OpenRaiser/Intern-Atlas huggingface dataset:
SE-GNN Seed Expanded-Aware Graph Neural Network With Iterative Optimization for Semi-Supervised Entity Alignment
Venue: Journal TKDE 2025
Year: 2025

Entity alignment aims to use pre-aligned seed pairs to find other equivalent entities from different knowledge graphs (KGs) and is widely used in graph fusion-related fields. However, as the scale of KGs increases, manually annotating pre-aligned seed pairs becomes difficult. Existing research utilizes entity embeddings obtained by aggregating single structural information to identify potential seed pairs, thus reducing the reliance on pre-aligned seed pairs. However, due to the structural heterogeneity of KGs, the quality of potential seed pairs obtained using only a single structural information is not ideal. In addition, although existing research improves the quality of potential seed pairs through semi-supervised iteration, they underestimate the impact of embedding distortion produced by noisy seed pairs on the alignment effect. In order to solve the above problems, we propose a seed expanded-aware graph neural network with iterative optimization for semi-supervised entity alignment, named SE-GNN. First, we utilize the semantic attributes and structural features of entities, combined with a conditional filtering mechanism, to obtain high-quality initial potential seed pairs. Next, we designed a local and global awareness mechanism. It introduces initial potential seed pairs and combines local and global information to obtain a more comprehensive entity embedding representation, which alleviates the impact of KGs structural heterogeneity and lays the foundation for the optimization of initial potential seed pairs. Then, we designed the threshold nearest neighbor embedding correction strategy. It combines the similarity threshold and the bidirectional nearest neighbor method as a filtering mechanism to select iterative potential seed pairs and also uses an embedding correction strategy to eliminate the embedding distortion.
Large Language Models are In-Context Molecule Learners
Venue: Journal TKDE 2025
Year: 2025

Large Language Models (LLMs) have demonstrated exceptional performance in biochemical tasks, especially the molecule caption translation task, which aims to bridge the gap between molecules and natural language texts. However, previous methods in adapting LLMs to the molecule-caption translation task required extra domain-specific pre-training stages, suffered weak alignment between molecular and textual spaces, or imposed stringent demands on the scale of LLMs. To resolve the challenges, we propose In-Context Molecule Adaptation (ICMA), as a new paradigm allowing LLMs to learn the molecule-text alignment from context examples via In-Context Molecule Tuning. Specifically, ICMA incorporates the following three stages: Hybrid Context Retrieval, Post-retrieval Re-ranking, and In-context Molecule Tuning. Initially, Hybrid Context Retrieval utilizes BM25 Caption Retrieval and Molecule Graph Retrieval to retrieve similar informative context examples. Additionally, Post-retrieval Re-ranking is composed of Sequence Reversal and Random Walk selection to further improve the quality of retrieval results. Finally, In-Context Molecule Tuning unlocks the in-context learning and reasoning capability of LLMs with the retrieved examples and adapts the parameters of LLMs for better alignment between molecules and texts. Experimental results demonstrate that ICMA can empower LLMs to achieve state-of-the-art or comparable performance without extra training corpora and intricate structures, showing that LLMs are inherently in-context molecule learners.
Tricolore Multi-Behavior User Profiling for Enhanced Candidate Generation in Recommender Systems
Venue: Journal TKDE 2025
Year: 2025

Online platforms aggregate extensive user feedback across diverse behaviors, providing a rich source for enhancing user engagement. Traditional recommender systems, however, typically optimize for a single target behavior and represent user preferences with a single vector, limiting their ability to handle multiple important behaviors or optimization objectives. This conventional approach also struggles to capture the full spectrum of user interests, resulting in a narrow item pool during candidate generation. To address these limitations, we present Tricolore, a versatile multi-vector learning framework that uncovers connections between different behavior types for more robust candidate generation. Tricolore's adaptive multi-task structure is also customizable to specific platform needs. To manage the variability in sparsity across behavior types, we incorporate a behavior-wise multi-view fusion module that dynamically enhances learning. Moreover, a popularity-balanced strategy ensures the recommendation list balances accuracy with item popularity, fostering diversity and improving overall performance. Extensive experiments on public datasets demonstrate Tricolore's effectiveness across various recommendation scenarios, from short video platforms to e-commerce. By leveraging a shared base embedding strategy, Tricolore also significantly improves the performance for cold-start users. The source code is publicly available at: https://github.com/abnering/Tricolore.
Ontology Embedding A Survey of Methods Applications and Resources
Venue: Journal TKDE 2025
Year: 2025

Ontologies are widely used for representing domain knowledge and meta data, playing an increasingly important role in Information Systems, the Semantic Web, Bioinformatics and many other domains. However, logical reasoning that ontologies can directly support are quite limited in learning, approximation and prediction. One straightforward solution is to integrate statistical analysis and machine learning. To this end, automatically learning vector representation for knowledge of an ontology i.e., ontology embedding has been widely investigated. Numerous papers have been published on ontology embedding, but a lack of systematic reviews hinders researchers from gaining a comprehensive understanding of this field. To bridge this gap, we write this survey paper, which first introduces different kinds of semantics of ontologies and formally defines ontology embedding as well as its property of faithfulness. Based on this, it systematically categorizes and analyses a relatively complete set of over 80 papers, according to the ontologies they aim at and their technical solutions including geometric modeling, sequence modeling and graph propagation. This survey also introduces the applications of ontology embedding in ontology engineering, machine learning augmentation and life sciences, presents a new library mOWL and discusses the challenges and future directions.
UniDyG A Unified and Effective Representation Learning Approach for Large Dynamic Graphs
Venue: Journal TKDE 2025
Year: 2025

Dynamic graphs are formulated in continuous-time or discrete-time dynamic graphs. They differ in temporal granularity: Continuous-Time Dynamic Graphs (CTDGs) exhibit rapid, localized changes, while Discrete-Time Dynamic Graphs (DTDGs) show gradual, global updates. This difference leads to isolated developments in representation learning for each type. To advance representation learning, recent research attempts to design a unified model capable of handling both CTDGs and DTDGs. However, it typically focuses on local dynamic propagation for temporal structure learning in the time domain, failing to accurately capture the structural evolution associated with each temporal granularity. In addition, existing works-whether specific or unified-often overlook the issue of temporal noise, compromising the model robustness and effectiveness. To better model both types of dynamic graphs, we propose UniDyG, a unified and effective representation learning approach, which scales to large dynamic graphs. We first propose a novel Fourier Graph Attention (FGAT) mechanism that can model local and global structural correlations based on recent neighbors and complex-number selective aggregation, while theoretically ensuring consistent representations of dynamic graphs over time. Based on approximation theory, we demonstrate that FGAT is well-suited to capture the underlying structures in CTDGs and DTDGs. We further enhance FGAT to resist temporal noise by designing an energy-gated unit, which adaptively filters out high-frequency noise according to the energy. Last, we leverage our FGAT mechanisms for temporal structure learning and employ the frequency-enhanced linear function for node-level dynamic updates, facilitating the generation of high-quality temporal embeddings. Extensive experiments show that our UniDyG achieves an average improvement of 14.4% over sixteen baselines across nine dynamic graphs.
Towards DS-NER Unveiling and Addressing Latent Noise in Distant Annotations
Venue: Journal TKDE 2025
Year: 2025

Distantly supervised named entity recognition (DS-NER) has emerged as a cheap and convenient alternative to traditional human annotation methods, enabling the automatic generation of training data by aligning text with external resources. Despite the many efforts in noise measurement methods, few works focus on the latent noise distribution between different distant annotation methods. In this work, we explore the effectiveness and robustness of DS-NER by two aspects: (1) distant annotation techniques, which encompasses both traditional rule-based methods and the innovative large language model supervision approach, and (2) noise assessment, for which we introduce a novel framework. This framework addresses the challenges by distinctly categorizing them into the unlabeled-entity problem (UEP) and the noisy-entity problem (NEP), subsequently providing specialized solutions for each. Our proposed method achieves significant improvements on eight real-world distant supervision datasets originating from three different data sources and involving four distinct annotation techniques, confirming its superiority over current state-of-the-art methods.
A Survey on Self-Supervised Graph Foundation Models Knowledge-Based Perspective
Venue: Journal TKDE 2025
Year: 2025

Graph self-supervised learning (SSL) is now a go-to method for pre-training graph foundation models (GFMs). There is a wide variety of knowledge patterns embedded in the graph data, such as node properties and clusters, which are crucial to learning generalized representations for GFMs. However, existing surveys of GFMs have several shortcomings: they lack comprehensiveness regarding the most recent progress, have unclear categorization of self-supervised methods, and take a limited architecture-based perspective that is restricted to only certain types of graph models. As the ultimate goal of GFMs is to learn generalized graph knowledge, we provide a comprehensive survey of self-supervised GFMs from a novel knowledge-based perspective. We propose a knowledge-based taxonomy, which categorizes self-supervised graph models by the specific graph knowledge utilized. Our taxonomy consists of microscopic (nodes, links, etc.), mesoscopic (context, clusters, etc.), and macroscopic knowledge (global structure, manifolds, etc.). It covers a total of 9 knowledge categories and more than 25 pretext tasks for pre-training GFMs, as well as various downstream task generalization strategies. Such a knowledge-based taxonomy allows us to re-examine graph models based on new architectures more clearly, such as graph language models, as well as provide more in-depth insights for constructing GFMs.
A Survey on Side Information-Driven Session-Based Recommendation From a Data-Centric Perspective
Venue: Journal TKDE 2025
Year: 2025

Session-based recommendation is gaining increasing attention due to its practical value in predicting the intents of anonymous users based on limited behaviors. Emerging efforts incorporate various side information to alleviate inherent data scarcity issues in this task, leading to impressive performance improvements. The core of side information-driven session-based recommendation is the discovery and utilization of diverse data. In this survey, we provide a comprehensive review of this task from a data-centric perspective. Specifically, this survey commences with a clear formulation of the task. This is followed by a detailed exploration of various benchmarks rich in side information that are pivotal for advancing research in this field. Afterwards, we delve into how different types of side information enhance the task, underscoring data characteristics and utility. Moreover, we discuss the usage of various side information, including data encoding, data injection, and involved techniques. A systematic review of research progress is then presented, with the taxonomy by the types of side information. Finally, we summarize the current limitations and present the future prospects of this vibrant topic.
RobGC Towards Robust Graph Condensation
Venue: Journal TKDE 2025
Year: 2025

Graph neural networks (GNNs) have attracted widespread attention for their impressive capability of graph representation learning. However, the increasing prevalence of large-scale graphs presents a significant challenge for GNN training due to their computational demands, limiting the applicability of GNNs in various scenarios. In response to this challenge, graph condensation (GC) is proposed as a promising acceleration solution, focusing on generating an informative compact graph that enables efficient training of GNNs while retaining performance. Despite the potential to accelerate GNN training, existing GC methods overlook the quality of large training graphs during both the training and inference stages. They indiscriminately emulate the training graph distributions, making the condensed graphs susceptible to noises within the training graph and significantly impeding the application of GC in intricate real-world scenarios. To address this issue, we propose robust graph condensation (RobGC), a plug-and-play approach for GC to extend the robustness and applicability of condensed graphs in noisy graph structure environments. Specifically, RobGC leverages the condensed graph as a feedback signal to guide the denoising process on the original training graph. A label propagation-based alternating optimization strategy is in place for the condensation and denoising processes, contributing to the mutual purification of the condensed graph and training graph. Additionally, as a GC method designed for inductive graph inference, RobGC facilitates test-time graph denoising by leveraging the noise-free condensed graph to calibrate the structure of the test graph. Extensive experiments show that RobGC is compatible with various GC methods, significantly boosting their robustness under different types and levels of graph structural noises.
DACAD Domain Adaptation Contrastive Learning for Anomaly Detection in Multivariate Time Series
Venue: Journal TKDE 2025
Year: 2025

In time series anomaly detection (TSAD), the scarcity of labeled data poses a challenge to the development of accurate models. Unsupervised domain adaptation (UDA) offers a solution by leveraging labeled data from a related domain to detect anomalies in an unlabeled target domain. However, existing UDA methods assume consistent anomalous classes across domains. To address this limitation, we propose a novel Domain Adaptation Contrastive learning model for Anomaly Detection in multivariate time series (DACAD), combining UDA with contrastive learning. DACAD utilizes an anomaly injection mechanism that enhances generalization across unseen anomalous classes, improving adaptability and robustness. Additionally, our model employs supervised contrastive loss for the source domain and self-supervised contrastive triplet loss for the target domain, ensuring comprehensive feature representation learning and domain-invariant feature extraction. Finally, an effective Center-based Entropy Classifier (CEC) accurately learns normal boundaries in the source domain. Extensive evaluations on multiple real-world datasets and a synthetic dataset highlight DACAD's superior performance in transferring knowledge across domains and mitigating the challenge of limited labeled data in TSAD.
UVTM Universal Vehicle Trajectory Modeling With ST Feature Domain Generation
Venue: Journal TKDE 2025
Year: 2025

Vehicle movement is frequently captured in the form of GPS trajectories, i.e., sequences of timestamped GPS locations. Such data is widely used for various tasks such as travel-time estimation, trajectory recovery, and trajectory prediction. A universal vehicle trajectory model could be applied to different tasks, removing the need to maintain multiple specialized models, thereby reducing computational and storage costs. However, creating such a model is challenging when the integrity of trajectory features is compromised, i.e., in scenarios where only partial features are available or the trajectories are sparse. To address these challenges, we propose the Universal Vehicle Trajectory Model (UVTM), which can effectively adapt to different tasks without excessive retraining. UVTM incorporates two specialized designs. First, it divides trajectory features into three distinct domains. Each domain can be masked and generated independently to accommodate tasks with only partially available features. Second, UVTM is pre-trained by reconstructing dense, feature-complete trajectories from sparse, feature-incomplete counterparts, enabling strong performance even when the integrity of trajectory features is compromised. Experiments involving four representative trajectory-related tasks on three real-world vehicle trajectory datasets provide insight into the performance of UVTM and offer evidence that it is capable of meeting its objectives.
Gaussian Process Latent Variable Modeling for Few-Shot Time Series Forecasting
Venue: Journal TKDE 2025
Year: 2025

Accurate time series forecasting is crucial for optimizing resource allocation, industrial production, and urban management, particularly with the growth of cyber-physical and IoT systems. However, limited training sample availability in fields like physics and biology poses significant challenges. Existing models struggle to capture long-term dependencies and to model diverse meta-knowledge explicitly in few-shot scenarios. To address these issues, we propose MetaGP, a meta-learning-based Gaussian process latent variable model that uses a Gaussian process kernel function to capture long-term dependencies and to maintain strong correlations in time series. We also introduce Kernel Association Search (KAS) as a novel meta-learning component to explicitly model meta-knowledge, thereby enhancing both interpretability and prediction accuracy. We study MetaGP on simulated and real-world few-shot datasets, showing that it is capable of state-of-the-art prediction accuracy. We also find that MetaGP can capture long-term dependencies and can model meta-knowledge, thereby providing valuable insights into complex time series patterns.
Unifying Lane-Level Traffic Prediction From a Graph Structural Perspective Benchmark and Baseline
Venue: Journal TKDE 2025
Year: 2025

Traffic prediction has long been a focal and pivotal area in research, witnessing both significant strides from city-level to road-level predictions in recent years. With the advancement of Vehicle-to-Everything (V2X) technologies, autonomous driving, and large-scale models in the traffic domain, lane-level traffic prediction has emerged as an indispensable direction. However, further progress in this field is hindered by the absence of comprehensive and unified evaluation standards, coupled with limited public availability of data and code. In this paper, we present the first systematic classification framework for lane-level traffic prediction, offering a structured taxonomy and analysis of existing methods. We construct three representative datasets from two real-world road networks, covering both regular and irregular lane configurations, and make them publicly available to support future research. We further establishes a unified spatial topology structure and prediction task formulation, and proposes a simple yet effective baseline model, GraphMLP, based on graph structure and MLP networks. This unified framework enables consistent evaluation across datasets and modeling paradigms. We also reproduce previously unavailable code from existing studies and conduct extensive experiments to assess a range of models in terms of accuracy, efficiency, and applicability, providing the first benchmark that jointly considers predictive performance and training cost for lane-level traffic scenarios. All datasets and code are released at https://github.com/ShuhaoLii/LaneLevel-Traffic-Benchmark.
Towards Robust Recommendation A Review and an Adversarial Robustness Evaluation Library
Venue: Journal TKDE 2025
Year: 2025

Recently, recommender system has achieved significant success. However, due to the openness of recommender systems, they remain vulnerable to malicious attacks. Additionally, natural noise in training data and issues such as data sparsity can also degrade the performance of recommender systems. Therefore, enhancing the robustness of recommender systems has become an increasingly important research topic. In this survey, we provide a comprehensive overview of the robustness of recommender systems. Based on our investigation, we categorize the robustness of recommender systems into adversarial robustness and non-adversarial robustness. In the adversarial robustness, we introduce the fundamental principles and classical methods of recommender system adversarial attacks and defenses. In the non-adversarial robustness, we analyze non-adversarial robustness from the perspectives of data sparsity, natural noise, and data imbalance. Additionally, we summarize commonly used datasets and evaluation metrics for evaluating the robustness of recommender systems. Finally, we also discuss the current challenges in the field of recommender system robustness and potential future research directions. Additionally, to facilitate fair and efficient evaluation of attack and defense methods in adversarial robustness, we propose an adversarial robustness evaluation library--ShillingREC, and we conduct evaluations of basic attack models and recommendation models. ShillingREC project is released at https://github.com/chengleileilei/ShillingREC.