scVAEDer: integrating deep diffusion models and variational autoencoders for single-cell transcriptomics analysis

被引:0
作者
Sadria, Mehrshad [1 ]
Layton, Anita [1 ,2 ,3 ,4 ]
机构
[1] Univ Waterloo, Dept Appl Math, Waterloo, ON, Canada
[2] Univ Waterloo, Cheriton Sch Comp Sci, Waterloo, ON, Canada
[3] Univ Waterloo, Dept Biol, Waterloo, ON, Canada
[4] Univ Waterloo, Sch Pharm, Waterloo, ON, Canada
来源
GENOME BIOLOGY | 2025年 / 26卷 / 01期
基金
加拿大健康研究院;
关键词
D O I
10.1186/s13059-025-03519-4
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Discovering a lower-dimensional embedding of single-cell data can improve downstream analysis. The embedding should encapsulate both the high-level features and low-level variations. While existing generative models attempt to learn such low-dimensional representations, they have limitations. Here, we introduce scVAEDer, a scalable deep-learning model that combines the power of variational autoencoders and deep diffusion models to learn a meaningful representation that retains both global structure and local variations. Using the learned embeddings, scVAEDer can generate novel scRNA-seq data, predict perturbation response on various cell types, identify changes in gene expression during dedifferentiation, and detect master regulators in biological processes.
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页数:17
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共 68 条
  • [1] Arjovsky M, 2017, PR MACH LEARN RES, V70
  • [2] Pioneer factors as master regulators of the epigenome and cell fate
    Balsalobre, Aurelio
    Drouin, Jacques
    [J]. NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2022, 23 (07) : 449 - 464
  • [3] Paternal Insulin-like Growth Factor 2 (Igf2) Regulates Stem Cell Activity During Adulthood
    Barroca, Vilma
    Lewandowski, Daniel
    Jaracz-Ros, Agnieszka
    Hardouin, Sylvie-Nathalie
    [J]. EBIOMEDICINE, 2017, 15 : 150 - 162
  • [4] Single-cell mapping of lineage and identity in direct reprogramming
    Biddy, Brent A.
    Kong, Wenjun
    Kamimoto, Kenji
    Guo, Chuner
    Waye, Sarah E.
    Sun, Tao
    Morris, Samantha A.
    [J]. NATURE, 2018, 564 (7735) : 219 - +
  • [5] Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types
    Carmona, Santiago J.
    Teichmann, Sarah A.
    Ferreira, Lauren
    Macaulay, Iain C.
    Stubbington, Michael J. T.
    Cvejic, Ana
    Gfeller, David
    [J]. GENOME RESEARCH, 2017, 27 (03) : 451 - 461
  • [6] Connective Tissue Growth Factor Activates Pluripotency Genes and Mesenchymal-Epithelial Transition in Head and Neck Cancer Cells
    Chang, Cheng-Chi
    Hsu, Wen-Hao
    Wang, Chen-Chien
    Chou, Chun-Hung
    Kuo, Mark Yen-Ping
    Lin, Been-Ren
    Chen, Szu-Ta
    Tai, Shyh-Kuan
    Kuo, Min-Liang
    Yang, Muh-Hwa
    [J]. CANCER RESEARCH, 2013, 73 (13) : 4147 - 4157
  • [7] Malat1 regulates myogenic differentiation and muscle regeneration through modulating MyoD transcriptional activity
    Chen, Xiaona
    He, Liangqiang
    Zhao, Yu
    Li, Yuying
    Zhang, Suyang
    Sun, Kun
    So, Karl
    Chen, Fengyuan
    Zhou, Liang
    Lu, Leina
    Wang, Lijun
    Zhu, Xihua
    Bao, Xichen
    Esteban, Miguel A.
    Nakagawa, Shinichi
    Prasanth, Kannanganattu V.
    Wu, Zhenguo
    Sun, Hao
    Wang, Huating
    [J]. CELL DISCOVERY, 2017, 3
  • [8] Banf1 is required to maintain the self-renewal of both mouse and human embryonic stem cells
    Cox, Jesse L.
    Mallanna, Sunil K.
    Ormsbee, Briana D.
    Desler, Michelle
    Wiebe, Matthew S.
    Rizzino, Angie
    [J]. JOURNAL OF CELL SCIENCE, 2011, 124 (15) : 2654 - 2665
  • [9] Dhariwal P, 2021, ADV NEUR IN
  • [10] Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces
    Ding, Jiarui
    Regev, Aviv
    [J]. NATURE COMMUNICATIONS, 2021, 12 (01)