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Quantum Autoencoder: An Efficient Representation Learner for Quantum Features

Shengxin Zhuang, Yusen Wu, Xavier F. Cadet, Du Huynh, Wei Liu, Philippe Charton, Cédric Damour, Frédéric Cadet, Jingbo Wang

Published May 20, 2026• 0 citations
Publisher

Abstract

Abstract Quantum machine learning methods often rely on fixed, hand-crafted quantum encodings that may not capture optimal features for downstream tasks. In this work, we study the power of quantum autoencoders in learning data-driven quantum representations. We first theoretically demonstrate that the quantum autoencoder method is efficient in terms of sample complexity throughout the entire training process. Then we numerically train the quantum autoencoder on 3 million peptide sequences, and evaluate their effectiveness across multiple peptide classification problems, including antihypertensive activity, blood–brain barrier-penetration, and cytotoxicity. The learned representations were compared against Hamiltonian-evolved baselines using a quantum kernel with support vector machines. Results show that quantum autoencoder learned representations achieve accuracy improvements ranging from 0.4% to 8.1% over Hamiltonian baselines across seven datasets, demonstrating effective generalization across biologically distinct datasets, with pre-training enabling effective transfer learning without task-specific fine-tuning. This work establishes that quantum autoencoder architectures can effectively learn from large-scale datasets (3 million samples) with compact parameterizations (~900 parameters), demonstrating their viability for practical quantum applications.

DOI
10.21203/rs.3.rs-9550061/v1

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Abstract Quantum machine learning methods often rely on fixed, hand-crafted quantum encodings that may not capture optimal features for downstream tasks. In this work, we study the power of quantum autoencoders in learning data-driven quantum representations. We first theoretically demonstrate that the quantum autoencoder method is efficient in terms of sample complexity throughout the entire training process. Then we numerically train the quantum autoencoder on 3 million peptide sequences, and evaluate their effectiveness across multiple peptide classification problems, including antihypertensive activity, blood–brain barrier-penetration, and cytotoxicity. The learned representations were compared against Hamiltonian-evolved baselines using a quantum kernel with support vector machines. Results show that quantum autoencoder learned representations achieve accuracy improvements ranging from 0.4% to 8.1% over Hamiltonian baselines across seven datasets, demonstrating effective generalization across biologically distinct datasets, with pre-training enabling effective transfer learning without task-specific fine-tuning. This work establishes that quantum autoencoder architectures can effectively learn from large-scale datasets (3 million samples) with compact parameterizations (~900 parameters), demonstrating their viability for practical quantum applications.
Quantum machine learning methods often rely on fixed, hand-crafted quantum encodings that may not capture optimal features for downstream tasks. In this work, we study the power of quantum autoencoders in learning data-driven quantum representations. We first theoretically demonstrate that the quantum autoencoder method is efficient in terms of sample complexity throughout the entire training process. Then we numerically train the quantum autoencoder on 3 million peptide sequences, and evaluate their effectiveness across multiple peptide classification problems including antihypertensive peptide prediction, blood-brain barrier-penetration, and cytotoxic activity detection. The learned representations were compared against Hamiltonian-evolved baselines using a quantum kernel with support vector machines. Results show that quantum autoencoder learned representations achieve accuracy improvements ranging from 0.4\% to 8.1\% over Hamiltonian baselines across seven datasets, demonstrating effective generalization to diverse downstream datasets with pre-training enabling effective transfer learning without task-specific fine-tuning. This work establishes that quantum autoencoder architectures can effectively learn from large-scale datasets (3 million samples) with compact parameterizations ($\sim$900 parameters), demonstrating their viability for practical quantum applications.
Data sets that are specified by a large number of features are currently outside the area of applicability for quantum machine learning algorithms. An immediate solution to this impasse is the application of dimensionality reduction methods before passing the data to the quantum algorithm. We investigate six conventional feature extraction algorithms and five autoencoder-based dimensionality reduction models to a particle physics data set with 67 features. The reduced representations generated by these models are then used to train a quantum support vector machine for solving a binary classification problem: whether a Higgs boson is produced in proton collisions at the LHC. We show that the autoencoder methods learn a better lower-dimensional representation of the data, with the method we design, the Sinkclass autoencoder, performing 40% better than the baseline. The methods developed here open up the applicability of quantum machine learning to a larger array of data sets. Moreover, we provide a recipe for effective dimensionality reduction in this context.
In order to leverage quantum computers for machine learning tasks such as image classification, consideration is required. Noisy Intermediate-Scale Quantum (NISQ) computers have limitations that include noise, scalability, read-in and read-out times, and gate operation times. Therefore, strategies should be devised to mitigate the impact complex datasets that can have on the overall efficiency of a quantum machine learning pipeline. This may otherwise lead to excessive resource demands or noise. We apply a classical feature extraction using a ResNet10-inspired convolutional autoencoder to reduce dataset dimensionality and extract abstract, meaningful features before feeding them into a quantum layer. The chosen quantum layer is a quantum-enhanced support vector machine (QSVM), as SVMs typically do not require large sample sizes to identify patterns in data and have short-depth quantum circuits, which limits the impact of noise. The autoencoder is trained to extract meaningful features through image reconstruction, aiming to minimize the mean squared error across a training set of images. We use three datasets to illustrate the pipeline: HTRU-1, MNIST, and CIFAR-10. We include a quantum-enhanced one-class support vector machine (QOCSVM) for the highly unbalanced HTRU-1 set, with classical machine learning results for comparison. HTRU-2 is also included to serve as a benchmark for a dataset with meaningful features. The autoencoder achieved near-perfect reconstruction and high accuracy for MNIST, while CIFAR-10 showed poorer performance due to image complexity, and HTRU-1 struggled due to the imbalance in the dataset. The varying performance across datasets highlights the need to balance dimensionality reduction and prediction performance using quantum methods.
Quantum-enhanced machine learning is a rapidly evolving field that aims to leverage the unique properties of quantum mechanics to enhance classical machine learning. However, the practical applicability of these methods remains an open question, particularly beyond the context of specifically crafted toy problems, and given the current limitations of quantum hardware. This study focuses on quantum kernel methods in the context of classification tasks. In particular, it examines the performance of quantum kernel estimation and quantum kernel training (QKT) in connection with two quantum feature mappings, namely, ZZFeatureMap and CovariantFeatureMap. Remarkably, these feature maps have been proposed in the literature under the conjecture of possible near-term quantum advantage and have shown promising performance in ad hoc datasets. This study aims to evaluate their versatility and generalization capabilities in a more general benchmark, encompassing both artificial and established reference datasets. Classical machine learning methods, specifically support vector machines and logistic regression, are also incorporated as baseline comparisons. Experimental results indicate that quantum methods exhibit varying performance across different datasets. Despite outperforming classical methods in ad hoc datasets, mixed results are obtained for the general case among standard classical benchmarks. The experimental data call into question a general added value of applying QKT optimization, for which the additional computational cost does not necessarily translate into improved classification performance. Instead, it is suggested that a careful choice of the quantum feature map in connection with proper hyperparameterization may prove more effective.
A key challenge in practical quantum machine learning (QML), particularly for discriminative tasks such as classification, is the limited capacity of near-term quantum devices to encode high-dimensional classical data into small quantum registers. In optimized basis-encoded (bit-bit) settings, this constraint leads to cross-class collisions, where samples with different labels are mapped to the same discrete bit-string and thus become indistinguishable to any downstream model. In this work, we investigate how data representation affects QML performance under such severe information bottlenecks. We introduce discretization-aware fine-tuning (DAFT), a method that adapts a pre-trained chemical foundation model to produce representations that remain informative after quantization. DAFT reduces collision probability through a differentiable soft collision loss. We evaluate both quantum and classical models under a controlled setting in which they receive identical discretized bit-string inputs, isolating the effect of representation from model architecture. On the blood-brain barrier penetration (BBBP) molecular property prediction benchmark using ChemBERTa-77M, DAFT reduces collision counts by several orders of magnitude and improves quantum classification accuracy by more than 12 percentage points compared to a frozen backbone. Importantly, without DAFT, classical models outperform QML under the same input constraints. With DAFT, however, this comparison reverses at higher qubit counts. At 10 qubits, the quantum model surpasses a matched classical baseline trained on identical bit-strings (0.883 vs. 0.855, p=0.026p = 0.026p=0.026). These results show that, in information-constrained regimes, achieving a quantum advantage critically depends on aligning continuous representations with discrete quantum encodings.
Abstract Classical autoencoders are neural networks that can learn efficient low-dimensional representations of data in higher-dimensional space. The task of an autoencoder is, given an input x , to map x to a lower dimensional point y such that x can likely be recovered from y . The structure of the underlying autoencoder network can be chosen to represent the data on a smaller dimension, effectively compressing the input. Inspired by this idea, we introduce the model of a quantum autoencoder to perform similar tasks on quantum data. The quantum autoencoder is trained to compress a particular data set of quantum states, where a classical compression algorithm cannot be employed. The parameters of the quantum autoencoder are trained using classical optimization algorithms. We show an example of a simple programmable circuit that can be trained as an efficient autoencoder. We apply our model in the context of quantum simulation to compress ground states of the Hubbard model and molecular Hamiltonians.