Interpreting Microbiome Relative Abundance Data Using Symbolic Regression

Understanding the complex interactions within the microbiome is crucial for developing effective diagnostic and therapeutic strategies. Traditional machine learning models often lack interpretability, which is essential for clinical and biological insights. This paper explores the application of symbolic regression (SR) to microbiome relative abundance data, with a focus on colorectal cancer (CRC). SR, known for its high interpretability, is compared against traditional machine learning models, e.g., random forest, gradient boosting decision trees. These models are evaluated based on performance metrics such as F1 score and accuracy. We utilize 71 studies encompassing, from various cohorts, over 10,000 samples across 749 species features. Our results indicate that SR not only competes reasonably well in terms of predictive performance, but also excels in model interpretability. SR provides explicit mathematical expressions that offer insights into the biological relationships within the microbiome, a crucial advantage for clinical and biological interpretation. Our experiments also show that SR can help understand complex models like XGBoost via knowledge distillation. To aid in reproducibility and further research, we have made the code openly available at https://github.com/swag2198/microbiome-symbolic-regression .