Jun 2026· arXiv.org· Vol abs/2606.28655· 0 citations· 5 references
Computer SciencePhysicsBiology
TL;DR
The results do not establish a general QML advantage, but they suggest that feature-map entanglement topology is a meaningful design variable for sparse biological screening tasks and warrants further evaluation with additional metrics, larger datasets, and noise-aware or hardware-based experiments.
Abstract
Parameterized quantum circuits (PQCs) provide a flexible substrate for hybrid quantum machine learning (QML), but their practical value on Noisy Intermediate-Scale Quantum (NISQ) devices remains an empirical question, especially because training depth and scale can introduce optimization challenges such as barren plateaus. Here we study how the number and topology of two-qubit entangling gates in the feature-map stage influence a fixed hybrid QNN workflow for classifying strong versus weak epitope-receptor binding in Porcine Reproductive and Respiratory Syndrome (PRRS) vaccine design. The dataset consists of docking-derived binding affinities for N=80 9-mer epitopes, labeled as Strong or Weak binding, and partitioned into training, validation, and test subsets using a 40:30:30 split. We compare a classical CNN benchmark with a hybrid Embedding-QNN architecture under four feature-map configurations: a non-entangling Z feature map, an all-to-all high-entanglement ZZ feature map, and two interleaved nearest-neighbour entanglement patterns of low and high depth. Among the configurations tested, the high-entanglement ZZ feature map is seen to provide the strongest evidence of reduced training-set overfit, with a lower training area under the accuracy curve (AUAC) and the highest test/training AUAC ratio, while preserving competitive test-set accuracy. These results do not establish a general QML advantage, but they suggest that feature-map entanglement topology is a meaningful design variable for sparse biological screening tasks and warrants further evaluation with additional metrics, larger datasets, and noise-aware or hardware-based experiments.
Quantum machine learning (QML) faces practical limitations due to noisy intermediate-scale quantum (NISQ) constraints, including noise, restricted qubit availability, and unstable optimization. This paper proposes HyQNet, a resource-aware hybrid quantum–classical framework designed to address these challenges through efficient circuit execution and adaptive optimization. The framework integrates optimized quantum circuits with classical learning strategies to improve scalability and stability under NISQ conditions. Experimental results on Iris, Wine, and Breast Cancer datasets show that HyQNet achieves an accuracy of 95.1% and F1-score of 94.8%, outperforming variational QNN (92.6%) and quantum SVM (91.2%). It also reduces runtime to 16.9 s compared to 20.5 s for VQNN, while maintaining efficient utilization of 8 qubits. Statistical analysis confirms significance (p < 0.05), and ablation studies validate the contribution of each component. The results demonstrate improved convergence stability and resource efficiency in hybrid quantum learning systems.
Sudheer Reddy K., Hastimal Jangid, Usha Desai· 2026 International Conferenc...· 0 citations
This work introduces Quantum Convolutional HLA Immunogenic Peptide Prediction (Q-CHIPP), a combinatorial framework integrating MHC binding and T-cell recognition that targets HLA-A*02:01–restricted 9-mer peptides and identifies those peptides known to be immunogenic, improving the prognostic impact of predicted neoantigen load.
Ryan Peters, Kahn Rhrissorrakrai, Prerana Bangalore Parthasarathy et al.· Science Advances· 0 citations
This work constitutes a reproducible baseline for noise-aware quantum machine learning on pharmaceutical data and shows that hardware-efficient entanglement structures—specifically alternating cost and mixer layers—provide a systematic advantage over purely rotational or diagonal encodings under realistic noise conditions.
Rania Derouich, N. Mathlouthi· bioRxiv· 0 citations
A structured perspective on the current state of QML is provided to identify opportunities in deploy it effectively in solve real-world problems and to identify opportunities in deploy it effectively in solve real-world problems.
Muhamad Akrom, Aprilyani Nur Safitri, N. Hidayat et al.· Journal of Multiscale Materi...· 0 citations
Deep generative models have become a leading approach for designing therapeutic molecules, yet efficiently exploring vast biomolecular sequence spaces remains difficult, particularly for targets with limited training data. The prior distribution that seeds a generative model shapes which regions of sequence space it explores, and recent work suggests that non-classical distributions sampled from quantum processors can serve as a structured alternative to the factorised Gaussian priors used by default. Whether such priors help on complex biological design tasks has been largely untested. Here we present what is, to our knowledge, the first end-to-end hybrid quantum-classical pipeline for de novo design of MHC class I-binding peptides, coupling a generative adversarial network (GAN) to latent vectors sampled from a real photonic quantum processor. Tested in silico across 131 HLA alleles, quantum-derived priors increased the yield of predicted strong binders, with the largest relative gains for understudied alleles where classical baselines perform worst. We selected three understudied alleles for further evaluation, finding that large gains coincided with broader sequence exploration at non-anchor positions while anchor specificity was preserved. On these three alleles, we validated the designs in vitro using peptide-MHC stability ELISAs, confirming that quantum-designed peptides are potent stabilisers of peptide-MHC class I complexes. These results establish structured, hardware-realisable non-classical priors as a useful inductive bias for generative peptide design, with direct relevance to personalised immunotherapies and vaccines.
E. S. Engdal, Jonathan Funk, O. Bacarreza et al.· bioRxiv· 0 citations
Results indicate that the topology-aligned inductive bias is the active ingredient driving parameter efficiency at QM9 scale, with implications for matched-baseline benchmarking in quantum machine learning.
