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Cui et al. |

scGPT: Gene Regulatory Network Inference on Pre-trained Models

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Genomics & Multi-Omics
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    • The h5ad format in scRNA-seq refers to the Hierarchical Data Format 5 (HDF5) Annotated Data format. It is commonly used to store single-cell gene expression data.
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scGPT (v0.2.1) is a foundation model for single-cell biology, based on generative pre-trained transformers trained on a vast repository of over 33 million cells. The scGPT model demonstrates the ability to extract valuable biological insights and can be further optimized through transfer learning for various downstream applications, including cell-type annotation, multi-batch integration, genetic perturbation prediction, and gene network inference.

Example use case: Gene regulatory network inference

Technology: Transformers

Limitation:

  • Some of the parameters were kept default. Please see this page for more details.
Citation:
scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI Haotian Cui, Chloe Wang, Hassaan Maan, Kuan Pang, Fengning Luo, Bo Wang bioRxiv 2023.04.30.538439; doi: https://doi.org/10.1101/2023.04.30.538439
Released:
Jul-19-2023
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