A t-SNE Based Classification Approach to Compositional Microbiome Data

Xu, Xueli and Xie, Zhongming and Yang, Zhenyu and Li, Dongfang and Xu, Ximing (2020) A t-SNE Based Classification Approach to Compositional Microbiome Data. Frontiers in Genetics, 11. ISSN 1664-8021

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Abstract

As a data-driven dimensionality reduction and visualization tool, t-distributed stochastic neighborhood embedding (t-SNE) has been successfully applied to a variety of fields. In recent years, it has also received increasing attention for classification and regression analysis. This study presented a t-SNE based classification approach for compositional microbiome data, which enabled us to build classifiers and classify new samples in the reduced dimensional space produced by t-SNE. The Aitchison distance was employed to modify the conditional probabilities in t-SNE to account for the compositionality of microbiome data. To classify a new sample, its low-dimensional features were obtained as the weighted mean vector of its nearest neighbors in the training set. Using the low-dimensional features as input, three commonly used machine learning algorithms, logistic regression (LR), support vector machine (SVM), and decision tree (DT) were considered for classification tasks in this study. The proposed approach was applied to two disease-associated microbiome datasets, achieving better classification performance compared with the classifiers built in the original high-dimensional space. The analytic results also showed that t-SNE with Aitchison distance led to improvement of classification accuracy in both datasets. In conclusion, we have developed a t-SNE based classification approach that is suitable for compositional microbiome data and may also serve as a baseline for more complex classification models.

Item Type: Article
Subjects: STM Academic > Medical Science
Depositing User: Unnamed user with email support@stmacademic.com
Date Deposited: 27 Jan 2023 08:09
Last Modified: 10 Feb 2024 04:10
URI: http://article.researchpromo.com/id/eprint/83

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