Bayesian Kinetic Modelling of Cocoa Bean Fermentation

ODE modelling of cocoa bean fermentation kinetics using Stan

Photo by Ly Le Minh

My core PhD research focused on developing kinetic models of cocoa bean fermentation using Bayesian methods coded in Stan to fit systems of ordinary differential equations to previously published fermentation trial data. This work allowed us to quantitatively describe how key biochemical compounds evolve during fermentation — a critical step in determining the final flavor profile of chocolate.

I presented a summary of this research at StanCon 2019 in Cambridge. You can view the accompanying notebook here.