Explainable Convolutional Neural Network for Phenotype Prediction from Genotype

In the realm of precision medicine, the prediction of phenotypic traits from genotype data plays a pivotal role in understanding disease susceptibility, drug response, and overall health outcomes. Machine learning models trained on genotype data offer promising avenues for phenotype prediction. However, the black-box nature of these models often hinders interpretabil-ity, raising concerns about their reliability and trustworthiness in clinical decision-making. This paper explores the application of SHapley Additive exPlanations (SHAP) and Local Interpretable Model-agnostic Explanations (LIME) on our existing CNN model to identify important features from genotype that contribute to phenotype prediction in yeast data. Both techniques on machine learning models include improving model transparency and interpretability by providing insights into prediction mechanisms. LIME focuses on local interpretability, explaining individual predictions tailored to specific instances swiftly, while SHAP computes feature importance using Shapley values, offering a comprehensive understanding of feature contributions. Our dataset contains 4,390 samples, each with 28,220 features in genotype which are used in the training, testing and validation of our existing CNN model. In our analysis of 20 phenotypes, we identify the number of relevant important features using SHAP, LIME methods, and the intersection which not only improves the Mean Squared Error (MSE) values compared to using all the features in the genotype data, but also the model training time.