Machine Learning Against Cancer: Accurate Diagnosis of Cancer by Machine Learning Classification of the Whole Genome Sequencing Data

TL;DR

This paper presents a novel machine learning approach that achieves perfect accuracy in classifying cancerous versus healthy tissues using whole genome sequencing data, including early-stage cancers, with privacy-preserving normalized data.

Contribution

The authors introduce MLAC, a new machine learning framework that attains perfect classification metrics across multiple cancer types using genomic data, even with limited samples.

Findings

Achieved perfect precision, sensitivity, and specificity for most tumor types.

Effective classification and clustering of cancerous and healthy samples.

Works well with normalized RNA sequencing data, preserving privacy.

Abstract

Machine learning can precisely identify different cancer tumors at any stage by classifying cancerous and healthy samples based on their genomic profile. We have developed novel methods of MLAC (Machine Learning Against Cancer) achieving perfect results with perfect precision, sensitivity, and specificity. We have used the whole genome sequencing data acquired by next-generation RNA sequencing techniques in The Cancer Genome Atlas and Genotype-Tissue Expression projects for cancerous and healthy tissues respectively. Moreover, we have shown that unsupervised machine learning clustering has great potential to be used for cancer diagnosis. Indeed, a creative way to work with data and general algorithms has resulted in perfect classification i.e. all precision, sensitivity, and specificity are equal to 1 for most of the different tumor types even with a modest amount of data, and the same method works well on a series of cancers and results in great clustering of cancerous and healthy samples too. Our system can be used in practice because once the classifier is trained, it can be used to classify any new sample of new potential patients. One advantage of our work is that the aforementioned perfect precision and recall are obtained on samples of all stages including very early stages of cancer; therefore, it is a promising tool for diagnosis of cancers in early stages. Another advantage of our novel model is that it works with normalized values of RNA sequencing data, hence people's private sensitive medical data will remain hidden, protected, and safe. This type of analysis will be widespread and economical in the future and people can even learn to receive their RNA sequencing data and do their own preliminary cancer studies themselves which have the potential to help the healthcare systems. It is a great step forward toward good health that is the main base of sustainable societies.