TB-DROP: deep learning-based drug resistance prediction of Mycobacterium tuberculosis utilizing whole genome mutations

The most widely practiced strategy for constructing the deep learning (DL) prediction model for drug resistance of Mycobacterium tuberculosis (MTB) involves the adoption of ready-made and state-of-the-art architectures usually proposed for non-biological problems. However, the ultimate goal is to construct a customized model for predicting the drug resistance of MTB and eventually for the biological phenotypes based on genotypes. Here, we constructed a DL training framework to standardize and modularize each step during the training process using the latest tensorflow 2 API. A systematic and comprehensive evaluation of each module in the three currently representative models, including Convolutional Neural Network, Denoising Autoencoder, and Wide & Deep, which were adopted by CNNGWP, DeepAMR, and WDNN, respectively, was performed in this framework regarding module contributions in order to assemble a novel model with proper dedicated modules. Based on the whole-genome level mutations, a de novo learning method was developed to overcome the intrinsic limitations of previous models that rely on known drug resistance-associated loci. A customized DL model with the multilayer perceptron architecture was constructed and achieved a competitive performance (the mean sensitivity and specificity were 0.90 and 0.87, respectively) compared to previous ones. The new model developed was applied in an end-to-end user-friendly graphical tool named TB-DROP (TuBerculosis Drug Resistance Optimal Prediction: https://github.com/nottwy/TB-DROP ), in which users only provide sequencing data and TB-DROP will complete analysis within several minutes for one sample. Our study contributes to both a new strategy of model construction and clinical application of deep learning-based drug-resistance prediction methods.