The topology of data: Opportunities for cancer research

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Abstract

Topological methods have recently emerged as a reliable and interpretable framework for extracting information from high-dimensional data, leading to the creation of a branch of applied mathematics called Topological Data Analysis (TDA). Since then, TDA has been progressively adopted in biomedical research. Biological data collection can result in enormous datasets, comprising thousands of features and spanning diverse datatypes. This presents a barrier to initial data analysis as the fundamental structure of the dataset becomes hidden, obstructing the discovery of important features and patterns. TDA provides a solution to obtain the underlying shape of datasets over continuous resolutions, corresponding to key topological features independent of noise. TDA has the potential to support future developments in healthcare as biomedical datasets rise in complexity and dimensionality. Previous applications extend across the fields of neuroscience, oncology, immunology, and medical image analysis. TDA has been used to reveal hidden subgroups of cancer patients, construct organisational maps of brain activity and classify abnormal patterns in medical images. The utility of TDA is broad and to understand where current achievements lie, we have evaluated the present state of TDA in cancer data analysis. This paper aims to provide an overview of TDA in Cancer Research. A brief introduction to the main concepts of TDA is provided to ensure that the paper is accessible to readers who are not familiar with this field. Following this, a focused literature review on the field is presented, discussing how TDA has been applied across heterogeneous datatypes for cancer research. [Abstract copyright: © The Author(s) (2021). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.]
Original languageEnglish
JournalBioinformatics (Oxford, England)
Early online date28 Jul 2021
DOIs
Publication statusEarly online date - 28 Jul 2021

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