期刊
BIOINFORMATICS
卷 38, 期 1, 页码 211-219出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btab594
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资金
- National Key R&D Program of China [2019YFA0709501]
- National Natural Science Foundation of China [61733018, 12071466]
- Shanghai Municipal Science and Technology Major Project [2021SHZDZX010]
- Fundamental Research Funds for the Central Universities
- LSC of CAS
Motivated by the need for effective approaches to integrate single-cell multi-omics data, this study presents Pamona, a partial Gromov-Wasserstein distance-based manifold alignment framework. It aims to delineate and represent the shared and dataset-specific cellular structures across modalities. Pamona demonstrates superior performance in accurately identifying shared and dataset-specific cells, recovering and aligning cellular structures, outperforming existing methods. The framework also allows for the incorporation of prior information to enhance alignment quality.
Motivation: Single-cell multi-omics sequencing data can provide a comprehensive molecular view of cells. However, effective approaches for the integrative analysis of such data are challenging. Existing manifold alignment methods demonstrated the state-of-the-art performance on single-cell multi-omics data integration, but they are often limited by requiring that single-cell datasets be derived from the same underlying cellular structure. Results: In this study, we present Pamona, a partial Gromov-Wasserstein distance-based manifold alignment framework that integrates heterogeneous single-cell multi-omics datasets with the aim of delineating and representing the shared and dataset-specific cellular structures across modalities. We formulate this task as a partial manifold alignment problem and develop a partial Gromov-Wasserstein optimal transport framework to solve it. Pamona identifies both shared and dataset-specific cells based on the computed probabilistic couplings of cells across datasets, and it aligns cellular modalities in a common low-dimensional space, while simultaneously preserving both shared and dataset-specific structures. Our framework can easily incorporate prior information, such as cell type annotations or cell-cell correspondence, to further improve alignment quality. We evaluated Pamona on a comprehensive set of publicly available benchmark datasets. We demonstrated that Pamona can accurately identify shared and dataset-specific cells, as well as faithfully recover and align cellular structures of heterogeneous single-cell modalities in a common space, outperforming the comparable existing methods.
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