Enhancing Privacy-Preserving Cancer Classification with Convolutional Neural Networks

Precision medicine significantly enhances patients prognosis, offering personalized treatments. Particularly for metastatic cancer, incorporating primary tumor location into the diagnostic process greatly improves survival rates. However, traditional methods rely on human expertise, requiring substantial time and financial resources. To address this challenge, Machine Learning (ML) and Deep Learning (DL) have proven particularly effective. Yet, their application to medical data, especially genomic data, must consider and encompass privacy due to the highly sensitive nature of data. In this paper, we propose OGHE, a convolutional neural network-based approach for privacy-preserving cancer classification designed to exploit spatial patterns in genomic data, while maintaining confidentiality by means of Homomorphic Encryption (HE). This encryption scheme allows the processing directly on encrypted data, guaranteeing its confidentiality during the entire computation. The design of OGHE is specific for privacy-preserving applications, taking into account HE limitations from the outset, and introducing an efficient packing mechanism to minimize the computational overhead introduced by HE. Additionally, OGHE relies on a novel feature selection method, VarScout, designed to extract the most significant features through clustering and occurrence analysis, while preserving inherent spatial patterns. Coupled with VarScout, OGHE has been compared with existing privacy-preserving solutions for encrypted cancer classification on the iDash 2020 dataset, demonstrating their effectiveness in providing accurate privacy-preserving cancer classification, and reducing latency thanks to our packing mechanism. The code is released to the scientific community.