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MarkerCapsule: Explainable Single Cell Typing using Capsule Networks

Sumanta Ray, Alexander Schönhuth
doi: https://doi.org/10.1101/2020.09.22.307512
Sumanta Ray
1Centrum Wiskunde & Informatica, Science Park 123, 1098 XG Amsterdam
3Department of Computer Science and Engineering, Aliah University, Kolkata, India
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  • For correspondence: sumantababai86@gmail.com
Alexander Schönhuth
1Centrum Wiskunde & Informatica, Science Park 123, 1098 XG Amsterdam
2Genome Data Science Unit, Bielefeld University, Germany
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ABSTRACT

Many single cell typing methods require manual annotation which casts problems with respect to resolution of (sub-)types, manpower resources and bias towards existing human knowledge. The integration of heterogeneous data and biologically meaningful interpretation of results are further current key challenges. We introduce MarkerCapsule, which leverages the landmark advantages of capsule networks achieved in their original applications in single cell typing. Thereby, the small amount of labeled data required and the naturally arising, biologically meaningful interpretation of cell types in terms of characteristic gene activity patterns are exemplary strengths, beyond outperforming the state of the art in terms of basic typing accuracy. MarkerCapsule is available at: https://github.com/sumantaray/MarkerCapsule.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵* A.Schoenhuth{at}cwi.nl

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 22, 2020.
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MarkerCapsule: Explainable Single Cell Typing using Capsule Networks
Sumanta Ray, Alexander Schönhuth
bioRxiv 2020.09.22.307512; doi: https://doi.org/10.1101/2020.09.22.307512
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MarkerCapsule: Explainable Single Cell Typing using Capsule Networks
Sumanta Ray, Alexander Schönhuth
bioRxiv 2020.09.22.307512; doi: https://doi.org/10.1101/2020.09.22.307512

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