Journal
NUCLEIC ACIDS RESEARCH
Volume 49, Issue 14, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkab380
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Funding
- National Key Research and Development Program of China [2017YFC0908500, 2016YFC1303205]
- National Natural Science Foundation of China [31970638, 61572361]
- Shanghai Natural Science Foundation [17ZR1449400]
- Shanghai Artificial Intelligence Technology Standard Project [19DZ2200900]
- Major Program of Development Fund for Shanghai Zhangjiang National Innovtaion Demonstration Zone [ZJ2018-ZD-004]
- Peak Disciplines (Type IV) of Institutions of Higher Learning in Shanghai
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Efficient single-cell assignment is crucial for analyzing single-cell sequencing data, and integrating multiple references can further improve single-cell assignment. The mtSC framework proposed in this study integrates multiple references based on multitask deep metric learning, demonstrating state-of-the-art effectiveness for integrative single-cell assignment with multiple references through evaluation on publicly available benchmark datasets.
Efficient single-cell assignment is essential for single-cell sequencing data analysis. With the explosive growth of single-cell sequencing data, multiple single-cell sequencing data sources are available for the same kind of tissue, which can be integrated to further improve single-cell assignment; however, an efficient integration strategy is still lacking due to the great challenges of data heterogeneity existing in multiple references. To this end, we present mtSC, a flexible single-cell assignment framework that integrates multiple references based on multitask deep metric learning designed specifically for cell type identification within tissues with multiple single-cell sequencing data as references. We evaluated mtSC on a comprehensive set of publicly available benchmark datasets and demonstrated its state-of-the-art effectiveness for integrative single-cell assignment with multiple references.
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