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Application of Aligned-UMAP to Longitudinal Biomedical Studies

19 Pages Posted: 8 Dec 2022 Publication Status: Published

See all articles by Anant Dadu

Anant Dadu

University of Illinois at Urbana-Champaign - Department of Computer Science

Vipul Satone

University of Illinois at Urbana-Champaign - Department of Industrial and Enterprise Systems Engineering

Rachneet Kaur

University of Illinois at Urbana-Champaign - Department of Industrial and Enterprise Systems Engineering

Mathew Koretsky

Government of the United States of America - National Institute of Neurological Disorders and Stroke (NINDS)

Hirotaka Iwaki

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD)

Yue Qi

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD); National Institutes of Health (NIH) - Thoracic and GI Malignancies Branch

Daniel M. Ramos

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD)

Brian Avants

Invicro - Image Analysis

Jacob Hesterman

Invicro - Image Analysis

Roger Gunn

Invicro - Image Analysis

Mark R. Cookson

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD); National Institutes of Health (NIH) - Cell Biology and Gene Expression Section

Michael E. Ward

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD); National Institutes of Health - National Institute of Neurological Disorders and Stroke

Andrew B. Singleton

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD); National Institute on Aging (NIA) - Molecular Genetics Section

Roy H. Campbell

University of Illinois at Urbana-Champaign - Department of Computer Science

Michael A. Nalls

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD); National Institutes of Health - Laboratory of Neurogenetics

Faraz Faghri

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD)

More...

Abstract

Longitudinal multi-dimensional biological datasets are ubiquitous and highly abundant. These datasets are essential to understanding disease progression, identifying subtypes, and drug discovery. Discovering meaningful patterns or disease pathophysiologies in these datasets is challenging due to their high dimensionality, making it difficult to visualize hidden patterns. Several methods have been developed for dimensionality reduction, but they are limited to cross-sectional datasets. Recently proposed Aligned-UMAP, an extension of the UMAP algorithm, can visualize high-dimensional longitudinal datasets. In this work, we applied Aligned-UMAP on a broad spectrum of clinical, imaging, proteomics, and single-cell datasets. Aligned-UMAP reveals time-dependent hidden patterns when color-coded with the metadata. We found that the algorithm parameters also play a crucial role and must be tuned carefully to utilize the algorithm's potential fully.

Altogether, based on its ease of use and our evaluation of  its performance on different modalities, we anticipate that Aligned-UMAP will be a valuable tool for the biomedical community. We also believe our benchmarking study becomes more important as more and more high-dimensional longitudinal data in biomedical research becomes available.

Keywords: Longitudinal biomedical data, Dimensionality reduction, Unsupervised learning

Suggested Citation

Dadu, Anant and Satone, Vipul and Kaur, Rachneet and Koretsky, Mathew and Iwaki, Hirotaka and Qi, Yue and Ramos, Daniel M. and Avants, Brian and Hesterman, Jacob and Gunn, Roger and Cookson, Mark R. and Ward, Michael E. and Singleton, Andrew B. and Campbell, Roy H. and Nalls, Michael A. and Faghri, Faraz, Application of Aligned-UMAP to Longitudinal Biomedical Studies. Available at SSRN: https://ssrn.com/abstract=4292603 or http://dx.doi.org/10.2139/ssrn.4292603
This version of the paper has not been formally peer reviewed.

Anant Dadu

University of Illinois at Urbana-Champaign - Department of Computer Science ( email )

Vipul Satone

University of Illinois at Urbana-Champaign - Department of Industrial and Enterprise Systems Engineering ( email )

Rachneet Kaur

University of Illinois at Urbana-Champaign - Department of Industrial and Enterprise Systems Engineering ( email )

Mathew Koretsky

Government of the United States of America - National Institute of Neurological Disorders and Stroke (NINDS) ( email )

Hirotaka Iwaki

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD) ( email )

Yue Qi

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD) ( email )

National Institutes of Health (NIH) - Thoracic and GI Malignancies Branch ( email )

United States

Daniel M. Ramos

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD) ( email )

Brian Avants

Invicro - Image Analysis ( email )

Jacob Hesterman

Invicro - Image Analysis ( email )

Roger Gunn

Invicro - Image Analysis ( email )

Mark R. Cookson

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD) ( email )

National Institutes of Health (NIH) - Cell Biology and Gene Expression Section ( email )

9000 Rockville Pike
Bethesda, MD 20892
United States

Michael E. Ward

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD) ( email )

National Institutes of Health - National Institute of Neurological Disorders and Stroke ( email )

9000 Rockville Pike
Bethesda, MD 20892
United States

Andrew B. Singleton

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD) ( email )

National Institute on Aging (NIA) - Molecular Genetics Section ( email )

Building 31, Room 5C27
31 Center Drive, MSC 2292
Bethesda, MD 20892
United States

Roy H. Campbell

University of Illinois at Urbana-Champaign - Department of Computer Science ( email )

Michael A. Nalls

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD) ( email )

National Institutes of Health - Laboratory of Neurogenetics ( email )

Bethesda, MD 20892
United States

Faraz Faghri (Contact Author)

Government of the United States of America - Center for Alzheimer's and Related Dementias (CARD) ( email )

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