Dataset Information

A deep manifold-regularized learning model for improving phenotype prediction from multi-modal data.

ABSTRACT: The phenotypes of complex biological systems are fundamentally driven by various multi-scale mechanisms. Multi-modal data, such as single cell multi-omics data, enables a deeper understanding of underlying complex mechanisms across scales for phenotypes. We developed an interpretable regularized learning model, deepManReg, to predict phenotypes from multi-modal data. First, deepManReg employs deep neural networks to learn cross-modal manifolds and then to align multi-modal features onto a common latent space. Second, deepManReg uses cross-modal manifolds as a feature graph to regularize the classifiers for improving phenotype predictions and also for prioritizing the multi-modal features and cross-modal interactions for the phenotypes. We applied deepManReg to (1) an image dataset of handwritten digits with multi-features and (2) single cell multi-modal data (Patch-seq data) including transcriptomics and electrophysiology for neuronal cells in the mouse brain. We show that deepManReg improved phenotype prediction in both datasets, and also prioritized genes and electrophysiological features for the phenotypes of neuronal cells.

SUBMITTER: Nguyen ND

PROVIDER: S-EPMC9038085 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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A deep manifold-regularized learning model for improving phenotype prediction from multi-modal data.

Nguyen Nam D ND Huang Jiawei J Wang Daifeng D

Nature computational science 20220131 1

The phenotypes of complex biological systems are fundamentally driven by various multi-scale mechanisms. Multi-modal data, such as single cell multi-omics data, enables a deeper understanding of underlying complex mechanisms across scales for phenotypes. We developed an interpretable regularized learning model, deepManReg, to predict phenotypes from multi-modal data. First, deepManReg employs deep neural networks to learn cross-modal manifolds and then to align multi-modal features onto a common ...[more]

PMID: 35480297

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Dataset Information

A deep manifold-regularized learning model for improving phenotype prediction from multi-modal data.

Publications

A deep manifold-regularized learning model for improving phenotype prediction from multi-modal data.

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