AUKAT: Conditional VAE-Driven Augmentation and Neural Modeling of Enzyme Turnover Numbers

Abstract

Accurate prediction of enzyme turnover numbers (kcat) is essential for applications in systems biology, metabolic engineering, and drug discovery, yet remains challenging due to the limited availability and uneven distribution of experimental data. Here, we present AUKAT, an integrated framework that combines conditional generative modeling with deep neural prediction to improve kcat estimation. A conditional variational autoencoder generates synthetic training instances in embedding space, followed by a selection pipeline that retains samples with strong agreement across independent evaluators, thereby ensuring data reliability. A hybrid convolutional neural network and transformer-based architecture is then used to predict kcat from substrate, enzyme functional, and species embeddings. Incorporating synthetic data improved predictive performance for both random forest and neural network models in five-fold cross-validation, with larger gains observed for the neural network architecture. Benchmarking against DLKcat demonstrated comparable predictive accuracy on the standard test set, while evaluation on stricter unseen subsets indicated improved generalization for low-similarity substrates and enzymes. Feature importance analysis further showed that AUKAT leverages substrate, enzyme functional, and species information in a more balanced manner rather than relying predominantly on a single feature source. In addition, AUKAT-human, a specialized model trained using a pre-training and fine-tuning strategy, achieved improved prediction accuracy for human enzyme kinetics. Overall, AUKAT provides a scalable approach for enzyme kinetics prediction and offers a practical solution to data scarcity in biochemical modeling.