Hybrid Deep Modeling of a GS115 (Mut+) Pichia pastoris Culture with State-Space Reduction

Hybrid modeling workflows combining machine learning with mechanistic process descriptions are becoming essential tools for bioprocess digitalization. In this study, a hybrid deep modeling method with state-space reduction was developed and showcased with a P. pastoris GS115 Mut+ strain expressing a single-chain antibody fragment (scFv). Deep feedforward neural networks (FFNN) with varying depths were connected in series with bioreactor macroscopic material balance equations. The hybrid model structure was trained with a deep learning technique based on the adaptive moment estimation method (ADAM), semidirect sensitivity equations and stochastic regularization. A state-space reduction method was investigated based on a principal component analysis (PCA) of the cumulative reacted amount. Data of nine fed-batch P. pastoris 50 L cultivations served to validate the method. Hybrid deep models were developed describing process dynamics as a function of critical process parameters (CPPs). The state-space reduction method succeeded to decrease the hybrid model complexity by 60% and to improve the predictive power by 18.5% in relation to the nonreduced version. An exploratory design space analysis showed that the optimization of the feed of methanol and of inorganic elements has the potential to increase the scFv endpoint titer by 30% and 80%, respectively, in relation to the reference condition.

Automated summary

In this study, a hybrid deep modeling method was developed and applied to a P. pastoris GS115 Mut+ strain expressing a single-chain antibody fragment (scFv). The hybrid model structure combined deep feedforward neural networks (FFNN) with bioreactor macroscopic material balance equations. The model was trained with a deep learning technique and a state-space reduction method was used to decrease complexity. The method was validated using experimental data and an exploratory design space analysis showed potential for increased scFv endpoint titer through optimization of methanol and inorganic element feeding.