We developed mixture model inference with discrete-coupled autoencoders (MMIDAS), an unsupervised variational framework that jointly learns discrete clusters and continuous cluster-specific variability. When applied to unimodal or multimodal single-cell omic data, MMIDAS learned single-cell representations with robust cell type definitions and interpretable, continuous within-cell type variability.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$32.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 digital issues and online access to articles
$119.00 per year
only $9.92 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout

References
Yao, Z. et al. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 624, 317–332 (2023). This paper presents a comprehensive mouse whole-brain cell type atlas, clustering cells into over 5,000 distinct types.
Fishell, G. & Heintz, N. The neuron identity problem: form meets function. Neuron 80, 602–612 (2013). This paper highlights the importance of identifying cell types in the nervous system and their distinct molecular ground states.
Gouwens, N. W. et al. Integrated morphoelectric and transcriptomic classification of cortical GABAergic cells. Cell 183, 935–953 (2020). This paper jointly profiles morphological, electrophysiological and transcriptomic features of GABAergic neurons in mouse visual cortex.
Scala, F. et al. Phenotypic variation of transcriptomic cell types in mouse motor cortex. Nature 598, 144–150 (2021). This paper jointly profiles morphological, electrophysiological, and transcriptomic features of neurons in mouse motor cortex.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
This is a summary of: Marghi, Y. et al. Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS. Nat. Comput. Sci. https://doi.org/10.1038/s43588-024-00683-8 (2024).
Rights and permissions
About this article
Cite this article
Joint inference of discrete and continuous factors captures variability across and within cell types. Nat Comput Sci 4, 733–734 (2024). https://doi.org/10.1038/s43588-024-00696-3
Published:
Issue date:
DOI: https://doi.org/10.1038/s43588-024-00696-3