Diagnostic Evidence GAuge of Single cells (DEGAS): A transfer learning framework to infer impressions of cellular and patient phenotypes between patients and single cells

Johnson, T. S.; Yu, C. Y.; Huang, Z.; Xu, S.; Wang, T.; Dong, C.; Shao, W.; Abu Zaid, M.; Wang, Y.; Bartlett, C.; Zhang, Y.; Liu, Y.; Zhang, J.; Huang, K.

doi:10.1101/2020.06.16.142984

bioRxiv · 10.1101/2020.06.16.142984

Diagnostic Evidence GAuge of Single cells (DEGAS): A transfer learning framework to infer impressions of cellular and patient phenotypes between patients and single cells

Johnson, T. S.·Yu, C. Y.·Huang, Z.·Xu, S.·Wang, T.·Dong, C.·Shao, W.·Abu Zaid, M.·Wang, Y.·Bartlett, C.·Zhang, Y.·Liu, Y.·Zhang, J.·Huang, K.

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Abstract

We propose DEGAS (Diagnostic Evidence GAuge of Single cells), a novel deep transfer learning framework, to transfer disease information from patients to cells. We call such transferrable information "impressions," which allow individual cells to be associated with disease attributes like diagnosis, prognosis, and response to therapy. Using simulated data and ten diverse single cell and patient bulk tissue transcriptomic datasets from Glioblastoma Multiforme (GBM), Alzheimers Disease (AD), and Multiple Myeloma (MM), we demonstrate the feasibility, flexibility, and broad applications of the DEGAS framework. DEGAS analysis on newly generated myeloma single cell transcriptomics led to the identification of PHF19high myeloma cells associated with progression.

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Johnson, T. S., Yu, C. Y., Huang, Z., Xu, S., Wang, T., Dong, C., Shao, W., Abu Zaid, M., Wang, Y., Bartlett, C., Zhang, Y., Liu, Y., Zhang, J., Huang, K.. 2020-06-16. Diagnostic Evidence GAuge of Single cells (DEGAS): A transfer learning framework to infer impressions of cellular and patient phenotypes between patients and single cells. https://doi.org/10.1101/2020.06.16.142984

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