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

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, et al. The human cell atlas. elife. 2017;6:e27041.

Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, et al. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016;167(7):1853-1866.e17.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schraivogel D, Gschwind AR, Milbank JH, Leonce DR, Jakob P, Mathur L, et al. Targeted Perturb-seq enables genome-scale genetic screens in single cells. Nat Methods. 2020;17(6):629–35.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ding J, Regev A. Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces. Nat Commun. 2021;12(1):2554.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sadria M, Layton A, Goyal S, Bader G. Fatecode: Cell fate regulator prediction using classification autoencoder perturbation. BioRxiv. 2022.

Flores M, Liu Z, Zhang T, Hasib MM, Chiu YC, Ye Z, et al. Deep learning tackles single-cell analysis—a survey of deep learning for scRNA-seq analysis. Brief Bioinform. 2022;23(1):bbab531.

Tran D, Nguyen H, Tran B, La Vecchia C, Luu HN, Nguyen T. Fast and precise single-cell data analysis using a hierarchical autoencoder. Nat Commun. 2021;12(1):1029.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Eraslan G, Simon LM, Mircea M, Mueller NS, Theis FJ. Single-cell RNA-seq denoising using a deep count autoencoder. Nat Commun. 2019;10(1):390.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang D, Gu J. VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder. Genomics Proteomics Bioinformatics. 2018;16(5):320–31.

Article  PubMed  PubMed Central  Google Scholar 

Marouf M, Machart P, Bansal V, Kilian C, Magruder DS, Krebs CF, et al. Realistic in silico generation and augmentation of single-cell RNA-seq data using generative adversarial networks. Nat Commun. 2020;11(1):166.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lotfollahi M, Wolf FA, Theis FJ. scGen predicts single-cell perturbation responses. Nat Methods. 2019;16(8):715–21.

Article  CAS  PubMed  Google Scholar 

Wei X, Dong J, Wang F. scPreGAN, a deep generative model for predicting the response of single cell expression to perturbation. Bioinformatics. 2022.

Xu J, Xu J, Meng Y, Lu C, Cai L, Zeng X, et al. Graph embedding and Gaussian mixture variational autoencoder network for end-to-end analysis of single-cell RNA sequencing data. Cell Rep Methods. 2023;3(1):100382.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lucas J, Tucker G, Grosse R, Norouzi M. Understanding Posterior Collapse in Generative Latent Variable Models. 2022.

Thanh-Tung H, Tran T. Catastrophic forgetting and mode collapse in gans. In: 2020 international joint conference on neural networks. Glasgow: IJCNN; 2020. p. 1–10.

Li H, Lindenbaum O, Cheng X, Cloninger A. Variational Diffusion Autoencoders with Random Walk Sampling. In: Vedaldi A, Bischof H, Brox T, Frahm J-M, editors. Computer vision – ECCV 2020: 16th european conference, glasgow, UK, august 23–28, 2020, proceedings, part XXIII. Cham: Springer International Publishing; 2020. p. 362–78.

Chapter  Google Scholar 

Arjovsky M, Chintala S, Bottou L. Wasserstein GAN. arXiv. 2017.

Lee KS, Tran NT, Cheung NM. Infomax-GAN: Improved adversarial image generation via information maximization and contrastive learning. In Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision. Waikoloa; 2021. p. 3942–52.

Kingma DP, Welling M. Auto-Encoding Variational Bayes. arXiv. 2013.

Kong Z, Ping W, Huang J, Zhao K, Catanzaro B. [2009.09761] DiffWave: A Versatile Diffusion Model for Audio Synthesis. arXiv. 2020 Sep 21.

Ho J, Jain A, Abbeel P. Denoising Diffusion Probabilistic Models. arXiv. 2020.

Kreis K, Dockhorn T, Li Z, Zhong E. Latent Space Diffusion Models of Cryo-EM Structures. arXiv. 2022.

Zeng X, Vahdat A, Williams F, Gojcic Z, Litany O, Fidler S, et al. LION: Latent Point Diffusion Models for 3D Shape Generation. arXiv. 2022.

Pandey K, Mukherjee A, Rai P, Kumar A. DiffuseVAE: Efficient, Controllable and High-Fidelity Generation from Low-Dimensional Latents. arXiv. 2022.

Rombach R, Blattmann A, Lorenz D, Esser P, Ommer B. High-Resolution Image Synthesis with Latent Diffusion Models. arXiv. 2021.

Vahdat A, Kreis K, Kautz J. Score-based Generative Modeling in Latent Space. Advances in Neural Information Processing Systems. 2021 Dec 6.

Kingma DP, Salimans T, Poole B, Ho J. Variational Diffusion Models. arXiv. 2021.

Dhariwal P, Nichol A. Diffusion Models Beat GANs on Image Synthesis. arXiv. 2021.

Preechakul K, Chatthee N, Wizadwongsa S, Suwajanakorn S. Diffusion Autoencoders: Toward a Meaningful and Decodable Representation. arXiv. 2021.

Shi C, Pamer EG. Monocyte recruitment during infection and inflammation. Nat Rev Immunol. 2011;11(11):762–74.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Isogai S, Yamamoto N, Hiramatsu N, Goto Y, Hayashi M, Kondo M, et al. Preparation of induced pluripotent stem cells using human peripheral blood monocytes. Cell Reprogram. 2018;20(6):347–55.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jung H, Kim MJ, Kim DO, Kim WS, Yoon S-J, Park Y-J, et al. TXNIP maintains the hematopoietic cell pool by switching the function of p53 under oxidative stress. Cell Metab. 2013;18(1):75–85.

Article  CAS  PubMed  Google Scholar 

Gribble SL, Kim H-S, Bonner J, Wang X, Dorsky RI. Tcf3 inhibits spinal cord neurogenesis by regulating sox4a expression. Development. 2009;136(5):781–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dumon S, Walton DS, Volpe G, Wilson N, Dassé E, Del Pozzo W, et al. Itga2b regulation at the onset of definitive hematopoiesis and commitment to differentiation. PLoS ONE. 2012;7(8):e43300.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cox JL, Mallanna SK, Ormsbee BD, Desler M, Wiebe MS, Rizzino A. Banf1 is required to maintain the self-renewal of both mouse and human embryonic stem cells. J Cell Sci. 2011;124(Pt 15):2654–65.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schlachetzki JCM, Prots I, Tao J, Chun HB, Saijo K, Gosselin D, et al. A monocyte gene expression signature in the early clinical course of Parkinson’s disease. Sci Rep. 2018;8(1):10757.

Article  PubMed  PubMed Central  Google Scholar 

Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJT, Cvejic A, et al. Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types. Genome Res. 2017;27(3):451–61.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huber R, Pietsch D, Panterodt T, Brand K. Regulation of C/EBPβ and resulting functions in cells of the monocytic lineage. Cell Signal. 2012;24(6):1287–96.

Article  CAS  PubMed  Google Scholar 

Hu Y, Hu Y, Xiao Y, Wen F, Zhang S, Liang D, et al. Genetic landscape and autoimmunity of monocytes in developing Vogt-Koyanagi-Harada disease. Proc Natl Acad Sci USA. 2020;117(41):25712–21.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, et al. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol. 2018;36(1):89–94.

Article  CAS  PubMed  Google Scholar 

Zheng M, Hu Z, Mei X, Ouyang L, Song Y, Zhou W, et al. Single-cell sequencing shows cellular heterogeneity of cutaneous lesions in lupus erythematosus. Nat Commun. 2022;13(1):7489.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhou D, Luo N, Wu Q, You Y, Zhai Z, Mou Z, et al. Transcellular distribution heterogeneity of Annexin A5 represents a protective response to lupus-related thrombophilia: a pilot Proteomics-based study. Biochem Biophys Res Commun. 2012;420(2):357–63.

Article  CAS  PubMed  Google Scholar 

Yanaba K, Asano Y, Noda S, Akamata K, Aozasa N, Taniguchi T, et al. Increased circulating fibrinogen-like protein 2 in patients with systemic sclerosis. Clin Rheumatol. 2013;32(1):43–7.

Article  PubMed  Google Scholar 

Santer DM, Wiedeman AE, Teal TH, Ghosh P, Elkon KB. Plasmacytoid dendritic cells and C1q differentially regulate inflammatory gene induction by lupus immune complexes. J Immunol. 2012;188(2):902–15.

Article  CAS  PubMed  Google Scholar 

Zhao Y, Zhou L, Li H, Sun T, Wen X, Li X, et al. Nuclear-Encoded lncRNA MALAT1 Epigenetically Controls Metabolic Reprogramming in HCC Cells through the Mitophagy Pathway. Mol Ther Nucleic Acids. 2021;23:264–76.

Article  CAS  PubMed 

Comments (0)

No login
gif