Understanding disease progression at the molecular pathway level usually requires capturing both structural dependencies between pathways and the temporal dynamics of disease evolution. In this work, we solve the former challenge by developing a biologically informed graph-forming method to efficiently construct pathway graphs for subjects from our newly curated JR5558 mouse transcriptomics dataset. We then develop Graph-level Pseudotime Analysis (GPA) to infer graph-level trajectories that reveal how disease progresses at the population level, rather than in individual subjects. Based on the trajectories estimated by GPA, we identify the most sensitive pathways that drive disease stage transitions. In addition, we measure changes in pathway features using neural stochastic differential equations (SDEs), which enables us to formally define and compute pathway stability and disease bifurcation points (points of no return), two fundamental problems in disease progression research. We further extend our theory to the case when pathways can interact with each other, enabling a more comprehensive and multi-faceted characterization of disease phenotypes. The comprehensive experimental results demonstrate the effectiveness of our framework in reconstructing the dynamics of the pathway, identifying critical transitions, and providing novel insights into the mechanistic understanding of disease evolution.

Graph Neural Networks (GNNs) have demonstrated remarkable effectiveness in various graph representation learning tasks. However, most existing GNNs focus primarily on capturing local information through explicit graph convolution, often neglecting global message-passing. This limitation hinders the establishment of a collaborative interaction between global and local information, which is crucial for comprehensively understanding graph data. To address these challenges, we propose a novel framework called Comprehensive Graph Representation Learning (ComGRL). ComGRL integrates local information into global information to derive powerful representations. It achieves this by implicitly smoothing local information through flexible graph contrastive learning, ensuring reliable representations for subsequent global exploration. Then ComGRL transfers the locally derived representations to a multi-head self-attention module, enhancing their discriminative ability by uncovering diverse and rich global correlations. To further optimize local information dynamically under the self-supervision of pseudo-labels, ComGRL employs a triple sampling strategy to construct mixed node pairs and applies reliable Mixup augmentation across attributes and structure for local contrastive learning. This approach broadens the receptive field and facilitates coordination between local and global representation learning, enabling them to reinforce each other. Experimental results across six widely used graph datasets demonstrate that ComGRL achieves excellent performance in node classification tasks. The code could be available at https://github.com/JinluWang1002/ComGRL.

Carbon emissions significantly contribute to climate change, and carbon credits have emerged as a key tool for mitigating environmental damage and helping organizations manage their carbon footprint. Despite their growing importance across sectors, fully leveraging carbon credits remains challenging. This study explores engineering practices and fintech solutions to enhance carbon emission management. We first review the negative impacts of carbon emission non-disclosure, revealing its adverse effects on financial stability and market value. Organizations are encouraged to actively manage emissions and disclose relevant data to mitigate risks. Next, we analyze factors influencing carbon prices and review advanced prediction algorithms that optimize carbon credit purchasing strategies, reducing costs and improving efficiency. Additionally, we examine corporate carbon emission prediction models, which offer accurate performance assessments and aid in planning future carbon credit needs. By integrating carbon price and emission predictions, we propose research directions, including corporate carbon management cost forecasting. This study provides a foundation for future quantitative research on the financial and market impacts of carbon management practices and is the first systematic review focusing on computing solutions and engineering practices for carbon credits.

Graph Neural Networks (GNNs) have excelled in handling graph-structured data, attracting significant research interest. However, two primary challenges have emerged: interference between topology and attributes distorting node representations, and the low-pass filtering nature of most GNNs leading to the oversight of valuable high-frequency information in graph signals. These issues are particularly pronounced in heterophilic graphs. To address these challenges, we propose Dual-Frequency Filtering Self-aware Graph Neural Networks (DFGNN). DFGNN integrates low-pass and high-pass filters to extract smooth and detailed topological features, using frequency-specific constraints to minimize noise and redundancy in the respective frequency bands. The model dynamically adjusts filtering ratios to accommodate both homophilic and heterophilic graphs. Furthermore, DFGNN mitigates interference by aligning topological and attribute representations through dynamic correspondences between their respective frequency bands, enhancing overall model performance and expressiveness. Extensive experiments conducted on benchmark datasets demonstrate that DFGNN outperforms state-of-the-art methods in classification performance, highlighting its effectiveness in handling both homophilic and heterophilic graphs.

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.

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.

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.

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.

Traffic flow prediction, a critical aspect of intelligent transportation systems, has been increasingly popular in the field of artificial intelligence, driven by the availability of extensive traffic data. The current challenges of traffic flow prediction lie in integrating diverse factors while balancing the trade-off between computational complexity and the precision necessary for effective long-range and large-scale predictions. To address these challenges, we introduce a Spatial-Temporal Selective State Space (ST-Mamba) model, which is the first to leverage the power of spatial-temporal learning in traffic flow prediction without using graph modeling. The ST-Mamba model can effectively capture the long-range dependency for traffic flow data, thereby avoiding the issue of over-smoothing. The proposed ST-Mamba model incorporates an effective Spatial-Temporal Mixer (ST-Mixer) to seamlessly integrate spatial and temporal data processing into a unified framework and employs a Spatial-Temporal Selective State Space (ST-SSM) block to improve computational efficiency. The proposed ST-Mamba model, specifically designed for spatial-temporal data, simplifies processing procedure and enhances generalization capabilities, thereby significantly improving the accuracy of long-range traffic flow prediction. Compared to the previous state-of-the-art (SOTA) model, the proposed ST-Mamba model achieves a 61.11\% improvement in computational speed and increases prediction accuracy by 0.67\%. Extensive experiments with real-world traffic datasets demonstrate that the \textsf{ST-Mamba} model sets a new benchmark in traffic flow prediction, achieving SOTA performance in computational efficiency for both long- and short-range predictions and significantly improving the overall efficiency and effectiveness of traffic management.

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.