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Abstract MotivationPredictive biological signatures provide utility as biomarkers for disease diagnosis and prognosis, as well as prediction of responses to vaccination or therapy. These signatures are identified from high-throughput profiling assays through a combination of dimensionality reduction and machine learning techniques. The genes, proteins, metabolites, and other biological analytes that compose signatures also generate hypotheses on the underlying mechanisms driving biological responses, thus improving biological understanding. Dimensionality reduction is a critical step in signature discovery to address the large number of analytes in omics datasets, especially for multi-omics profiling studies with tens of thousands of measurements. Latent factor models, which can account for the structural heterogeneity across diverse assays, effectively integrate multi-omics data and reduce dimensionality to a small number of factors that capture correlations and associations among measurements. These factors provide biologically interpretable features for predictive modeling. However, multi-omics integration and predictive modeling are generally performed independently in sequential steps, leading to suboptimal factor construction. Combining these steps can yield better multi-omics signatures that are more predictive while still being biologically meaningful. ResultsWe developed a supervised variational Bayesian factor model that extracts multi-omics signatures from high-throughput profiling datasets that can span multiple data types. Signature-based multiPle-omics intEgration via lAtent factoRs (SPEAR) adaptively determines factor rank, emphasis on factor structure, data relevance and feature sparsity. The method improves the reconstruction of underlying factors in synthetic examples and prediction accuracy of coronavirus disease 2019 severity and breast cancer tumor subtypes. Availability and implementationSPEAR is a publicly available R-package hosted at https://bitbucket.org/kleinstein/SPEAR.
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UnCOT-AD: Unpaired Cross-Omics Translation Enables Multi-Omics Integration for Alzheimer’s Disease Prediction
Abstract Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder, posing a growing public health challenge. Traditional machine learning models for AD prediction have relied on single omics data or phenotypic assessments, limiting their ability to capture the disease’s molecular complexity and resulting in poor performance. Recent advances in high-throughput multi-omics have provided deeper biological insights. However, due to the scarcity of paired omics datasets, existing multi-omics AD prediction models rely on unpaired omics data, where different omics profiles are combined without being derived from the same biological sample, leading to biologically less meaningful pairings and causing less accurate predictions. To address these issues, we propose UnCOT-AD, a novel deep learning framework for Unpaired Cross-Omics Translation enabling effective multi-omics integration for AD prediction. Our method introduces the first-ever cross-omics translation model trained on unpaired omics datasets, using two coupled Variational Autoencoders and a novel cycle consistency mechanism to ensure accurate bidirectional translation between omics types. We integrate adversarial training to ensure that the generated omics profiles are biologically realistic. Moreover, we employ contrastive learning to capture the disease specific patterns in latent space to make the cross-omics translation more accurate and biologically relevant. We rigorously validate UnCOT-AD on both cross-omics translation and AD prediction tasks. Results show that UnCOT-AD empowers multi-omics based AD prediction by combining real omics profiles with corresponding omics profiles generated by our cross-omics translation module and achieves state-of-the-art performance in accuracy and robustness. Source code is available at https://github.com/abrarrahmanabir/UnCOT-AD
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- PAR ID:
- 10630914
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Briefings in Bioinformatics
- Volume:
- 26
- Issue:
- 4
- ISSN:
- 1467-5463
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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