将单细胞表达数据转化为自然语言描述,让机器读懂细胞的“身份说明书”。
Cell2Text: Multimodal LLM for Generating Single-Cell Descriptions from RNA-Seq Data
- 用大模型把基因表达数据转成结构化文字描述
- 在分类准确率和语义一致性上超越现有方法
- 适合需要解释性结果的生物研究者快速理解新细胞
单细胞RNA测序使基因表达在细胞层面的测量成为可能,为细胞类型、状态及疾病背景提供信息。近年来,单细胞基础模型作为强大工具,直接从表达谱中学习可迁移表征,提升了分类与聚类性能。然而,这些模型受限于离散预测头,将细胞复杂性压缩为预定义标签,难以捕捉生物学家所需的丰富上下文解释。我们提出Cell2Text,一种多模态生成框架,可将scRNA-seq谱型转化为结构化的自然语言描述。通过整合单细胞基础模型的基因级嵌入与预训练大语言模型,Cell2Text生成涵盖细胞身份、组织来源、疾病关联和通路活性的连贯摘要,并能泛化至未见细胞。实验表明,Cell2Text在分类准确率上优于基线,使用基于PageRank的相似性度量展现强本体一致性,且文本生成具有高语义保真度。结果表明,将表达数据与自然语言结合,不仅提升预测性能,还实现内在可解释输出,为无标签高效表征未知细胞提供了可扩展路径。
原文摘要 · Abstract (English)
Single-cell RNA sequencing has transformed biology by enabling the measurement of gene expression at cellular resolution, providing information for cell types, states, and disease contexts. Recently, single-cell foundation models have emerged as powerful tools for learning transferable representations directly from expression profiles, improving performance on classification and clustering tasks. However, these models are limited to discrete prediction heads, which collapse cellular complexity into predefined labels that fail to capture the richer, contextual explanations biologists need. We introduce Cell2Text, a multimodal generative framework that translates scRNA-seq profiles into structured natural language descriptions. By integrating gene-level embeddings from single-cell foundation models with pretrained large language models, Cell2Text generates coherent summaries that capture cellular identity, tissue origin, disease associations, and pathway activity, generalizing to unseen cells. Empirically, Cell2Text outperforms baselines on classification accuracy, demonstrates strong ontological consistency using PageRank-based similarity metrics, and achieves high semantic fidelity in text generation. These results demonstrate that coupling expression data with natural language offers both stronger predictive performance and inherently interpretable outputs, pointing to a scalable path for label-efficient characterization of unseen cells.
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