Single-cell RNA sequencing (scRNA-seq) is a widely used technique for characterizing individual cells and studying gene expression at the single-cell level. Clustering plays a vital role in grouping similar cells together for various downstream analyses. However, the high sparsity and dimensionality of large scRNA-seq data pose challenges to clustering performance. Although several deep learning-based clustering algorithms have been proposed, most existing clustering methods have limitations in capturing the precise distribution types of the data or fully utilizing the relationships between cells, leaving a considerable scope for improving the clustering performance, particularly in detecting rare cell populations from large scRNA-seq data. We introduce DeepScena, a novel single-cell hierarchical clustering tool that fully incorporates nonlinear dimension reduction, negative binomial-based convolutional autoencoder for data fitting, and a self-supervision model for cell similarity enhancement. In comprehensive evaluation using multiple large-scale scRNA-seq datasets, DeepScena consistently outperformed seven popular clustering tools in terms of accuracy. Notably, DeepScena exhibits high proficiency in identifying rare cell populations within large datasets that contain large numbers of clusters. When applied to scRNA-seq data of multiple myeloma cells, DeepScena successfully identified not only previously labeled large cell types but also subpopulations in CD14 monocytes, T cells and natural killer cells, respectively.
In the form of multidimensional arrays, tensor data have become increasingly prevalent in modern scientific studies and biomedical applications such as computational biology, brain imaging analysis, and process monitoring system. These data are intrinsically heterogeneous with complex dependencies and structure. Therefore, ad‐hoc dimension reduction methods on tensor data may lack statistical efficiency and can obscure essential findings. Model‐based clustering is a cornerstone of multivariate statistics and unsupervised learning; however, existing methods and algorithms are not designed for tensor‐variate samples. In this article, we propose a tensor envelope mixture model (TEMM) for simultaneous clustering and multiway dimension reduction of tensor data. TEMM incorporates tensor‐structure‐preserving dimension reduction into mixture modeling and drastically reduces the number of free parameters and estimative variability. An expectation‐maximization‐type algorithm is developed to obtain likelihood‐based estimators of the cluster means and covariances, which are jointly parameterized and constrained onto a series of lower dimensional subspaces known as the tensor envelopes. We demonstrate the encouraging empirical performance of the proposed method in extensive simulation studies and a real data application in comparison with existing vector and tensor clustering methods.
more » « less- NSF-PAR ID:
- 10397033
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Biometrics
- Volume:
- 78
- Issue:
- 3
- ISSN:
- 0006-341X
- Format(s):
- Medium: X Size: p. 1067-1079
- Size(s):
- ["p. 1067-1079"]
- Sponsoring Org:
- National Science Foundation
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