Mixed-effect Bayesian network reveals personal effects of nutrition

Nutrition experts know by their experience that people can react very differently to the same nutrition. If we could systematically quantify these differences, it would enable more personal dietary understanding and guidance. This work proposes a mixed-effect Bayesian network as a method for modeling the multivariate system of nutrition effects. Estimation of this network reveals a system of both population-wide and personal correlations between nutrients and their biological responses. Fully Bayesian estimation in the method allows managing the uncertainty in parameters and incorporating the existing nutritional knowledge into the model. The method is evaluated by modeling data from a dietary intervention study, called Sysdimet, which contains personal observations from food records and the corresponding fasting concentrations of blood cholesterol, glucose, and insulin. The model's usefulness in nutritional guidance is evaluated by predicting personally if a given diet increases or decreases future levels of concentrations. The proposed method is shown to be comparable with the well-performing Extreme Gradient Boosting (XGBoost) decision tree method in classifying the directions of concentration increases and decreases. In addition to classification, we can also predict the precise concentration level and use the biologically interpretable model parameters to understand what personal effects contribute to the concentration. We found considerable personal differences in the contributing nutrients, and while these nutritional effects are previously known at a population level, recognizing their personal differences would result in more accurate estimates and more effective nutritional guidance.