Deep Discriminative Fine-Tuning for Cancer Type Classification
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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 on point mutations as features (1). Tumor classification accuracy can be greatly improved (to over 90 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 classes on The Cancer Genome Atlas (TCGA) dataset. Using our method, we achieve state-of-the-art tumor type classification accuracy of 78.3 classes relying on DNA point mutations in the tumor only.
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