scPlantLLM: A Foundation Model for Exploring Single-cell Expression Atlases in Plants.
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| Main Authors: | , , , , , , , , |
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| Format: | Artículo científico |
| Language: | en |
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Genomics, proteomics & bioinformatics
2025
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| _version_ | 1868266228872642561 |
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| author | Cao, Guangshuo Chao, Haoyu Zheng, Wenqi Lan, Yangming Lu, Kaiyan Wang, Yueyi Chen, Ming Zhang, He Chen, Dijun |
| author_facet | Cao, Guangshuo Chao, Haoyu Zheng, Wenqi Lan, Yangming Lu, Kaiyan Wang, Yueyi Chen, Ming Zhang, He Chen, Dijun Cao, Guangshuo Chao, Haoyu Zheng, Wenqi Lan, Yangming Lu, Kaiyan Wang, Yueyi Chen, Ming Zhang, He Chen, Dijun |
| collection | PubMed - marine biology |
| contents | scPlantLLM: A Foundation Model for Exploring Single-cell Expression Atlases in Plants. Cao, Guangshuo Chao, Haoyu Zheng, Wenqi Lan, Yangming Lu, Kaiyan Wang, Yueyi Chen, Ming Zhang, He Chen, Dijun Single-Cell Analysis Arabidopsis Gene Regulatory Networks Software Gene Expression Regulation, Plant Sequence Analysis, RNA Gene Expression Profiling Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into plant cellular diversity by enabling high-resolution analyses of gene expression at the single-cell level. However, the complexity of scRNA-seq data, including challenges in batch integration, cell type annotation, and gene regulatory network (GRN) inference, demands advanced computational approaches. To address these challenges, we developed scPlantLLM, a Transformer model trained on millions of plant single-cell data points. Using a sequential pretraining strategy incorporating masked language modeling and cell type annotation tasks, scPlantLLM generates robust and interpretable single-cell data embeddings. When applied to Arabidopsis thaliana datasets, scPlantLLM excels in clustering, cell type annotation, and batch integration, achieving an accuracy of up to 0.91 in zero-shot learning scenarios. Furthermore, the model demonstrates an ability to identify biologically meaningful GRNs and subtle cellular subtypes, showcasing its potential to advance plant biology research. Compared to traditional methods, scPlantLLM outperforms in key metrics such as adjusted rand index (ARI), normalized mutual information (NMI), and silhouette score (SIL), highlighting its superior clustering accuracy and biological relevance. scPlantLLM represents a foundation model for exploring plant single-cell expression atlases, offering unprecedented capabilities to resolve cellular heterogeneity and regulatory dynamics across diverse plant systems. The code used in this study is available at https://github.com/compbioNJU/scPlantLLM. |
| format | Artículo científico |
| id | pubmed_40094454 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Genomics, proteomics & bioinformatics |
| record_format | pubmed |
| spellingShingle | scPlantLLM: A Foundation Model for Exploring Single-cell Expression Atlases in Plants. Cao, Guangshuo Chao, Haoyu Zheng, Wenqi Lan, Yangming Lu, Kaiyan Wang, Yueyi Chen, Ming Zhang, He Chen, Dijun Single-Cell Analysis Arabidopsis Gene Regulatory Networks Software Gene Expression Regulation, Plant Sequence Analysis, RNA Gene Expression Profiling scPlantLLM: A Foundation Model for Exploring Single-cell Expression Atlases in Plants. Cao, Guangshuo Chao, Haoyu Zheng, Wenqi Lan, Yangming Lu, Kaiyan Wang, Yueyi Chen, Ming Zhang, He Chen, Dijun Single-Cell Analysis Arabidopsis Gene Regulatory Networks Software Gene Expression Regulation, Plant Sequence Analysis, RNA Gene Expression Profiling Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into plant cellular diversity by enabling high-resolution analyses of gene expression at the single-cell level. However, the complexity of scRNA-seq data, including challenges in batch integration, cell type annotation, and gene regulatory network (GRN) inference, demands advanced computational approaches. To address these challenges, we developed scPlantLLM, a Transformer model trained on millions of plant single-cell data points. Using a sequential pretraining strategy incorporating masked language modeling and cell type annotation tasks, scPlantLLM generates robust and interpretable single-cell data embeddings. When applied to Arabidopsis thaliana datasets, scPlantLLM excels in clustering, cell type annotation, and batch integration, achieving an accuracy of up to 0.91 in zero-shot learning scenarios. Furthermore, the model demonstrates an ability to identify biologically meaningful GRNs and subtle cellular subtypes, showcasing its potential to advance plant biology research. Compared to traditional methods, scPlantLLM outperforms in key metrics such as adjusted rand index (ARI), normalized mutual information (NMI), and silhouette score (SIL), highlighting its superior clustering accuracy and biological relevance. scPlantLLM represents a foundation model for exploring plant single-cell expression atlases, offering unprecedented capabilities to resolve cellular heterogeneity and regulatory dynamics across diverse plant systems. The code used in this study is available at https://github.com/compbioNJU/scPlantLLM. |
| title | scPlantLLM: A Foundation Model for Exploring Single-cell Expression Atlases in Plants. |
| topic | Single-Cell Analysis Arabidopsis Gene Regulatory Networks Software Gene Expression Regulation, Plant Sequence Analysis, RNA Gene Expression Profiling |
| url | https://pubmed.ncbi.nlm.nih.gov/40094454/ |