Transport models underpin the design and optimisation of chemical processes, yet their constitutive laws are typically hand-picked, their experimental initial conditions are assumed exact, and their computational cost restricts optimisation to a handful of process variables. Here we introduce a differentiable hybrid modelling framework that embeds neural networks within a GPU-accelerated population balance equation solver to discover constitutive laws and assimilate initial conditions directly from experimental crystallisation data. Using thirteen real experiments with multi-dimensional size and shape measurements, we show that treating measured initial conditions as exact yields a physically inconsistent rate law despite improved predictive accuracy, whereas assimilating them recovers a physically consistent, non-linear law and reduces trajectory error sevenfold relative to conventional modelling. End-to-end differentiability further enables gradient-based optimisation of high-dimensional operating profiles, identifying a 300-variable temperature profile that reduces crystal aspect ratio by 25% at constant mass, facilitating superior product attributes. Our framework augments, rather than replaces, mechanistic modelling, offering a general route to learning transport models from data and optimising processes with them.

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