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    Ensemble learning models that predict surface protein abundance from single-cell multimodal omics data

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    Authors
    Xu, F.
    Wang, S.
    Dai, X.
    Mundra, Piyushkumar A
    Zheng, J.
    Affiliation
    School of Information Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
    Issue Date
    2020
    
    Metadata
    Show full item record
    Abstract
    Single-cell protein abundance is a fundamental type of information to characterize cell states. Due to high cost and technical barriers, however, direct quantification of proteins is difficult. Single-cell RNA sequencing (scRNA-seq) data, serving as a cost-effective substitute of single-cell proteomics, may not accurately reflect protein expression levels due to measurement error, noise, post-transcriptional and translational regulation, etc. The recently emerging single-cell multimodal omics data, e.g. CITE-seq and REAP-seq, can simultaneously profile RNA and protein abundances in single cells, providing labeled data for predictive modeling in a supervised learning framework. Deep neural network-based transfer learning method has been applied to imputation of surface protein abundance from single-cell transcriptomic data. However, it is unclear if the artificial neural network is the best model, and it is desirable to improve the prediction performance (e.g. accuracy, interpretability) of machine learning models. In this paper, we compared several tree-based ensemble learning methods with neural network models, and found that ensemble learning often performed better than neural network, and Random Forest (RF) performed the best overall. Moreover, we used the feature importance scores from RF to interpret biological mechanisms underlying the prediction. Our study demonstrates the effectiveness of ensemble learning for reliable protein abundance prediction using single-cell multimodal omics data, and paves the way for knowledge discovery by mining single-cell multi-omics data in large scale.
    Citation
    Xu F, Wang S, Dai X, Mundra PA, Zheng J. Ensemble learning models that predict surface protein abundance from single-cell multimodal omics data. Methods. 2020.
    Journal
    Methods
    URI
    http://hdl.handle.net/10541/623452
    DOI
    10.1016/j.ymeth.2020.10.001
    PubMed ID
    33039573
    Additional Links
    https://dx.doi.org/10.1016/j.ymeth.2020.10.001
    Type
    Article
    ae974a485f413a2113503eed53cd6c53
    10.1016/j.ymeth.2020.10.001
    Scopus Count
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    All Paterson Institute for Cancer Research

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