Temporal knowledge graph reasoning aims to predict future events with knowledge of existing facts and plays a key role in various downstream tasks. Previous methods focused on either graph structure learning or semantic reasoning, failing to integrate dual reasoning perspectives to handle different prediction scenarios. Moreover, they lack the capability to capture the inherent differences between historical and non-historical events, which limits their generalization across different temporal contexts. To this end, we propose a Multi-Expert Structural-Semantic Hybrid (MESH) framework that employs three kinds of expert modules to integrate both structural and semantic information, guiding the reasoning process for different events. Extensive experiments on three datasets demonstrate the effectiveness of our approach.
Accurate weather forecasts are essential for supporting a wide range of activities and decision-making processes, as well as mitigating the impacts of adverse weather events. While traditional numerical weather prediction (NWP) remains the cornerstone of operational forecasting, machine learning is emerging as a powerful alternative for fast, flexible, and scalable predictions. We introduce PeakWeather, a high-quality dataset of surface weather observations collected every 10 minutes over more than 8 years from the ground stations of the Federal Office of Meteorology and Climatology MeteoSwiss's measurement network. The dataset includes a diverse set of meteorological variables from 302 station locations distributed across Switzerland's complex topography and is complemented with topographical indices derived from digital height models for context. Ensemble forecasts from the currently operational high-resolution NWP model are provided as a baseline forecast against which to evaluate new approaches. The dataset's richness supports a broad spectrum of spatiotemporal tasks, including time series forecasting at various scales, graph structure learning, imputation, and virtual sensing. As such, PeakWeather serves as a real-world benchmark to advance both foundational machine learning research, meteorology, and sensor-based applications.
Research on Graph Structure Learning (GSL) provides key insights for graph-based clustering, yet current methods like Graph Neural Networks (GNNs), Graph Attention Networks (GATs), and contrastive learning often rely heavily on the original graph structure. Their performance deteriorates when the original graph's adjacency matrix is too sparse or contains noisy edges unrelated to clustering. Moreover, these methods depend on learning node embeddings and using traditional techniques like k-means to form clusters, which may not fully capture the underlying graph structure between nodes. To address these limitations, this paper introduces DeSE, a novel unsupervised graph clustering framework incorporating Deep Structural Entropy. It enhances the original graph with quantified structural information and deep neural networks to form clusters. Specifically, we first propose a method for calculating structural entropy with soft assignment, which quantifies structure in a differentiable form. Next, we design a Structural Learning layer (SLL) to generate an attributed graph from the original feature data, serving as a target to enhance and optimize the original structural graph, thereby mitigating the issue of sparse connections between graph nodes. Finally, our clustering assignment method (ASS), based on GNNs, learns node embeddings and a soft assignment matrix to cluster on the enhanced graph. The ASS layer can be stacked to meet downstream task requirements, minimizing structural entropy for stable clustering and maximizing node consistency with edge-based cross-entropy loss. Extensive comparative experiments are conducted on four benchmark datasets against eight representative unsupervised graph clustering baselines, demonstrating the superiority of the DeSE in both effectiveness and interpretability.
Knowledge components (KCs) are the fundamental units of knowledge in the field of education. A KC graph illustrates the relationships and dependencies between KCs. An accurate KC graph can assist educators in identifying the root causes of learners' poor performance on specific KCs, thereby enabling targeted instructional interventions. To achieve this, we have developed a KC graph structure learning algorithm, named MAS-KCL, which employs a multi-agent system driven by large language models for adaptive modification and optimization of the KC graph. Additionally, a bidirectional feedback mechanism is integrated into the algorithm, where AI agents leverage this mechanism to assess the value of edges within the KC graph and adjust the distribution of generation probabilities for different edges, thereby accelerating the efficiency of structure learning. We applied the proposed algorithm to 5 synthetic datasets and 4 real-world educational datasets, and experimental results validate its effectiveness in learning path recognition. By accurately identifying learners' learning paths, teachers are able to design more comprehensive learning plans, enabling learners to achieve their educational goals more effectively, thus promoting the sustainable development of education.
Graph structure learning is a core problem in graph-based machine learning, essential for uncovering latent relationships and ensuring model interpretability. However, most existing approaches are ill-suited for large-scale and dynamically evolving graphs, as they often require complete re-learning of the structure upon the arrival of new nodes and incur substantial computational and memory costs. In this work, we propose GraphFLEx: a unified and scalable framework for Graph Structure Learning in Large and Expanding Graphs. GraphFLEx mitigates the scalability bottlenecks by restricting edge formation to structurally relevant subsets of nodes identified through a combination of clustering and coarsening techniques. This dramatically reduces the search space and enables efficient, incremental graph updates. The framework supports 48 flexible configurations by integrating diverse choices of learning paradigms, coarsening strategies, and clustering methods, making it adaptable to a wide range of graph settings and learning objectives. Extensive experiments across 26 diverse datasets and Graph Neural Network architectures demonstrate that GraphFLEx achieves state-of-the-art performance with significantly improved scalability.
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene regulatory networks (GRN) is essential to understand and predict the effects of genetic perturbations. However, current methods fail to fully leverage gene-related information, and solely rely on simple evaluation metrics to construct coarse-grained GRN. More importantly, they ignore functional differences between biotypes, limiting the ability to capture potential gene interactions. In this work, we leverage pre-trained large language model and DNA sequence model to extract features from gene descriptions and DNA sequence data, respectively, which serve as the initialization for gene representations. Additionally, we introduce gene biotype information for the first time in genetic perturbation, simulating the distinct roles of genes with different biotypes in regulating cellular processes, while capturing implicit gene relationships through graph structure learning (GSL). We propose GRAPE, a heterogeneous graph neural network (HGNN) that leverages gene representations initialized with features from descriptions and sequences, models the distinct roles of genes with different biotypes, and dynamically refines the GRN through GSL. The results on publicly available datasets show that our method achieves state-of-the-art performance.
Concept Factorization (CF) models have attracted widespread attention due to their excellent performance in data clustering. In recent years, many variant models based on CF have achieved great success in clustering by taking into account the internal geometric manifold structure of the dataset and using graph regularization techniques. However, their clustering performance depends greatly on the construction of the initial graph structure. In order to enable adaptive learning of the graph structure of the data, we propose a Concept Factorization Based on Self-Representation and Adaptive Graph Structure Learning (CFSRAG) Model. CFSRAG learns the affinity relationship between data through a self-representation method, and uses the learned affinity matrix to implement dynamic graph regularization constraints, thereby ensuring dynamic learning of the internal geometric structure of the data. Finally, we give the CFSRAG update rule and convergence analysis, and conduct comparative experiments on four real datasets. The results show that our model outperforms other state-of-the-art models.
Existing programming knowledge tracing methods have not deeply explored the relationships between knowledge concepts and programming questions or students’ codes, which leads to insufficient representation of programming questions and students’ codes and insufficient tracing of students’ knowledge states. To address these problems, this study proposes a programming knowledge tracing method based on a heterogeneous graph representation. We constructed a heterogeneous graph, where nodes represent the knowledge concept, programming question, and student code, and edges represent the relationships among knowledge concepts, programming questions, and student code. Subsequently, we leverage a graph structure learning algorithm to exploit the potential connections among them, aiming to enhance the graph structure information. Based on the graph, we further fully integrated the knowledge concept information into the representations of programming questions and student codes through the graph convolutional representation learning algorithm. Moreover, an attention mechanism is utilized to compute the effect of programming questions and student codes on the knowledge state and update the student’s knowledge state in conjunction with the corresponding answer results. Furthermore, the proposed method provides an assessment of the mastery level for each knowledge concept rather than only assessing each question using traditional methods. Experiments on two datasets, CodeWorkout and CodeNet, show that the proposed method achieves an average improvement of 4.28% in ACC and 6.48% in AUC compared with the baseline models, validating the effectiveness of the proposed method.
Recently, the emergence of LLMs has prompted researchers to integrate language descriptions into graphs, aiming to enhance model encoding capabilities from a data-centric perspective. This graph representation is called text-attributed graphs (TAGs). A review of prior advancements highlights that graph structure learning (GSL) is a pivotal technique for improving data utility, making it highly relevant to efficient TAG learning. However, most GSL methods are tailored for traditional graphs without textual information, underscoring the necessity of developing a new GSL paradigm. Despite clear motivations, it remains challenging: (1) How can we define a reasonable optimization objective for GSL in the era of LLMs, considering the massive parameters in LLM? (2) How can we design an efficient model architecture that enables seamless integration of LLM for this optimization objective? For Question 1, we reformulate existing GSL optimization objectives as a tree optimization framework, shifting the focus from obtaining a well-trained edge predictor to a language-aware tree sampler. For Question 2, we propose decoupled and training-free model design principles for LLM integration, shifting the focus from computation-intensive fine-tuning to more efficient inference. Based on this, we propose Large Language and Tree Assistant (LLaTA), which leverages tree-based LLM in-context learning to enhance the understanding of topology and text, enabling reliable inference and generating improved graph structure. Extensive experiments on 10 datasets demonstrate that LLaTA enjoys flexibility-incorporated with any backbone; scalability-outperforms other LLM-enhanced graph learning methods; effectiveness-achieves SOTA predictive performance.
Node classification in graphs aims to predict the categories of unlabeled nodes by utilizing a small set of labeled nodes. However, weighted graphs often contain noisy edges and anomalous edge weights, which can distort fine-grained relationships between nodes and hinder accurate classification. We propose the Edge Weight-aware Graph Structure Learning (EWGSL) method, which combines weight learning and graph structure learning to address these issues. EWGSL improves node classification by redefining attention coefficients in graph attention networks to incorporate node features and edge weights. It also applies graph structure learning to sparsify attention coefficients and uses a modified InfoNCE loss function to enhance performance by adapting to denoised graph weights. Extensive experimental results show that EWGSL has an average Micro-F1 improvement of 17.8% compared with the best baseline.
Earthquake detection is essential for earthquake early warning (EEW) systems. Traditional methods struggle with low signal-to-noise ratios and single-station reliance, limiting their effectiveness. We propose a Spatio-Temporal Graph Convolutional Network (GCN) using Spectral Structure Learning Convolution (Spectral SLC) to model static and dynamic relationships across seismic stations. Our approach processes multi-station waveform data and generates station-specific detection probabilities. Experiments show superior performance over a conventional GCN baseline in terms of true positive rate (TPR) and false positive rate (FPR), highlighting its potential for robust multi-station earthquake detection. The code repository for this study is available at https://github.com/SuchanunP/eq_detector.
Inferring the graph structure from observed data is a key task in graph machine learning to capture the intrinsic relationship between data entities. While significant advancements have been made in learning the structure of homogeneous graphs, many real-world graphs exhibit heterogeneous patterns where nodes and edges have multiple types. This paper fills this gap by introducing the first approach for heterogeneous graph structure learning (HGSL). To this end, we first propose a novel statistical model for the data-generating process (DGP) of heterogeneous graph data, namely hidden Markov networks for heterogeneous graphs (H2MN). Then we formalize HGSL as a maximum a-posterior estimation problem parameterized by such DGP and derive an alternating optimization method to obtain a solution together with a theoretical justification of the optimization conditions. Finally, we conduct extensive experiments on both synthetic and real-world datasets to demonstrate that our proposed method excels in learning structure on heterogeneous graphs in terms of edge type identification and edge weight recovery.
Graph Neural Networks (GNNs) have become a prominent approach for learning from graph-structured data. However, their effectiveness can be significantly compromised when the graph structure is suboptimal. To address this issue, Graph Structure Learning (GSL) has emerged as a promising technique that refines node connections adaptively. Nevertheless, we identify two key limitations in existing GSL methods: 1) Most methods primarily focus on node similarity to construct relationships, while overlooking the quality of node information. Blindly connecting low-quality nodes and aggregating their ambiguous information can degrade the performance of other nodes. 2) The constructed graph structures are often constrained to be symmetric, which may limit the model's flexibility and effectiveness. To overcome these limitations, we propose an Uncertainty-aware Graph Structure Learning (UnGSL) strategy. UnGSL estimates the uncertainty of node information and utilizes it to adjust the strength of directional connections, where the influence of nodes with high uncertainty is adaptively reduced. Importantly, UnGSL serves as a plug-in module that can be seamlessly integrated into existing GSL methods with minimal additional computational cost. In our experiments, we implement UnGSL into six representative GSL methods, demonstrating consistent performance improvements.
The exploration of cellular heterogeneity within the tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) is essential for understanding cancer progression and response to therapy. Current scRNA-seq approaches, however, lack spatial context and rely on incomplete datasets of ligand-receptor interactions (LRIs), limiting accurate cell type annotation and cell-cell communication (CCC) inference. This study addresses these challenges using a novel graph neural network (GNN) model that enhances cell type prediction and cell interaction analysis. Our study utilized a dataset consisting of 49,020 cells from 19 patients across three cancer types: Leukemia, Breast Invasive Carcinoma, and Colorectal Cancer. The proposed scGSL model demonstrated robust performance, achieving an average accuracy of 84.83%, precision of 86.23%, recall of 81.51%, and an F1 score of 80.92% across all datasets. These metrics represent a significant enhancement over existing methods, which typically exhibit lower performance metrics. Additionally, by reviewing existing literature on gene interactions within the TME, the scGSL model proves to robustly identify biologically meaningful gene interactions in an unsupervised manner, validated by significant expression differences in key gene pairs across various cancers. The source code and data used in this paper can be found in https://github.com/LiYuechao1998/scGSL.
Identifying protein-protein interactions (PPI) is crucial for gaining in-depth insights into numerous biological processes within cells and holds significant guiding value in areas such as drug development and disease treatment. Currently, most PPI prediction methods focus primarily on the study of protein sequences, neglecting the critical role of the internal structure of proteins. This paper proposes a novel PPI prediction method named MgslaPPI, which utilizes graph attention to mine protein structural information and enhances the expressive power of the protein encoder through multitask learning strategy. Specifically, we decompose the end-to-end PPI prediction process into two stages: amino acid residue reconstruction (A2RR) and protein interaction prediction (PIP). In the A2RR stage, we employ a graph attention-based residue reconstruction method to explore the internal relationships and features of proteins. In the PIP stage, in addition to the basic interaction prediction task, we introduce two auxiliary tasks, i.e., protein feature reconstruction (PFR) and masked interaction prediction (MIP). The PFR task aims to reconstruct the representation of proteins in the PIP stage, while the MIP task uses partially masked protein features for PPI prediction, with both working in concert to prompt MgslaPPI to capture more useful information. Experimental results demonstrate that MgslaPPI significantly outperforms existing state-of-the-art methods under various data partitioning schemes.
Spectral clustering is a powerful technique for clustering high-dimensional data, utilizing graph-based representations to detect complex, non-linear structures and non-convex clusters. The construction of a similarity graph is essential for ensuring accurate and effective clustering, making graph structure learning (GSL) central for enhancing spectral clustering performance in response to the growing demand for scalable solutions. Despite advancements in GSL, there is a lack of comprehensive surveys specifically addressing its role within spectral clustering. To bridge this gap, this survey presents a comprehensive review of spectral clustering methods, emphasizing on the critical role of GSL. We explore various graph construction techniques, including pairwise, anchor, and hypergraph-based methods, in both fixed and adaptive settings. Additionally, we categorize spectral clustering approaches into single-view and multi-view frameworks, examining their applications within one-step and two-step clustering processes. We also discuss multi-view information fusion techniques and their impact on clustering data. By addressing current challenges and proposing future research directions, this survey provides valuable insights for advancing spectral clustering methodologies and highlights the pivotal role of GSL in tackling large-scale and high-dimensional data clustering tasks.
With the rapid development of machine learning technologies, data-driven spectrum prediction enables intelligent dynamic spectrum access to alleviate the bottleneck of spectrum resource scarcity and congestion. However, spectrum prediction still faces some key challenges, including how to exploit the implicit but crucial multi-band correlations in wideband spectrum data, and how to capture the temporal dynamics across different bands. Due to the ignorance of such crucial features inherent from spectrum occupancy patterns, existing learning-based spectrum prediction methods unfortunately suffer from inaccurate prediction performance. To fill this gap, this paper develops a novel model of graph convolutional regression neural network (GCRNN), by introducing efficient graph structure learning (GSL-GCRNN) for dynamic multi-band spectrum prediction. The proposed GSL-GCRNN model is designed to adaptively learn both the multi-band and temporal correlations in dynamic wideband spectrum scenarios. Empowered by the graph structure estimator, graph convolutional networks are fueled to effectively extract the correlations in the frequency domain, followed by gated recurrent unit networks to further extract the temporal correlations of each band. It is worth noting that the graph structure estimator further enables to learn the multi-band correlations across different time periods on-the-fly, enhancing the accuracy of wideband spectrum prediction in dynamic environments. Simulation results verify that our GSLGCRNN approach outperforms the benchmark methods.
Soft sensing of hard-to-measure variables is often crucial in industrial processes. Current practices rely heavily on conventional modeling techniques that show success in improving accuracy. However, they overlook the non-linear nature, dynamics characteristics, and non-Euclidean dependencies between complex process variables. To tackle these challenges, we present a framework known as a Knowledge discovery graph Attention Network for effective Soft sensing (KANS). Unlike the existing deep learning soft sensor models, KANS can discover the intrinsic correlations and irregular relationships between the multivariate industrial processes without a predefined topology. First, an unsupervised graph structure learning method is introduced, incorporating the cosine similarity between different sensor embedding to capture the correlations between sensors. Next, we present a graph attention-based representation learning that can compute the multivariate data parallelly to enhance the model in learning complex sensor nodes and edges. To fully explore KANS, knowledge discovery analysis has also been conducted to demonstrate the interpretability of the model. Experimental results demonstrate that KANS significantly outperforms all the baselines and state-of-the-art methods in soft sensing performance. Furthermore, the analysis shows that KANS can find sensors closely related to different process variables without domain knowledge, significantly improving soft sensing accuracy.
Spatial-temporal data collected across different geographic locations often suffer from missing values, posing challenges to data analysis. Existing methods primarily leverage fixed spatial graphs to impute missing values, which implicitly assume that the spatial relationship is roughly the same for all features across different locations. However, they may overlook the different spatial relationships of diverse features recorded by sensors in different locations. To address this, we introduce the multi-scale Graph Structure Learning framework for spatial-temporal Imputation (GSLI) that dynamically adapts to the heterogeneous spatial correlations. Our framework encompasses node-scale graph structure learning to cater to the distinct global spatial correlations of different features, and feature-scale graph structure learning to unveil common spatial correlation across features within all stations. Integrated with prominence modeling, our framework emphasizes nodes and features with greater significance in the imputation process. Furthermore, GSLI incorporates cross-feature and cross-temporal representation learning to capture spatial-temporal dependencies. Evaluated on six real incomplete spatial-temporal datasets, GSLI showcases the improvement in data imputation.
Temporal Graph Networks (TGNs) have shown remarkable performance in learning representation for continuous-time dynamic graphs. However, real-world dynamic graphs typically contain diverse and intricate noise. Noise can significantly degrade the quality of representation generation, impeding the effectiveness of TGNs in downstream tasks. Though structure learning is widely applied to mitigate noise in static graphs, its adaptation to dynamic graph settings poses two significant challenges. i) Noise dynamics. Existing structure learning methods are ill-equipped to address the temporal aspect of noise, hampering their effectiveness in such dynamic and ever-changing noise patterns. ii) More severe noise. Noise may be introduced along with multiple interactions between two nodes, leading to the re-pollution of these nodes and consequently causing more severe noise compared to static graphs. In this paper, we present RDGSL, a representation learning method in continuous-time dynamic graphs. Meanwhile, we propose dynamic graph structure learning, a novel supervisory signal that empowers RDGSL with the ability to effectively combat noise in dynamic graphs. To address the noise dynamics issue, we introduce the Dynamic Graph Filter, where we innovatively propose a dynamic noise function that dynamically captures both current and historical noise, enabling us to assess the temporal aspect of noise and generate a denoised graph. We further propose the Temporal Embedding Learner to tackle the challenge of more severe noise, which utilizes an attention mechanism to selectively turn a blind eye to noisy edges and hence focus on normal edges, enhancing the expressiveness for representation generation that remains resilient to noise. Our method demonstrates robustness towards downstream tasks, resulting in up to 5.1% absolute AUC improvement in evolving classification versus the second-best baseline.