ArticleGenome biology2025
MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- ParTIpy: a scalable framework for archetypal analysis and Pareto task inference.Molecular systems biology · 2026Article
- Omics landscapes in molecular mechanisms withFood chemistry. Molecular sciences · 2025Review
- Epigenetic Heritability of Cell Plasticity Drives Cancer Drug Resistance through a One-to-Many Genotype-to-Phenotype Paradigm.Cancer research · 2025Article
- Applications and advances of multi-omics technologies in gastrointestinal tumors.Frontiers in medicine · 2025Review
- Chrysalis: decoding tissue compartments in spatial transcriptomics with archetypal analysis.Communications biology · 2024Article
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Authors and funding
3 authors.
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Abstract
High-throughput multi-omic molecular profiling allows the probing of biological systems at unprecedented resolution. However, integrating and interpreting high-dimensional, sparse, and noisy multimodal datasets remains challenging. Deriving new biological insights with current methods is difficult because they are not rooted in biological principles but prioritise tasks like dimensionality reduction. Here, we introduce a framework that combines archetypal analysis, an approach grounded in biological principles, with deep learning. Using archetypes based on evolutionary trade-offs and Pareto optimality, MIDAA finds extreme data points that define the geometry of the latent space, preserving the complexity of biological interactions while retaining an interpretable output. We demonstrate that these extreme points represent cellular programmes reflecting the underlying biology. Moreover, we show that, compared to alternative methods, MIDAA can identify parsimonious, interpretable, and biologically relevant patterns from real and simulated multi-omics.
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Registered trials
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