Deep Semi-Supervised Survival Analysis for Predicting Cancer Prognosis

TL;DR

This paper introduces Cox-MT, a deep semi-supervised learning model that leverages both labeled and unlabeled data to improve cancer prognosis prediction accuracy using neural network-based survival analysis.

Contribution

The paper develops a novel deep semi-supervised Cox model using the Mean Teacher framework, enhancing survival prediction with limited labeled data and multi-modal data integration.

Findings

Cox-MT outperforms existing ANN-based Cox models like Cox-nnet.

Performance improves with more unlabeled data.

Multi-modal Cox-MT surpasses single-modal models.

Abstract

The Cox Proportional Hazards (PH) model is widely used in survival analysis. Recently, artificial neural network (ANN)-based Cox-PH models have been developed. However, training these Cox models with high-dimensional features typically requires a substantial number of labeled samples containing information about time-to-event. The limited availability of labeled data for training often constrains the performance of ANN-based Cox models. To address this issue, we employed a deep semi-supervised learning (DSSL) approach to develop single- and multi-modal ANN-based Cox models based on the Mean Teacher (MT) framework, which utilizes both labeled and unlabeled data for training. We applied our model, named Cox-MT, to predict the prognosis of several types of cancer using data from The Cancer Genome Atlas (TCGA). Our single-modal Cox-MT models, utilizing TCGA RNA-seq data or whole slide images, significantly outperformed the existing ANN-based Cox model, Cox-nnet, using the same data set across four types of cancer considered. As the number of unlabeled samples increased, the performance of Cox-MT significantly improved with a given set of labeled data. Furthermore, our multi-modal Cox-MT model demonstrated considerably better performance than the single-modal model. In summary, the Cox-MT model effectively leverages both labeled and unlabeled data to significantly enhance prediction accuracy compared to existing ANN-based Cox models trained solely on labeled data.