinear interactions between nodes in the graph. This approach allows us to capture complex dynamics within the graph accurately and efficiently. We theoretically establish a connection between the DMD-estimated operator and the original dynamic operator between system states. Building upon this foundation, we introduce a family of DMD-GNN models that effectively leverage the low-rank eigenfunctions provided by the DMD algorithm. We further discuss the potential of enhancing our approach by incorporating domain-specific constraints such as symmetry into the DMD computation, allowing the corresponding GNN models to respect known physical properties of the underlying system. Our work paves the path for applying advanced dynamical system analysis tools via GNNs. We validate our approach through extensive experiments on various learning tasks, including directed graphs, large-scale graphs, long-range interactions, and spatial-temporal graphs. We also empirically verify that our proposed models can serve as powerful encoders for link prediction tasks. The results demonstrate that our DMD-enhanced GNNs achieve state-of-the-art performance, highlighting the effectiveness of integrating DMD into GNN frameworks.

Diffusing to the Top: Boost Graph Neural Networks with Minimal Hyperparameter Tuning

Graph Neural Networks (GNNs) are proficient in graph representation learning and achieve promising performance on versatile tasks such as node classification and link prediction. Usually, a comprehensive hyperparameter tuning is essential for fully unlocking GNN's top performance, especially for complicated tasks such as node classification on large graphs and long-range graphs. This is usually associated with high computational and time costs and careful design of appropriate search spaces. This work introduces a graph-conditioned latent diffusion framework (GNN-Diff) to generate high-performing GNNs based on the model checkpoints of sub-optimal hyperparameters selected by a light-tuning coarse search. We validate our method through 166 experiments across four graph tasks: node classification on small, large, and long-range graphs, as well as link prediction. Our experiments involve 10 classic and state-of-the-art target models and 20 publicly available datasets. The results consistently demonstrate that GNN-Diff: (1) boosts the performance of GNNs with efficient hyperparameter tuning; and (2) presents high stability and generalizability on unseen data across multiple generation runs. The code is available at https://github.com/lequanlin/GNN-Diff.

A Riemannian Approach to Ground Metric Learning for Optimal Transport

Optimal transport (OT) theory has attracted much attention in machine learning and signal processing applications. OT defines a notion of distance between probability distributions of source and target data points. A crucial factor that influences OT-based distances is the ground metric of the embedding space in which the source and target data points lie. In this work, we propose to learn a suitable latent ground metric parameterized by a symmetric positive definite matrix. We use the rich Riemannian geometry of symmetric positive definite matrices to jointly learn the OT distance along with the ground metric. Empirical results illustrate the efficacy of the learned metric in OT-based domain adaptation.

Machine Learning-Based Prediction of Key Genes Correlated to the Subretinal Lesion Severity in a Mouse Model of Age-Related Macular Degeneration

Age-related macular degeneration (AMD) is a major cause of blindness in older adults, severely affecting vision and quality of life. Despite advances in understanding AMD, the molecular factors driving the severity of subretinal scarring (fibrosis) remain elusive, hampering the development of effective therapies. This study introduces a machine learning-based framework to predict key genes that are strongly correlated with lesion severity and to identify potential therapeutic targets to prevent subretinal fibrosis in AMD. Using an original RNA sequencing (RNA-seq) dataset from the diseased retinas of JR5558 mice, we developed a novel and specific feature engineering technique, including pathway-based dimensionality reduction and gene-based feature expansion, to enhance prediction accuracy. Two iterative experiments were conducted by leveraging Ridge and ElasticNet regression models to assess biological relevance and gene impact. The results highlight the biological significance of several key genes and demonstrate the framework's effectiveness in identifying novel therapeutic targets. The key findings provide valuable insights for advancing drug discovery efforts and improving treatment strategies for AMD, with the potential to enhance patient outcomes by targeting the underlying genetic mechanisms of subretinal lesion development.

STLLM-DF: A Spatial-Temporal Large Language Model with Diffusion for Enhanced Multi-Mode Traffic System Forecasting

The rapid advancement of Intelligent Transportation Systems (ITS) presents challenges, particularly with missing data in multi-modal transportation and the complexity of handling diverse sequential tasks within a centralized framework. To address these issues, we propose the Spatial-Temporal Large Language Model Diffusion (STLLM-DF), an innovative model that leverages Denoising Diffusion Probabilistic Models (DDPMs) and Large Language Models (LLMs) to improve multi-task transportation prediction. The DDPM's robust denoising capabilities enable it to recover underlying data patterns from noisy inputs, making it particularly effective in complex transportation systems. Meanwhile, the non-pretrained LLM dynamically adapts to spatial-temporal relationships within multi-modal networks, allowing the system to efficiently manage diverse transportation tasks in both long-term and short-term predictions. Extensive experiments demonstrate that STLLM-DF consistently outperforms existing models, achieving an average reduction of 2.40\% in MAE, 4.50\% in RMSE, and 1.51\% in MAPE. This model significantly advances centralized ITS by enhancing predictive accuracy, robustness, and overall system performance across multiple tasks, thus paving the way for more effective spatio-temporal traffic forecasting through the integration of frozen transformer language models and diffusion techniques.

Hierarchical Multi-modal Transformer for Cross-modal Long Document Classification

Long Document Classification (LDC) has gained significant attention recently. However, multi-modal data in long documents such as texts and images are not being effectively utilized. Prior studies in this area have attempted to integrate texts and images in document-related tasks, but they have only focused on short text sequences and images of pages. How to classify long documents with hierarchical structure texts and embedding images is a new problem and faces multi-modal representation difficulties. In this paper, we propose a novel approach called Hierarchical Multi-modal Transformer (HMT) for cross-modal long document classification. The HMT conducts multi-modal feature interaction and fusion between images and texts in a hierarchical manner. Our approach uses a multi-modal transformer and a dynamic multi-scale multi-modal transformer to model the complex relationships between image features, and the section and sentence features. Furthermore, we introduce a new interaction strategy called the dynamic mask transfer module to integrate these two transformers by propagating features between them. To validate our approach, we conduct cross-modal LDC experiments on two newly created and two publicly available multi-modal long document datasets, and the results show that the proposed HMT outperforms state-of-the-art single-modality and multi-modality methods.

Unleash Graph Neural Networks from Heavy Tuning

Graph Neural Networks (GNNs) are deep-learning architectures designed for graph-type data, where understanding relationships among individual observations is crucial. However, achieving promising GNN performance, especially on unseen data, requires comprehensive hyperparameter tuning and meticulous training. Unfortunately, these processes come with high computational costs and significant human effort. Additionally, conventional searching algorithms such as grid search may result in overfitting on validation data, diminishing generalization accuracy. To tackle these challenges, we propose a graph conditional latent diffusion framework (GNN-Diff) to generate high-performing GNNs directly by learning from checkpoints saved during a light-tuning coarse search. Our method: (1) unleashes GNN training from heavy tuning and complex search space design; (2) produces GNN parameters that outperform those obtained through comprehensive grid search; and (3) establishes higher-quality generation for GNNs compared to diffusion frameworks designed for general neural networks.

ST-MambaSync: The Complement of Mamba and Transformers for Spatial-Temporal in Traffic Flow Prediction

Accurate traffic flow prediction is crucial for optimizing traffic management, enhancing road safety, and reducing environmental impacts. Existing models face challenges with long sequence data, requiring substantial memory and computational resources, and often suffer from slow inference times due to the lack of a unified summary state. This paper introduces ST-MambaSync, an innovative traffic flow prediction model that combines transformer technology with the ST-Mamba block, representing a significant advancement in the field. We are the pioneers in employing the Mamba mechanism which is an attention mechanism integrated with ResNet within a transformer framework, which significantly enhances the model's explainability and performance. ST-MambaSync effectively addresses key challenges such as data length and computational efficiency, setting new benchmarks for accuracy and processing speed through comprehensive comparative analysis. This development has significant implications for urban planning and real-time traffic management, establishing a new standard in traffic flow prediction technology.

ST-MambaSync: The Confluence of Mamba Structure and Spatio-Temporal Transformers for Precipitous Traffic Prediction

Balancing accuracy with computational efficiency is paramount in machine learning, particularly when dealing with high-dimensional data, such as spatial-temporal datasets. This study introduces ST-MambaSync, an innovative framework that integrates a streamlined attention layer with a simplified state-space layer. The model achieves competitive accuracy in spatial-temporal prediction tasks. We delve into the relationship between attention mechanisms and the Mamba component, revealing that Mamba functions akin to attention within a residual network structure. This comparative analysis underpins the efficiency of state-space models, elucidating their capability to deliver superior performance at reduced computational costs.

ST-SSMs: Spatial-Temporal Selective State of Space Model for Traffic Forecasting

Accurate and efficient traffic prediction is crucial for planning, management, and control of intelligent transportation systems. Most state-of-the-art methods for traffic prediction effectively predict both long-term and short-term by employing spatio-temporal neural networks as prediction models, together with transformers to learn global information on prediction objects (e.g., traffic states of road segments). However, these methods often have a high computational cost to obtain good performance. This paper introduces an innovative approach to traffic flow prediction, the Spatial-Temporal Selective State Space Model (ST-SSMs), featuring the novel ST-Mamba block, which can achieve good prediction accuracy with less computational cost. A comparative analysis highlights the ST-Mamba layer's efficiency, revealing its equivalence to three attention layers, yet with markedly reduced processing time. Through rigorous testing on diverse real-world datasets, the ST-SSMs model demonstrates exceptional improvements in prediction accuracy and computational simplicity, setting new benchmarks in the domain of traffic flow forecasting