arXiv:2607.19426q-bio.GNcs.AI2026-07

提出可追溯的单细胞数据压缩方法,保留真实细胞和基因信息。

Making Single-Cell Data Distillation Auditable: Traceable Real-Cell Coresets via Discrete Min--Max Selection

论文配图:Making Single-Cell Data Distillation Auditable: Traceable Real-Cell Coresets via Discrete Min--Max Selection
图 1 · 摘自论文原文
  • 通过离散极小极大选择,交替筛选关键细胞和基因。
  • 在五个基准上平均保持95.3%的宏F1,优于合成基线10.4%~17.4%。
  • 保留原始细胞索引与基因符号,支持生物学溯源分析。

大规模单细胞数据存储、整理和重复训练成本高昂。数据蒸馏可通过构建更小的训练集缓解此问题,但现有方法多依赖合成细胞,无法对应实际细胞与基因,限制了源级可追溯性。此外,真实表达矩阵常稀疏且含噪。为此,我们提出Minmax-CF,一种标签感知的特征函数选择器,实现可追溯的单细胞数据蒸馏。该方法将压缩建模为特征函数方向上的离散极小极大选择问题,采用熵正则化最大化最小保留方向,贪心最小化按权重误差降低程度排序细胞与基因。在五种粗谱系基准和五种压缩预算下,平均保留全参考宏F1的95.3%,差距超过每种子标准差。同时保留精确源细胞索引与原始基因符号。相较于大小匹配的合成PCA-中心点与分布匹配(DM)基线,Minmax-CF在25次对比中有24次表现更优,平均提升10.4%与17.4%。保留细胞可投影至独立计算的嵌入空间,实现直接生物解释。

原文摘要 · Abstract (English)

Large single-cell datasets are expensive to store, curate, and repeatedly reuse for model training. Data distillation can reduce this burden by building smaller training sets. However, many existing methods rely on synthetic cells. These synthetic cells do not retain direct correspondence with assayed cells and genes. This limits source-level inspection and biological traceability. Moreover, real-cell expression matrices are often sparse and noisy. In light of these challenges, we propose Minmax-CF, a label-aware characteristic-function selector for traceable single-cell data distillation. Minmax-CF formulates compression as a discrete min--max selection problem over characteristic-function directions. It uses entropy-regularized maximization to emphasize the least preserved directions. Greedy minimization ranks cells and genes by how much they reduce the resulting weighted error. The method alternates cell and gene selection under explicit axis-specific budgets. Across five coarse-lineage benchmarks and five compression budgets, Minmax-CF retains 95.3% of the Full-reference macro-F1 on average, with gaps that exceed one per-seed standard deviation. It also retains exact source-cell indices and original gene symbols. Compared with size-matched synthetic PCA-Centroid and Distribution Matching (DM) baselines, Minmax-CF achieves higher coarse-lineage macro-F1 in 24 of 25 comparisons against each baseline. It exceeds their average performance by 10.4% and 17.4%, respectively. Retained cells can also be projected onto independently computed embeddings for direct biological interpretation.

单细胞数据蒸馏可追溯压缩

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