Computational genomic algorithms for miRNA-based diagnosis of lung cancer: the potential of machine learning

TL;DR

This paper compares traditional and machine learning algorithms for miRNA-based lung cancer diagnosis, demonstrating that machine learning achieves higher accuracy and offers valuable confidence intervals, with potential for broader disease applications.

Contribution

The study develops and evaluates a machine learning algorithm for miRNA-based lung cancer diagnosis, showing improved accuracy over traditional methods and highlighting its potential for complex disease classification.

Findings

Machine learning achieves 97% accuracy for cancer samples.

Traditional methods have lower diagnostic accuracy.

Machine learning provides confidence intervals for diagnosis.

Abstract

The advent of large scale, high-throughput genomic screening has introduced a wide range of tests for diagnostic purposes. Prominent among them are tests using miRNA expression levels. Genomics and proteomics now provide expression levels of hundreds of miRNAs at a time. However, for actual diagnostic tools to become reality requires the simultaneous development of methods to interpret the large amounts of miRNA expression data that can be generated from a single patient sample. Because these data are in numeric form, quantitative methods must be developed. Statistics such as p-values and log fold change give some insight, but the diagnostic effectiveness of each miRNA test must first be evaluated. Here, the author has developed a traditional, sensitivity- and specificity-based algorithm, as well as a modern machine learning algorithm, and evaluated their diagnostic potential for lung cancer against a publicly available database. The findings suggest that the machine learning algorithm achieves higher accuracy (97% for cancerous and 73% for normal samples), in addition to providing confidence intervals that could provide valuable diagnostic support. The machine learning algorithm also has significant potential for expansion to more complex diagnoses of lung cancer sub-types, to other cancers as well diseases beyond cancer. Both algorithms are available on the Github repo: https://github.com/neerja-g/machine-learning-miRNA.