H H Peng

Pu Li, Yantuan Xian, Hao Peng et al.

Community detection is a critical task in graph theory, social network analysis, and bioinformatics, where communities are defined as clusters of densely interconnected nodes. However, detecting communities in large-scale networks with millions of nodes and billions of edges remains challenging due to the inefficiency and unreliability of existing methods. Moreover, many existing methods are limited to specific types of graph structures (such as unweighted or undirected graphs) or are designed solely for detecting static communities, reducing their broader applicability. To address these issues, we propose a novel heuristic community detection algorithm, termed CoDeSEG, which identifies communities by minimizing the network's two-dimensional (2D) structural entropy within a potential game framework. In the game, nodes decide to stay in the current community or move to another based on a strategy that maximizes the 2D structural entropy utility function. Additionally, we introduce a structural entropy-based node overlapping heuristic for detecting overlapping communities, with a near-linear time complexity. Furthermore, we design a cascading influence propagation-based adaptive community update strategy, which dynamically identifies and processes nodes whose community affiliations may change during graph evolution, thereby effectively extending CoDeSEG to dynamic community detection scenarios. Experimental results on fourteen large-scale networks demonstrate that CoDeSEG achieves state-of-the-art performance across three community detection tasks (overlapping, non-overlapping, dynamic), while also delivering substantial improvements in detection efficiency.

Songhan Wang, Haoang Chi, He Li et al.

Spatial and Single-cell transcriptomics are transformative in deciphering cellular dynamics. As the fundamental paradigm for reconstructing cell developmental paths, trajectory inference (TI) is critical. However, existing methods require extensive manual intervention and proficiency in heterogeneous tools, posing a significant barrier to efficient TI analysis. To bridge this gap, we propose SpaCellAgent, an autonomous large language model (LLM) multi-agent framework that automates end-to-end spatiotemporal analysis and narrative generation. SpaCellAgent utilizes a multi-agent architecture for strategic workflow planning, a dynamic tool-orchestration engine for adaptive algorithm selection, and a self-evolution module that iteratively refines performance through feedback. We evaluate SpaCellAgent on six heterogeneous datasets encompassing complex temporal developmental trajectories, diverse sequencing platforms, and spatially-resolved tissue architectures. SpaCellAgent consistently demonstrates over 40\% improvement in analytical efficiency while maintaining expert-aligned performance. By converting natural language specifications into optimized analytical workflows and fully automating the pipeline, SpaCellAgent democratizes advanced spatiotemporal modeling and establishes a scalable, agent-driven paradigm for computational biology. The code and materials are available at https://github.com/LittleXH-shw/SpaCellAgent.

Jingyun Zhang, Hao Peng, Jianxin Li et al.

Unsupervised graph clustering is a fundamental technique for uncovering underlying semantic patterns in large-scale networks. Although Graph Contrastive Learning has demonstrated promising performance, existing methods often suffer from the "structural isolation" issue during mini-batch training, making it challenging to capture cohesive community structures that characterize the global topological distribution. To address these challenges, we propose SCISE, a Scalable unsupervised graph Clustering framework that preserves structural Integrity by synergizing community-aware sampling with constrained Structural Entropy. Specifically, we first introduce the Structural Entropy Community Constraint operator (SECC), which optimizes structural information within a constrained solution space to mitigate community fragmentation and enhance partition cohesion. Second, to prevent global information loss during batch training, we design a Community-Aware Sampling Expansion (CSampE) mechanism that incorporates the community context of target nodes into sampling batches, effectively breaking structural barriers and preserving topological integrity. Finally, we devise a Structural Contrastive Learning (StructCL) module that refines edge weights based on intra-batch structural similarity, guiding the encoder to learn representations in a higher-order structural space. Extensive experiments on six mainstream benchmark datasets demonstrate that SCISE significantly outperforms state-of-the-art algorithms, with ablation studies and robustness analyses further validating its effectiveness and reliability for real-world large-scale graphs.