arXiv subjects

Junbin Gao

Publications and source records attributed to Junbin Gao.

At least 55 records · Page 3Linked to original sources

arXiv2025

Combating Confirmation Bias: A Unified Pseudo-Labeling Framework for Entity Alignment

Entity alignment (EA) aims at identifying equivalent entity pairs across different knowledge graphs (KGs) that refer to the same real-world identity. To circumvent the shortage of seed alignments provided for training, recent EA models utilize pseudo-labeling strategies to iteratively add unaligned entity pairs predicted with high confidence to the seed alignments for model training. However, the adverse impact of confirmation bias during pseudo-labeling has been largely overlooked, thus hindering entity alignment performance. To systematically combat confirmation bias for pseudo-labeling-based entity alignment, we propose a Unified Pseudo-Labeling framework for Entity Alignment (UPL-EA) that explicitly eliminates pseudo-labeling errors to boost the accuracy of entity alignment. UPL-EA consists of two complementary components: (1) Optimal Transport (OT)-based pseudo-labeling uses discrete OT modeling as an effective means to determine entity correspondences and reduce erroneous matches across two KGs. An effective criterion is derived to infer pseudo-labeled alignments that satisfy one-to-one correspondences; (2) Parallel pseudo-label ensembling refines pseudo-labeled alignments by combining predictions over multiple models independently trained in parallel. The ensembled pseudo-labeled alignments are thereafter used to augment seed alignments to reinforce subsequent model training for alignment inference. The effectiveness of UPL-EA in eliminating pseudo-labeling errors is both theoretically supported and experimentally validated. Our extensive results and in-depth analyses demonstrate the superiority of UPL-EA over 15 competitive baselines and its utility as a general pseudo-labeling framework for entity alignment.

cs.AI↗

arXiv2025

Graph Pseudotime Analysis and Neural Stochastic Differential Equations for Analyzing Retinal Degeneration Dynamics and Beyond

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.

cs.LG↗

arXiv2025

Contrastive Learning Meets Pseudo-label-assisted Mixup Augmentation: A Comprehensive Graph Representation Framework from Local to Global

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.

cs.LG↗

arXiv2024

HC-LLM: Historical-Constrained Large Language Models for Radiology Report Generation

Radiology report generation (RRG) models typically focus on individual exams, often overlooking the integration of historical visual or textual data, which is crucial for patient follow-ups. Traditional methods usually struggle with long sequence dependencies when incorporating historical information, but large language models (LLMs) excel at in-context learning, making them well-suited for analyzing longitudinal medical data. In light of this, we propose a novel Historical-Constrained Large Language Models (HC-LLM) framework for RRG, empowering LLMs with longitudinal report generation capabilities by constraining the consistency and differences between longitudinal images and their corresponding reports. Specifically, our approach extracts both time-shared and time-specific features from longitudinal chest X-rays and diagnostic reports to capture disease progression. Then, we ensure consistent representation by applying intra-modality similarity constraints and aligning various features across modalities with multimodal contrastive and structural constraints. These combined constraints effectively guide the LLMs in generating diagnostic reports that accurately reflect the progression of the disease, achieving state-of-the-art results on the Longitudinal-MIMIC dataset. Notably, our approach performs well even without historical data during testing and can be easily adapted to other multimodal large models, enhancing its versatility.

cs.CV↗

arXiv2024

Dual-Frequency Filtering Self-aware Graph Neural Networks for Homophilic and Heterophilic Graphs

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.

cs.LG↗

arXiv2024

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.

cs.LG↗

arXiv2024

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.

cs.LG↗

arXiv2024

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.

cs.LG↗

arXiv2024

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.

q-bio.GN↗

arXiv2024

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.

cs.LG↗

arXiv2024

SpecSTG: A Fast Spectral Diffusion Framework for Probabilistic Spatio-Temporal Traffic Forecasting

Traffic forecasting, a crucial application of spatio-temporal graph (STG) learning, has traditionally relied on deterministic models for accurate point estimations. Yet, these models fall short of quantifying future uncertainties. Recently, many probabilistic methods, especially variants of diffusion models, have been proposed to fill this gap. However, existing diffusion methods typically deal with individual sensors separately when generating future time series, resulting in limited usage of spatial information in the probabilistic learning process. In this work, we propose SpecSTG, a novel spectral diffusion framework, to better leverage spatial dependencies and systematic patterns inherent in traffic data. More specifically, our method generates the Fourier representation of future time series, transforming the learning process into the spectral domain enriched with spatial information. Additionally, our approach incorporates a fast spectral graph convolution designed for Fourier input, alleviating the computational burden associated with existing models. Compared with state-of-the-arts, SpecSTG achieves up to 8% improvements on point estimations and up to 0.78% improvements on quantifying future uncertainties. Furthermore, SpecSTG's training and validation speed is 3.33X of the most efficient existing diffusion method for STG forecasting. The source code for SpecSTG is available at https://anonymous.4open.science/r/SpecSTG.

cs.LG↗

arXiv2024

Quasi-Framelets: Robust Graph Neural Networks via Adaptive Framelet Convolution

This paper aims to provide a novel design of a multiscale framelet convolution for spectral graph neural networks (GNNs). While current spectral methods excel in various graph learning tasks, they often lack the flexibility to adapt to noisy, incomplete, or perturbed graph signals, making them fragile in such conditions. Our newly proposed framelet convolution addresses these limitations by decomposing graph data into low-pass and high-pass spectra through a finely-tuned multiscale approach. Our approach directly designs filtering functions within the spectral domain, allowing for precise control over the spectral components. The proposed design excels in filtering out unwanted spectral information and significantly reduces the adverse effects of noisy graph signals. Our approach not only enhances the robustness of GNNs but also preserves crucial graph features and structures. Through extensive experiments on diverse, real-world graph datasets, we demonstrate that our framelet convolution achieves superior performance in node classification tasks. It exhibits remarkable resilience to noisy data and adversarial attacks, highlighting its potential as a robust solution for real-world graph applications. This advancement opens new avenues for more adaptive and reliable spectral GNN architectures.

cs.LG↗

arXiv2024

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.

cs.CV↗

arXiv2024

Design Your Own Universe: A Physics-Informed Agnostic Method for Enhancing Graph Neural Networks

Physics-informed Graph Neural Networks have achieved remarkable performance in learning through graph-structured data by mitigating common GNN challenges such as over-smoothing, over-squashing, and heterophily adaption. Despite these advancements, the development of a simple yet effective paradigm that appropriately integrates previous methods for handling all these challenges is still underway. In this paper, we draw an analogy between the propagation of GNNs and particle systems in physics, proposing a model-agnostic enhancement framework. This framework enriches the graph structure by introducing additional nodes and rewiring connections with both positive and negative weights, guided by node labeling information. We theoretically verify that GNNs enhanced through our approach can effectively circumvent the over-smoothing issue and exhibit robustness against over-squashing. Moreover, we conduct a spectral analysis on the rewired graph to demonstrate that the corresponding GNNs can fit both homophilic and heterophilic graphs. Empirical validations on benchmarks for homophilic, heterophilic graphs, and long-term graph datasets show that GNNs enhanced by our method significantly outperform their original counterparts.

cs.LG↗

arXiv2024

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.

cs.LG↗

arXiv2024

ST-Mamba: Spatial-Temporal Selective State Space Model for Traffic Flow Prediction

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.

cs.LG↗

arXiv2024

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.

cs.LG↗

arXiv2024

CCDSReFormer: Traffic Flow Prediction with a Criss-Crossed Dual-Stream Enhanced Rectified Transformer Model

Accurate, and effective traffic forecasting is vital for smart traffic systems, crucial in urban traffic planning and management. Current Spatio-Temporal Transformer models, despite their prediction capabilities, struggle with balancing computational efficiency and accuracy, favoring global over local information, and handling spatial and temporal data separately, limiting insight into complex interactions. We introduce the Criss-Crossed Dual-Stream Enhanced Rectified Transformer model (CCDSReFormer), which includes three innovative modules: Enhanced Rectified Spatial Self-attention (ReSSA), Enhanced Rectified Delay Aware Self-attention (ReDASA), and Enhanced Rectified Temporal Self-attention (ReTSA). These modules aim to lower computational needs via sparse attention, focus on local information for better traffic dynamics understanding, and merge spatial and temporal insights through a unique learning method. Extensive tests on six real-world datasets highlight CCDSReFormer's superior performance. An ablation study also confirms the significant impact of each component on the model's predictive accuracy, showcasing our model's ability to forecast traffic flow effectively.

cs.LG↗