将单细胞基因表达转为图像,用视觉模型提升细胞分类与基因程序识别准确率。
A vision foundation model for single-cell biology via spatial gene cartography

- 把每个细胞当作图像,用最优传输固定基因位置,使共表达基因在空间上相邻。
- 在6个独立数据集上零样本分类准确率领先,且无需微调即可恢复基因程序。
- 适合单细胞生物信息学、生物图像分析及无需标注数据的研究者使用。
大多数单细胞基础模型基于语言模型,将每个细胞表示为基因标记序列,忽略了基因间关系和表达量大小。我们提出scVision,一种视觉基础模型,将每个细胞渲染为连续图像。通过最优传输,将基因固定于共享的跨组织布局中,使共表达基因成为空间邻近点,将转录组转化为图像,其中基因程序表现为局部纹理。在7200万个人类细胞上通过掩码图像建模预训练视觉变换器,并以冻结编码器进行零样本评估。在六个独立保留研究中,scVision是精度最高的细胞类型注释器,能无监督恢复基因程序,优于现有基础模型和经典基线;在多研究整合任务中表现媲美最强的基于标记的模型,同时最大程度保留生物结构,且从未见过批次标签。固定网络下打乱基因布局导致准确率显著下降,远超移除视觉变换器的影响,表明生物学意义的位置而非网络本身承载信号。通过保留表达量和基因关系,scVision将单细胞表征学习重构为视觉问题,连接计算机视觉成熟方法。
原文摘要 · Abstract (English)
Most single-cell foundation models are adapted from language models, representing each cell as a sequence of gene tokens. This discards the relationships among genes and often the magnitude of their expression. We present scVision, a vision foundation model that instead renders each cell as a continuous image. Using optimal transport, it places genes at fixed positions on a single shared, pan-tissue layout so that co-expressed genes become spatial neighbours, turning a transcriptome into an image in which gene programs appear as local texture. We pretrain a vision transformer by masked image modelling on 72 million human cells and use the frozen encoder with no fine-tuning. In zero-shot evaluations on six independent, held-out studies, scVision is the most accurate cell-type annotator and recovers gene programs without supervision, ahead of existing foundation models and classical baselines; on multi-study integration it matches the strongest token-based model while conserving the most biological structure, without ever seeing a batch label. Permuting the gene layout with the network fixed sharply lowers accuracy, more than removing the vision transformer itself, showing that biologically meaningful position, not the network, carries the signal. By preserving expression magnitude and gene relationships, scVision reframes single-cell representation learning as a vision problem, connecting it to the mature methods of computer vision.
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