Abstract
The high cost of functional molecular assays, and prevalence of missing modalities and unmatched samples in computational biology, create significant barriers to comprehensive multi-omic profiling, essential for capturing and reasoning over molecules, cells, tissues, and organisms. This work proposes a model that learns meaningful representations from multi-omics cancer data supporting the reconstruction of missing and unpaired modalities. Contrary to increasingly complex, larger models, e.g. Foundation Models (FMs), ARO prioritizes practical applicability in limited or incomplete data settings. ARO optimally reconstructs missing modalities (MSE of $0.15$ on the validation and test data in the Unmasked settings), with its learned latent embeddings enabling a downstream cancer classification task. Our findings indicate that analyzing diverse molecular layers as a single integrated system offers a reliable and cost-efficient approach, reducing dependence on large-scale experimental testing, while still supporting multi-omic exploration in limited data settings.
Keywords
Publication details
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- Open access
- Green open access
Cite this article
APA 7
Singh, A., Shah, Y., D'Ercoli, C., Mehrjou, A., Schwab, P., Jones, T., & Liò, P. (2026). ARO: Aligned Representation learning for multi-Omics data. https://omanscience.com/en/articles/aro-aligned-representation-learning-for-multi-omics-data
MLA 9
Singh, Amogh, et al. "ARO: Aligned Representation learning for multi-Omics data." https://omanscience.com/en/articles/aro-aligned-representation-learning-for-multi-omics-data.
Chicago (author–date)
Singh, Amogh, Yash Shah, Chiara D'Ercoli, Arash Mehrjou, Patrick Schwab, Timothy Jones, and Pietro Liò. 2026. "ARO: Aligned Representation learning for multi-Omics data." https://omanscience.com/en/articles/aro-aligned-representation-learning-for-multi-omics-data.
Harvard
Singh, A., Shah, Y., D'Ercoli, C., Mehrjou, A., Schwab, P., Jones, T. and Liò, P. (2026) 'ARO: Aligned Representation learning for multi-Omics data', Available at: https://omanscience.com/en/articles/aro-aligned-representation-learning-for-multi-omics-data.
Vancouver
Singh A, Shah Y, D'Ercoli C, Mehrjou A, Schwab P, Jones T, et al. ARO: Aligned Representation learning for multi-Omics data. https://omanscience.com/en/articles/aro-aligned-representation-learning-for-multi-omics-data
IEEE
A. Singh, Y. Shah, C. D'Ercoli, A. Mehrjou, P. Schwab, T. Jones, and P. Liò, "ARO: Aligned Representation learning for multi-Omics data," https://omanscience.com/en/articles/aro-aligned-representation-learning-for-multi-omics-data.