Harnessing the deep learning power of foundation models in single-cell omics

Bommasani, R. et al. Picking on the same person: Does algorithmic monoculture lead to outcome homogenization? Adv. Neural Inf. Process. Syst. 35, 3663–3678 (2022).

Google Scholar 

Baysoy, A. et al. The technological landscape and applications of single-cell multi-omics. Nat. Rev. Mol. Cell Biol. 24, 695–713 (2023).

Article  CAS  PubMed  Google Scholar 

Ma, Q. & Xu, D. Deep learning shapes single-cell data analysis. Nat. Rev. Mol. Cell Biol. 23, 303–304 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cui, H. et al. scGPT: toward building a foundation model for single-cell multi-omics using generative AI. Nat. Methods https://doi.org/10.1038/s41592-024-02201-0 (2024).

Theodoris, C. V. et al. Transfer learning enables predictions in network biology. Nature 618, 616–624 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stuart, T. & Satija, R. Integrative single-cell analysis. Nat. Rev. Genet. 20, 257–272 (2019).

Article  CAS  PubMed  Google Scholar 

Thirunavukarasu, A. J. et al. Large language models in medicine. Nat. Med. 29, 1930–1940 (2023).

Article  CAS  PubMed  Google Scholar 

Wang, W. et al. A survey of zero-shot learning: Settings, methods, and applications. ACM Trans. Intell. Syst. Technol. 10, 1–37 (2019).

Article  Google Scholar 

Liu, T. et al. Evaluating the utilities of large language models in single-cell data analysis. Preprint at bioRxiv https://doi.org/10.1101/2023.09.08.555192 (2023).

Rosen, Y. et al. Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN. Nat. Methods https://doi.org/10.1038/s41592-024-02191-z (2024).

Janizek, J. D. et al. Uncovering expression signatures of synergistic drug responses via ensembles of explainable machine-learning models. Nat. Biomed. Eng. 7, 811–829 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Van de Sande, B. et al. Applications of single-cell RNA sequencing in drug discovery and development. Nat. Rev. Drug Discov. 22, 496–520 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Wang, X. et al. MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer. Nat. Commun. 15, 338 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cao, Z. J. & Gao, G. Multi-omics single-cell data integration and regulatory inference with graph-linked embedding. Nat. Biotechnol. 40, 1458–1466 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Moor, M. et al. Foundation models for generalist medical artificial intelligence. Nature 616, 259–265 (2023).

Article  CAS  PubMed  Google Scholar 

留言 (0)

沒有登入
gif