Transfer learning efficiently maps bone marrow cell types from mouse to human using single-cell RNA sequencing

Communications Biology, vol. 3, pp. 736

Abstract

Biomedical research often involves conducting experiments on model organisms in the anticipation that the biology learnt will transfer to humans. Previous comparative studies of mouse and human tissues were limited by the use of bulk-cell material. Here we show that transfer learning-the branch of machine learning that concerns passing information from one domain to another-can be used to efficiently map bone marrow biology between species, using data obtained from single-cell RNA sequencing. We first trained a multiclass logistic regression model to recognize different cell types in mouse bone marrow achieving equivalent performance to more complex artificial neural networks. Furthermore, it was able to identify individual human bone marrow cells with 83% overall accuracy. However, some human cell types were not easily identified, indicating important differences in biology. When re-training the mouse classifier using data from human, less than 10 human cells of a given type were needed to accurately learn its representation. In some cases, human cell identities could be inferred directly from the mouse classifier via zero-shot learning. These results show how simple machine learning models can be used to reconstruct complex biology from limited data, with broad implications for biomedical research.

Authors 14

1. Patrick S. Stumpf corresponding Aachen Joint Research Centre for Computational Biomedicine (JRC-COMBINE)

   University of Southampton · RWTH Aachen University

   Affiliation as printed

   Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK. pstumpf@ukaachen.de

   Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, 52074, Germany. pstumpf@ukaachen.de

   Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK

2. Haruka Imanishi

   Kyushu University

   Affiliation as printed

   Kyushu University, Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan

3. Yuya Kunisaki

   Kyushu University Hospital

   Affiliation as printed

   Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka, 812-8582, Japan

4. Yuichiro Semba

   Kyushu University

   Affiliation as printed

   Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan

5. Timothy J. Noble

   University of Southampton

   Affiliation as printed

   Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK

6. Rosanna C. G. Smith

   University of Southampton

   Affiliation as printed

   Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK

7. Matthew J.J. Rose-Zerilli

   University of Southampton

   Affiliation as printed

   Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK

8. Jonathan J. West

   University of Southampton

   Affiliation as printed

   Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK

   Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK

9. Richard O. C. Oreffo

   University of Southampton

   Affiliation as printed

   Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK

   Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK

10. Katayoun Farrahi

    University of Southampton

    Affiliation as printed

    Electronics and Computer Sciences, University of Southampton, Southampton, SO17 1BJ, UK

11. Mahesan Niranjan

    University of Southampton

    Affiliation as printed

    Electronics and Computer Sciences, University of Southampton, Southampton, SO17 1BJ, UK

12. Koichi Akashi

    Kyushu University

    Affiliation as printed

    Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan

13. Fumio Arai corresponding

    Kyushu University

    Affiliation as printed

    Kyushu University, Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan. farai@med.kyushu-u.ac.jp

    Kyushu University, Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan

14. Ben D. MacArthur corresponding

    The Alan Turing Institute · University of Southampton

    Affiliation as printed

    Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK. bdm@soton.ac.uk

    Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK. bdm@soton.ac.uk

    Mathematical Sciences, University of Southampton, Southampton, SO17 1BJ, UK. bdm@soton.ac.uk

    The Alan Turing Institute, London, NW1 2DB, UK. bdm@soton.ac.uk

    Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK