通过对比学习动态构建细胞图,提升单细胞聚类精度。
scAGC: Learning Adaptive Cell Graphs with Contrastive Guidance for Single-Cell Clustering
- 用可微分采样动态调整细胞间连接关系
- 在9个数据集上均优于现有方法,NMI和ARI领先
- 适合处理零膨胀、长尾分布的单细胞数据
准确的细胞类型注释是分析单细胞RNA测序(scRNA-seq)数据的关键步骤,有助于揭示细胞异质性。然而,由于scRNA-seq数据高维且零值众多,传统聚类方法面临显著的统计与计算挑战。尽管一些先进方法使用图神经网络建模细胞间关系,但通常依赖静态图结构,对噪声敏感,并难以捕捉单细胞群体中的长尾分布特征。为此,我们提出scAGC,一种基于对比引导的自适应细胞图学习方法。该方法端到端地联合优化特征表示与细胞图结构。具体而言,引入拓扑自适应图自编码器,利用可微分的Gumbel-Softmax采样策略,在训练中动态重构图结构,缓解长尾度分布问题,促进更均衡的邻域结构。为建模scRNA-seq数据的离散性、过度分散性和零膨胀特性,集成零膨胀负二项式(ZINB)损失以实现鲁棒特征重建。此外,引入对比学习目标,正则化图学习过程,防止拓扑突变,确保稳定性并加速收敛。在9个真实scRNA-seq数据集上的全面实验表明,scAGC在9个数据集上取得最优NMI分数,在7个数据集上取得最优ARI分数。代码已公开于匿名GitHub。
原文摘要 · Abstract (English)
Accurate cell type annotation is a crucial step in analyzing single-cell RNA sequencing (scRNA-seq) data, which provides valuable insights into cellular heterogeneity. However, due to the high dimensionality and prevalence of zero elements in scRNA-seq data, traditional clustering methods face significant statistical and computational challenges. While some advanced methods use graph neural networks to model cell-cell relationships, they often depend on static graph structures that are sensitive to noise and fail to capture the long-tailed distribution inherent in single-cell populations.To address these limitations, we propose scAGC, a single-cell clustering method that learns adaptive cell graphs with contrastive guidance. Our approach optimizes feature representations and cell graphs simultaneously in an end-to-end manner. Specifically, we introduce a topology-adaptive graph autoencoder that leverages a differentiable Gumbel-Softmax sampling strategy to dynamically refine the graph structure during training. This adaptive mechanism mitigates the problem of a long-tailed degree distribution by promoting a more balanced neighborhood structure. To model the discrete, over-dispersed, and zero-inflated nature of scRNA-seq data, we integrate a Zero-Inflated Negative Binomial (ZINB) loss for robust feature reconstruction. Furthermore, a contrastive learning objective is incorporated to regularize the graph learning process and prevent abrupt changes in the graph topology, ensuring stability and enhancing convergence. Comprehensive experiments on 9 real scRNA-seq datasets demonstrate that scAGC consistently outperforms other state-of-the-art methods, yielding the best NMI and ARI scores on 9 and 7 datasets, respectively.Our code is available at Anonymous Github.
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