Transfer Learning Assessment of Data-driven Crystallisation Processes via Constrained Neural Ordinary Differential Equations
Daniele PessinaiD, Wenqing TianiD, Oliver L Watson, Jerry Y. Y. HengiD, Maria M. PapathanasiouiD
Abstract
Modelling complex crystallisation processes remains challenging due to limited experimental datasets, high measurement noise, and the need for generalisability across varying operating conditions. Neural Ordinary Differential Equations (NODEs) and transfer learning (TL) offer promising tools to overcome these limitations by providing data-efficient, flexible, and transferable modelling frameworks. This work investigates the use of NODEs to model protein crystallisation dynamics under data-scarce conditions. A NODE trained on a data-rich source system successfully captures solute consumption and particle size dynamics, but when applied to data-sparse target systems, scratch-trained NODEs exhibit limited generalisation and unphysical behaviours. To address this, several TL strategies are evaluated, including layer freezing, parameter deviation penalisation, and system-embedding within the neural architecture. Results show that layer freezing and deviation penalty consistently improve knowledge transfer, while system-embedding offers robustness in noisy or undersampled datasets. In addition, physics-informed NODEs, constrained to enforce monotonic concentration decay and crystal growth, demonstrate greater stability under high noise and sparse measurement regimes, ensuring physically consistent predictions. Overall, the combination of constrained NODEs with appropriate TL strategies provides a robust framework for accurate, transferable modelling of crystallisation systems in low-data regimes.
02 /Specification & Classification
Click any tag to browse matching papers- Citations
- 0
- FWCI
- 0.00
- Field percentile
- 13th percentile
- Approach
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Transferable Coarse Graining via Contrastive Learning of Graph Neural Networks
- CHiMP: Deep Learning Tools Trained on Protein Crystallisation Micrographs to Enable Automation of Experiments
Oliver N. F. King, K. E. Levik, … Mark Basham·Acta Crystallographica Section D Structural BiologyPeer-reviewed·Sep 25, 2024
- Noise-Transfer2Clean: Denoising cryo-EM images based on noise modeling and transfer
Hongjia Li, Hui Zhang, … Fa Zhang·BioinformaticsPeer-reviewed·Jan 28, 2022
- PartiNet is a dynamic adaptive neural network for high-performance particle picking in cryo-electron microscopy
Mihin Perera, Winnie Tan, … Shabih Shakeel·bioRxiv·Jan 23, 2026
- Not getting in too deep: a practical deep learning approach to routine crystallisation image classification
Jamie Milne, Qian Chen, … Julie C. Wilson·PLoS ONEPeer-reviewed·Mar 9, 2023
- Physics-Guided Deep Neural Networks: Correcting Physical Distortions in Protein Phase Separation Prediction
Mengmei Wang, Tonggan Lu, … yangxin Li·bioRxiv·Apr 21, 2026