Quantum Interaction Manifolds for Cancer Genomics: A Theoretical Framework and Proof-of-Concept Quantum Machine Learning for Early Diagnosis and Drug Response Modeling
Abstract Understanding and predicting cancer phenotypes from genomic data requires models capableof capturing high-order interactions among genes and biological pathways. We introduce Quantum Interaction Manifolds (QIMs), a theoretical framework that represents gene expression profiles as quantumstates evolved under biologically informed Hamiltonians. We show that QIM embeddings induce hypothesisclasses that cannot be efficiently approximated by classical learners under standard complexity assumptions,providing a principled quantum advantage in representing nonlinear genomic dependencies. Using noisysimulations on reduced-dimensional datasets, we demonstrate that QIM-based quantum kernels achievecompetitive accuracy in cancer classification tasks, while variational quantum models trained on QIMrepresentations learn continuous drug response signals with stable convergence. Together, these results establish QIMs as a quantum-native approach for modeling genomic interactions and highlight the potentialof structured quantum machine learning to support future developments in computational oncology
Abstract Understanding and predicting cancer phenotypes from genomic data requires models capableof capturing high-order interactions among genes and biological pathways. We introduce Quantum Interaction Manifolds (QIMs), a theoretical framework that represents gene expression profiles as quantumstates evolved under biologically informed Hamiltonians. We show that QIM embeddings induce hypothesisclasses that cannot be efficiently approximated by classical learners under standard complexity assumptions,providing a principled quantum advantage in representing nonlinear genomic dependencies. Using noisysimulations on reduced-dimensional datasets, we demonstrate that QIM-based quantum kernels achievecompetitive accuracy in cancer classification tasks, while variational quantum models trained on QIMrepresentations learn continuous drug response signals with stable convergence. Together, these results establish QIMs as a quantum-native approach for modeling genomic interactions and highlight the potentialof structured quantum machine learning to support future developments in computational oncology
Multi-omics integration has become a cornerstone of personalized medicine, enabling researchers to connect genomic, transcriptomic, proteomic, metabolomic, and epigenomic data to reveal complex biological mechanisms and individualized disease signatures. However, the extreme dimensionality, heterogeneity, and nonlinear interactions across omics layers challenge even the most advanced classical machine learning methods. Quantum Machine Learning (QML) offers a powerful alternative by exploiting quantum superposition, entanglement, and high-dimensional feature embeddings to model multi-omics interactions more efficiently. This study proposes a hybrid quantum–classical framework that combines quantum kernel estimation, variational quantum classifiers, and quantum-enhanced feature fusion networks to generate integrative biological signatures for precision diagnostics. Simulation results using benchmark multi-omics datasets demonstrate improved classification accuracy, enhanced sensitivity to weak biological signals, and reduced computational overhead compared to classical baselines. These findings highlight the potential of QML to accelerate multi-omics insights and pave the way toward truly personalized, predictive healthcare.
The rapid advancements in genomics and the availability of large-scale genetic datasets have revolutionized our understanding of genetic diseases. However, the complexity and high dimensionality of genomic data pose significant computational challenges for classical machine learning (ML) algorithms. Quantum machine learning (QML), an emerging interdisciplinary field that combines quantum computing with ML techniques, offers a promising solution to address these challenges. This paper explores the application of QML algorithms for diagnosing genetic diseases by leveraging the unique properties of quantum computing, such as superposition, entanglement, and quantum parallelism. A novel hybrid quantum-classical approach is proposed to enhance the accuracy and efficiency of disease diagnosis using genomic datasets. The methodology involves encoding genetic data into quantum states, applying quantum-enhanced feature selection and classification algorithms, and validating the results on publicly available datasets, such as the UK Biobank and the Cancer Genome Atlas (TCGA). Experimental results demonstrate that the proposed QML framework achieves higher classification accuracy and faster computation times compared to classical counterparts. Equations, tables, and charts are used to illustrate the effectiveness of the approach. This research highlights the transformative potential of QML in precision medicine and lays the groundwork for future investigations into quantum-enabled healthcare solutions.
Quantum machine learning (QML) presents novel opportunities for resolving, accelerating, and refining computational biology challenges. In biomedical research and personalized medicine, multi-omics integration offers a comprehensive understanding of complex biological systems, bridging the gap between basic research and clinical applications. Recent advancements in quantum computing could enhance multi-omics integration by leveraging unique quantum principles, potentially revealing intricate patterns in multi-omics datasets and offering new insights into the molecular landscape of lung cancer. This study focuses on the integration, feature selection, diagnostic classification, and biomarker identification of lung cancer types-LUAD primary tumor and solid tissue normal-using QML. Given the heterogeneity and high dimensionality of the data, we aim to assess the performance of QML in feature selection, reduction, encoding, and diagnostic classification in integrated multi-omics cancer datasets. We demonstrate the efficacy of Quantum Neural Networks (QNNs) for classifying multi-omics lung cancer data from The Cancer Genome Atlas, comparing our framework with 16 and 64 dimensions of feature using QML. Our results show that the Multi-omic Quantum Machine Learning (MQML) framework achieves superior classification performance with smaller training datasets, as determined by significant and non-significant p-values. This study provides empirical evidence for the potential application of unconventional computing approaches in biomed-ical sciences, particularly in oncology research, including cancer subtype diagnostic, survival, and stage classification. Key results include the identification of sixteen genes and thirty-two genes with the hybrid quantum-classical neural net-work model, with notable genes such as MIR632, CYP19A1, RP11-108K3.1, C14orf39, THUMPD1, ACSM3, GSC, MIR92a-2, DYRK1B, DNAJA1, IRX1, FMR1, POU2F2, MIR9-2, ZNF274, MIR196a-1, MIR3653, MIR33b, MIR301a, MIR182, MIR520a, PYGO2, EMX2OS, EMX2, RP11-550F7.1, RPS11, MIR20a, EIF4G2, IGLV1-47, RP11-180M15.7, SCYL3, AC107081.5, C2orf47, FST, MIR7-1, SLC22A18, CLDN5, and AC007879.7 identified as having significant and non-significant p-values asso-ciated with LUAD patient predictions.
Quantum computing has reintroduced itself as a breakthrough technology for machine learning, especially in the analysis of massive datasets, especially the genomic ones. The present research focuses on using QML, namely QSVM, to parse sequences, discover features relating to multiple genetic alterations, biomarkers, and gene expression patterns. The data type under consideration, namely genomic data, is high-dimensional and complex, which presents some problems to the computational methods originating from traditional mathematics. QSVM is designed to work with the mathematical foundations of quantum mechanics including superposition and entanglement and for this reason, it solves problems associated with large scale genomic data more efficiently and accurately. The application of QSVM in MEPs confirms its superiority over classical counterparts in classifying gene mutations, clustering of expression profiles or prediction of disease susceptibility. In addition, through feature mapping, QSVM offers better insights into biological information contained on genomic data, as compared to linear correlations. Furthermore, the ability of QML frameworks to expand to fit the increasing amount of data produced by next-generation sequencing technologies is assessed. Leveraging on this research QSVM has been recognised to redefine precision medicine by rapidly diagnosing diseases and providing unique therapeutic options. The results re-echo the potential of QML in transforming CG and promoting future innovations in biomedicine and health.
Quantum machine learning (QML) algorithms have demonstrated the power of quantum computing for solving complex problems and big data in certain tasks. In this study, we explore the capabilities of QML for the classification of real-world biological large datasets including ten different cancer types based on gene expression values. By comparing the classification results obtained from the quantum algorithm with those from classical approaches, we disclose that the QML algorithm overall achieves comparable and reliable results. Moreover, we identify novel biomarkers that can contribute to the understanding of cancer biology. Some of these biomarkers are consistent with DNA promoter methylation. Our findings highlight the potential of QML in cancer classification and biomarker discovery, paving the way for future advancements in other disease research and clinical applications.
Identification of cancer driver genes is fundamental for the development of targeted therapeutic interventions. The integration of mutational profiles with protein-protein-interaction (PPI) networks offers a promising avenue for their detection [Horn , ; Nourbakhsh , ], but scaling to large network datasets is computationally demanding. Quantum computing offers compact representations and potential complexity reductions. Motivated by the classical method of Gumpinger [], in this work we introduce a supervised quantum framework that combines mutation scores with network topology via a state-preparation scheme we call quantum multiorder moment embedding (QMME). QMME encodes low-order statistical moments over the mutation scores of a node's immediate and second-order neighbors and encodes this information into quantum states. These states are used as inputs to a kernel-based quantum binary classifier that discriminates known driver genes from others. Simulations on an empirical PPI network demonstrate competitive performance, with a 12.6% recall gain over a classical baseline. The pipeline performs explicit quantum state preparation and requires no classical training, enabling an efficient, nearly end-to-end quantum workflow. A brief complexity analysis suggests the approach could achieve a quantum speedup in network-based cancer-gene prediction. This work underscores the potential of supervised quantum-graph-learning frameworks to advance biological discovery.