Deep Discriminative Fine-Tuning for Cancer Type Classification

TL;DR

This paper introduces a deep discriminative fine-tuning approach that significantly improves tumor type classification accuracy using DNA point mutation data, achieving over 78% accuracy across 29 classes, which surpasses previous methods.

Contribution

The authors develop a novel deep transfer learning and fine-tuning method that enhances classification accuracy on sparse mutation data, outperforming existing approaches in tumor origin prediction.

Findings

Achieved 78.3% accuracy for 29 tumor classes using DNA mutations.

Reduced classification error by over 30% compared to previous methods.

Outperformed state-of-the-art models on TCGA dataset.

Abstract

Determining the primary site of origin for metastatic tumors is one of the open problems in cancer care because the efficacy of treatment often depends on the cancer tissue of origin. Classification methods that can leverage tumor genomic data and predict the site of origin are therefore of great value. Because tumor DNA point mutation data is very sparse, only limited accuracy (64.5% for 12 tumor classes) was previously demonstrated by methods that rely on point mutations as features (1). Tumor classification accuracy can be greatly improved (to over 90% for 33 classes) by relying on gene expression data (2). However, this additional data is often not readily available in clinical setting, because point mutations are better profiled and targeted by clinical mutational profiling. Here we sought to develop an accurate deep transfer learning and fine-tuning method for tumor sub-type classification, where predicted class is indicative of the primary site of origin. Our method significantly outperforms the state-of-the-art for tumor classification using DNA point mutations, reducing the error by more than 30% at the same time discriminating over many more classes on The Cancer Genome Atlas (TCGA) dataset. Using our method, we achieve state-of-the-art tumor type classification accuracy of 78.3% for 29 tumor classes relying on DNA point mutations in the tumor only.