Wengen Li

Jihong Guan, Jiaqi Wang, Wengen Li et al.

Knowledge Graphs (KGs) are composed of triples, and the goal of Knowledge Graph Completion (KGC) is to infer the missing factual triples. Traditional KGC tasks predict missing elements in a triple given one or two of its elements. As a more realistic task, the Triple Set Prediction (TSP) task aims to infer the set of missing triples conditioned only on the observed knowledge graph, without assuming any partial information about the missing triples. Existing TSP methods predict the set of missing triples in a triple-by-triple manner, falling short in capturing the dependencies among the predicted triples to ensure consistency. To address this issue, we propose a novel discrete diffusion model termed DiffTSP that treats TSP as a generative task. DiffTSP progressively adds noise to the KG through a discrete diffusion process, achieved by masking relational edges. The reverse process then gradually recovers the complete KG conditioned on the incomplete graph. To this end, we design a structure-aware denoising network that integrates a relational context encoder with a relational graph diffusion transformer for knowledge graph generation. DiffTSP can generate the complete set of triples in a one-pass manner while ensuring the dependencies among the predicted triples. Our approach achieves state-of-the-art performance on three public datasets. Code: https://github.com/ADMIS-TONGJI/DiffTSP.

Hanchen Yang, Wengen Li, Shuyu Wang et al.

With the rapid amassing of spatial-temporal (ST) ocean data, many spatial-temporal data mining (STDM) studies have been conducted to address various oceanic issues, including climate forecasting and disaster warning. Compared with typical ST data (e.g., traffic data), ST ocean data is more complicated but with unique characteristics, e.g., diverse regionality and high sparsity. These characteristics make it difficult to design and train STDM models on ST ocean data. To the best of our knowledge, a comprehensive survey of existing studies remains missing in the literature, which hinders not only computer scientists from identifying the research issues in ocean data mining but also ocean scientists to apply advanced STDM techniques. In this paper, we provide a comprehensive survey of existing STDM studies for ocean science. Concretely, we first review the widely-used ST ocean datasets and highlight their unique characteristics. Then, typical ST ocean data quality enhancement techniques are explored. Next, we classify existing STDM studies in ocean science into four types of tasks, i.e., prediction, event detection, pattern mining, and anomaly detection, and elaborate on the techniques for these tasks. Finally, promising research opportunities are discussed. This survey can help scientists from both computer science and ocean science better understand the fundamental concepts, key techniques, and open challenges of STDM for ocean science.

Yangmin Li, Ruiqi Zhu, Wengen Li

Multimodal sentiment analysis is an active research area that combines multiple data modalities, e.g., text, image and audio, to analyze human emotions and benefits a variety of applications. Existing multimodal sentiment analysis methods can be classified as modality interaction-based methods, modality transformation-based methods and modality similarity-based methods. However, most of these methods highly rely on the strong correlations between modalities, and cannot fully uncover and utilize the correlations between modalities to enhance sentiment analysis. Therefore, these methods usually achieve bad performance for identifying the sentiment of multimodal data with weak correlations. To address this issue, we proposed a two-stage semi-supervised model termed Correlation-aware Multimodal Transformer (CorMulT) which consists pre-training stage and prediction stage. At the pre-training stage, a modality correlation contrastive learning module is designed to efficiently learn modality correlation coefficients between different modalities. At the prediction stage, the learned correlation coefficients are fused with modality representations to make the sentiment prediction. According to the experiments on the popular multimodal dataset CMU-MOSEI, CorMulT obviously surpasses state-of-the-art multimodal sentiment analysis methods.

Yi Liu, Jia Ma, Wengen Li et al.

Recent advances in Image Restoration (IR) have been largely driven by generative methods such as Diffusion Models and Flow Matching, which excel in synthesizing realistic textures while suffering from slow multi-step inference and compromised pixel fidelity. In contrast, classical regression-based IR methods excel precisely in these aspects, offering single-step efficiency and high pixel-level reconstruction fidelity. To bridge this gap, we propose DiSI, a unified framework that Disentangles the underlying Stochastic Interpolant process into independent generation and regression components. This decoupling endows DiSI with remarkable versatility, enabling a continuous and controllable transition from a pure regression process to a fully generative one. Technically, we instantiate this framework with two specific sampling trajectories, accompanied by a unified sampler for high-quality, few-step inference on arbitrary trajectories. Furthermore, we design a dual-branch U-Net style transformer network in pixel space, using a dedicated branch to enhance conditional guidance while ensuring high throughput. Extensive experiments demonstrate that DiSI efficiently achieves competitive results on various IR tasks, while uniquely offering the inference-time flexibility to control the distortion-perception trade-off within a single model.

Xudong Jiang, Mingshan Loo, Hanchen Yang et al.

Accurate long-term time series forecasting (LTSF) requires the capture of complex long-range dependencies and dynamic periodic patterns. Recent advances in frequency-domain analysis offer a global perspective for uncovering temporal characteristics. However, real-world time series often exhibit pronounced cross-domain heterogeneity where variables that appear synchronized in the time domain can differ substantially in the frequency domain. Existing frequency-based LTSF methods often rely on implicit assumptions of cross-domain homogeneity, which limits their ability to adapt to such intricate variability. To effectively integrate frequency-domain analysis with temporal dependency learning, we propose AdaMamba, a novel framework that endogenizes adaptive and context-aware frequency analysis within the Mamba state-space update process. Specifically, AdaMamba introduces an interactive patch encoding module to capture inter-variable interaction dynamics. Then, we develop an adaptive frequency-gated state-space module that generates input-dependent frequency bases, and generalizes the conventional temporal forgetting gate into a unified time-frequency forgetting gate. This allows dynamic calibration of state transitions based on learned frequency-domain importance, while preserving Mamba's capability in modeling long-range dependencies. Extensive experiments on seven public LTSF benchmarks and two domain-specific datasets demonstrate that AdaMamba consistently outperforms state-of-the-art methods in forecasting accu racy while maintaining competitive computational efficiency. The code of AdaMamba is available at https://github.com/XDjiang25/AdaMamba.

Ming Shan Loo, Wengen Li, Xudong Jiang et al.

The reconstruction of ocean subsurface temperature (OST) using satellite remote sensing data holds significant scientific value for advancing the understanding of ocean dynamics and climate variability. However, the scarcity of subsurface observations, combined with the high degree of nonlinearity and spatiotemporal heterogeneity in subsurface processes, poses substantial challenges to the accuracy and generalization capability of traditional reconstruction methods. To address these limitations, this study proposes an adaptive framework that could capture both vertical structural dependencies and temporal variation patterns of OST via spatio-temporal clustering. By incorporating this framework with various deep learning models, e.g., dual-path convolutional neural networks (DP-CNN), Attention U-Net, and Vision Transformer (ViT), the OST field can be accurately reconstructed at a global scale only using surface observations, i.e., sea surface temperature (SST), sea surface salinity (SSS), sea surface height (SSH), and sea surface wind (SSW). Experimental results demonstrate that multiple deep learning methods using the proposed framework largely outperform their original counterparts, yielding improvements in RMSE ranging from 12.4\% to 27.2\%. This study provides a reliable solution for subsurface temperature reconstruction, offering important implications for meteorological modeling and climate change assessment.

Yi Liu, Wengen Li, Jihong Guan et al.

Cloud removal (CR) remains a challenging task in remote sensing image processing. Although diffusion models (DM) exhibit strong generative capabilities, their direct applications to CR are suboptimal, as they generate cloudless images from random noise, ignoring inherent information in cloudy inputs. To overcome this drawback, we develop a new CR model EMRDM based on mean-reverting diffusion models (MRDMs) to establish a direct diffusion process between cloudy and cloudless images. Compared to current MRDMs, EMRDM offers a modular framework with updatable modules and an elucidated design space, based on a reformulated forward process and a new ordinary differential equation (ODE)-based backward process. Leveraging our framework, we redesign key MRDM modules to boost CR performance, including restructuring the denoiser via a preconditioning technique, reorganizing the training process, and improving the sampling process by introducing deterministic and stochastic samplers. To achieve multi-temporal CR, we further develop a denoising network for simultaneously denoising sequential images. Experiments on mono-temporal and multi-temporal datasets demonstrate the superior performance of EMRDM. Our code is available at https://github.com/Ly403/EMRDM.

Lingbai Kong, Wengen Li, Hanchen Yang et al.

Temporal causal discovery is a crucial task aimed at uncovering the causal relations within time series data. The latest temporal causal discovery methods usually train deep learning models on prediction tasks to uncover the causality between time series. They capture causal relations by analyzing the parameters of some components of the trained models, e.g., attention weights and convolution weights. However, this is an incomplete mapping process from the model parameters to the causality and fails to investigate the other components, e.g., fully connected layers and activation functions, that are also significant for causal discovery. To facilitate the utilization of the whole deep learning models in temporal causal discovery, we proposed an interpretable transformer-based causal discovery model termed CausalFormer, which consists of the causality-aware transformer and the decomposition-based causality detector. The causality-aware transformer learns the causal representation of time series data using a prediction task with the designed multi-kernel causal convolution which aggregates each input time series along the temporal dimension under the temporal priority constraint. Then, the decomposition-based causality detector interprets the global structure of the trained causality-aware transformer with the proposed regression relevance propagation to identify potential causal relations and finally construct the causal graph. Experiments on synthetic, simulated, and real datasets demonstrate the state-of-the-art performance of CausalFormer on discovering temporal causality. Our code is available at https://github.com/lingbai-kong/CausalFormer.

Siyuan Guo, Lexuan Wang, Chang Jin et al.

This paper introduces M$^{3}$-20M, a large-scale Multi-Modal Molecule dataset that contains over 20 million molecules, with the data mainly being integrated from existing databases and partially generated by large language models. Designed to support AI-driven drug design and discovery, M$^{3}$-20M is 71 times more in the number of molecules than the largest existing dataset, providing an unprecedented scale that can highly benefit the training or fine-tuning of models, including large language models for drug design and discovery tasks. This dataset integrates one-dimensional SMILES, two-dimensional molecular graphs, three-dimensional molecular structures, physicochemical properties, and textual descriptions collected through web crawling and generated using GPT-3.5, offering a comprehensive view of each molecule. To demonstrate the power of M$^{3}$-20M in drug design and discovery, we conduct extensive experiments on two key tasks: molecule generation and molecular property prediction, using large language models including GLM4, GPT-3.5, GPT-4, and Llama3-8b. Our experimental results show that M$^{3}$-20M can significantly boost model performance in both tasks. Specifically, it enables the models to generate more diverse and valid molecular structures and achieve higher property prediction accuracy than existing single-modal datasets, which validates the value and potential of M$^{3}$-20M in supporting AI-driven drug design and discovery. The dataset is available at https://github.com/bz99bz/M-3.

Mingrui Zhang, Hanchen Yang, Wengen Li et al.

Large vision models (LVMs) have recently proven to be surprisingly effective time series forecasters, simply by rendering temporal data as images. This success, how ever, rests on a largely unexamined premise: the rendered time series images are sufficiently close to natural images for knowledge in pre-trained models to transfer effectively. We argue that two gaps still remain, i.e., spectral and structural gaps, fundamentally limiting the potential of LVMs for time series forecasting. Spectrally, we systematically reveal that rendered time series images exhibit a markedly shallower power spectrum than the natural images LVMs are pre-trained to recognize. Structurally, reshaping 1D temporal sequences into 2D grids fabricates spurious spatial adjacencies while severing genuine temporal continuities, misleading the spatial inductive biases of pre-trained LVMs. To bridge these gaps, we propose SSDA, a dual-branch network that spectrally and structurally adapts to unlock the full potential of LVMs for time series forecasting. At the data level, a Spectral Magnitude Aligner (SMA) applies 2D FFT to selectively enhance the magnitude spectrum toward natural-image statistics while preserving phase. At the model level, a Structural-Guided Low-Rank Adaptation (SG-LoRA) injects position-aware temporal encodings into patch embeddings and adapts at tention via low-rank updates. The two branches are further adaptively fused to produce the final forecast. Extensive experiments on seven real-world benchmarks demonstrate that SSDA consistently outperforms strong LVM- and LLM-based baselines under both full-shot and few-shot settings. Code is publicly available at https://anonymous.4open.science/r/SSDA-8C5B.

Hanchen Yang, Jiaqi Wang, Jiannong Cao et al.

Sea surface temperature (SST) prediction is a critical task in ocean science, supporting various applications, such as weather forecasting, fisheries management, and storm tracking. While existing data-driven methods have demonstrated significant success, they often neglect to leverage the rich domain knowledge accumulated over the past decades, limiting further advancements in prediction accuracy. The recent emergence of large language models (LLMs) has highlighted the potential of integrating domain knowledge for downstream tasks. However, the application of LLMs to SST prediction remains underexplored, primarily due to the challenge of integrating ocean domain knowledge and numerical data. To address this issue, we propose Ocean Knowledge Graph-enhanced LLM (OKG-LLM), a novel framework for global SST prediction. To the best of our knowledge, this work presents the first systematic effort to construct an Ocean Knowledge Graph (OKG) specifically designed to represent diverse ocean knowledge for SST prediction. We then develop a graph embedding network to learn the comprehensive semantic and structural knowledge within the OKG, capturing both the unique characteristics of individual sea regions and the complex correlations between them. Finally, we align and fuse the learned knowledge with fine-grained numerical SST data and leverage a pre-trained LLM to model SST patterns for accurate prediction. Extensive experiments on the real-world dataset demonstrate that OKG-LLM consistently outperforms state-of-the-art methods, showcasing its effectiveness, robustness, and potential to advance SST prediction. The codes are available in the online repository.

Wuchao Liu, Han Peng, Wengen Li et al.

Single-cell multi-omics data contain huge information of cellular states, and analyzing these data can reveal valuable insights into cellular heterogeneity, diseases, and biological processes. However, as cell differentiation \& development is a continuous and dynamic process, it remains challenging to computationally model and infer cell interaction patterns based on single-cell multi-omics data. This paper presents scI2CL, a new single-cell multi-omics fusion framework based on intra- and inter-omics contrastive learning, to learn comprehensive and discriminative cellular representations from complementary multi-omics data for various downstream tasks. Extensive experiments of four downstream tasks validate the effectiveness of scI2CL and its superiority over existing peers. Concretely, in cell clustering, scI2CL surpasses eight state-of-the-art methods on four widely-used real-world datasets. In cell subtyping, scI2CL effectively distinguishes three latent monocyte cell subpopulations, which are not discovered by existing methods. Simultaneously, scI2CL is the only method that correctly constructs the cell developmental trajectory from hematopoietic stem and progenitor cells to Memory B cells. In addition, scI2CL resolves the misclassification of cell types between two subpopulations of CD4+ T cells, while existing methods fail to precisely distinguish the mixed cells. In summary, scI2CL can accurately characterize cross-omics relationships among cells, thus effectively fuses multi-omics data and learns discriminative cellular representations to support various downstream analysis tasks.