Back to PublicationsQOBRA: A Quantum Operator-Based Autoencoder for De Novo Molecular Design
QOBRA: A Quantum Operator-Based Autoencoder for De Novo Molecular Design #442
bioRxiv 2025.07.15.665010
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2025
Authors
Yue Yu, Francesco Calcagno, Haote Li, Victor S. Batista
Abstract
We introduce a variational quantum autoencoder tailored for de novo molecular design named QOBRA (Quantum Operator-Based Real-Amplitude autoencoder). QOBRA leverages circuits for real-amplitude encoding and the SWAP test to estimate reconstruction and latent-space regularization errors during back-propagation. Adjoint encoder and decoder operator unitary transformations and a generative process that ensures accurate reconstruction as well as novelty, uniqueness, and validity of the generated samples. We showcase the QOBRA as applied to de novo design of Ca^{2+}-, Mg^{2+}-, and Zn^{2+}-binding metalloproteins after training the generative model with a modest dataset.