Constructing and Visualizing Models using Mime-based Machine-learning Framework

The widespread high-throughput sequencing technology has significantly enhanced our understanding of biology and cancer heterogeneity. Machine learning algorithms on transcriptional data have become vital for predicting patient prognosis and clinical responses. Despite advancements in machine learning algorithms, an open-source platform that incorporates the most sophisticated machine learning algorithms on transcriptional data remains absent. To address this gap, we developed Mime, a versatile machine-learning framework to enhance the construction and visualization of predictive models for clinical characteristics and gene signatures. By integrating diverse datasets and employing the most advanced feature selection techniques, Mime addresses critical challenges in clinical predictions. It provides three main functions, including model construction, feature selection, and data visualization. Model construction encompasses a range of machine learning algorithms, including but not limited to decision trees, support vector machines, and ensemble methods, allowing researchers to select the best-fitted approach for their specific analysis. Feature selection utilizes advanced algorithms such as Recursive Feature Elimination and LASSO regression to streamline the dataset and focus on the most informative features. The framework supports customizable parameter tuning through cross-validation methods, optimizing model performance while mitigating overfitting risks. Visualization tools integrated within Mime enable researchers to interpret model outcomes effectively, providing graphical representations of feature importance and predictive performance metrics. In this manuscript, we provide a detailed tutorial on the stepwise procedures of this versatile machine-learning framework.