Journal Article

A topological data analysis based classification method for multiple measurements

Ramanujam, Ryan, Riihimäki, Henri, Hillert, Jan, Chachólski, Wojciech, Theorell, Jakob

2020

Overview

Background Machine learning models for repeated measurements are limited. Using topological data analysis (TDA), we present a classifier for repeated measurements which samples from the data space and builds a network graph based on the data topology. A machine learning model with cross-validation is then applied for classification. When test this on three case studies, accuracy exceeds an alternative support vector machine (SVM) voting model in most situations tested, with additional benefits such as reporting data subsets with high purity along with feature values. Results For 100 examples of 3 different tree species, the model reached 80% classification accuracy after 30 datapoints, which was improved to 90% after increased sampling to 400 datapoints. The alternative SVM classifier achieved a maximum accuracy of 68.7%. Using data from 100 examples from each class of 6 different random point processes, the classifier achieved 96.8% accuracy, vastly outperforming the SVM. Using two outcomes in neuron spiking data, the TDA classifier was similarly accurate to the SVM in one case (both converged to 97.8% accuracy), but was outperformed in the other (relative accuracies 79.8% and 92.2%, respectively). Conclusions This algorithm and software can be beneficial for repeated measurement data common in biological sciences, as both an accurate classifier and a feature selection tool.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Accuracy / Algorithms / Analysis / Bioinformatics / Biomedical and Life Sciences / Breast cancer / Case studies / Classification / Classifiers / Clustering / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Data analysis / Datasets / Firing pattern / Gene expression / Information management / Learning algorithms / Life Sciences / Machine learning / Machine Learning and Artificial Intelligence in Bioinformatics / Measurement / Medical prognosis / Methods / Microarrays / Model accuracy / Multiple measurement analysis / Plant species / Research Article / Software / Support vector machines / Topological data analysis / Topology