The discovery of biomarker sets for a targeted pathway is a challenging problem in biomedical medicine, which is computationally prohibited on classical algorithms due to the massive search space. Here, I present a quantum algorithm named QuantAnts Machine to address the task. The proposed algorithm is a quantum analog of the classical Ant Colony Optimization (ACO). We create the mixture of multi-domain from genetic networks by representation theory, enabling the search of biomarkers from the multi-modality of the human genome. Although the proposed model can be generalized, we investigate the RAS-mutational activation in this work. To the end, QuantAnts Machine discovers rarely-known biomarkers in clinical-associated domain for RAS-activation pathway, including COL5A1, COL5A2, CCT5, MTSS1 and NCAPD2. Besides, the model also suggests several therapeutic-targets such as JUP, CD9, CD34 and CD74.
The discovery of biomarker sets for a targeted pathway is a challenging problem in biomedical medicine, which is computationally prohibited on classical algorithms due to the massive search space. Here, I present a quantum algorithm named QuantAnts Machine to address the task. The proposed algorithm is a quantum analog of the classical Ant Colony Optimization (ACO). We create the mixture of multi-domain from genetic networks by representation theory, enabling the search of biomarkers from the multi-modality of the human genome. Although the proposed model can be generalized, we investigate the RAS-mutational activation in this work. To the end, QuantAnts Machine discovers rarely-known biomarkers in clinical-associated domain for RAS-activation pathway, including COL5A1, COL5A2, CCT5, MTSS1 and NCAPD2. Besides, the model also suggests several therapeutic-targets such as JUP, CD9, CD34 and CD74.
Abstract In this work, we introduce a quantum algorithm for biomarker identification in oncology, named QuantAnts machines, pronounced "quantant machine." Our proposed machine intelligence allows sampling biomarker-verse for the targeted RAS signaling activation, revealing combinations of biomarkers with therapeutic applications. Notable, the QuantAnts for Clinical Oncology model, ASCO(ant-4) discovers the complex CD9, CD34, and CD74 as targeting for RAS pathway for some cancer phenotypes such as gastric, colorectal (with/without metastasis), ovarian, breast and brain cancer. To the end, we show the generalization of QuantAnts machines by altering the model for genetic code designs (named QuantAnts-CRISPR), which enabling optimized sgRNA for CRISPR-Cas9 to target the complex CD9, CD34, and CD74 all-together. The found sgRNA designs are optimized by reversing mutation processes over the targeted complex, i.e., balancing the mutated contents over the input biomarker-verse.
BACKGROUND: Biomarker discovery is a challenging task due to the massive search space. Quantum computing and quantum Artificial Intelligence (quantum AI) can be used to address the computational problem of biomarker discovery from genetic data. METHOD: We propose a Quantum Neural Networks architecture to discover genetic biomarkers for input activation pathways. The Maximum Relevance-Minimum Redundancy criteria score biomarker candidate sets. Our proposed model is economical since the neural solution can be delivered on constrained hardware. RESULTS: We demonstrate the proof of concept on four activation pathways associated with CTLA4, including (1) CTLA4-activation stand-alone, (2) CTLA4-CD8A-CD8B co-activation, (3) CTLA4-CD2 co-activation, and (4) CTLA4-CD2-CD48-CD53-CD58-CD84 co-activation. CONCLUSION: The model indicates new genetic biomarkers associated with the mutational activation of CLTA4-associated pathways, including 20 genes: CLIC4, CPE, ETS2, FAM107A, GPR116, HYOU1, LCN2, MACF1, MT1G, NAPA, NDUFS5, PAK1, PFN1, PGAP3, PPM1G, PSMD8, RNF213, SLC25A3, UBA1, and WLS. We open source the implementation at: https://github.com/namnguyen0510/Biomarker-Discovery-with-Quantum-Neural-Networks .
Biomarkers play a central role in medicine's gradual progress toward proactive, personalized precision diagnostics and interventions. However, finding biomarkers that provide very early indicators of a change in health status, for example, for multifactorial diseases, has been challenging. The discovery of such biomarkers stands to benefit significantly from advanced information processing and means to detect complex correlations, which quantum computing offers. In this perspective, quantum algorithms, particularly in machine learning, are mapped to key applications in biomarker discovery. The opportunities and challenges associated with the algorithms and applications are discussed. The analysis is structured according to different data types-multidimensional, time series, and erroneous data-and covers key data modalities in healthcare-electronic health records, omics, and medical images. An outlook is provided concerning open research challenges.
The convergence of quantum computing and artificial intelligence (AI) presents a paradigm shift in healthcare, revolutionizing complex biological simulations, genomic data processing, and drug discovery innovations. Traditional computational methods, despite their advancements, often struggle with the sheer scale and complexity of biological data, limiting the speed and accuracy of medical breakthroughs. Quantum computing, with its ability to process vast datasets exponentially faster than classical computers, coupled with AI's predictive capabilities, offers a transformative solution for accelerating biomedical research and clinical applications. This paper explores quantum machine learning’s role in optimizing AI-driven molecular dynamics simulations for drug discovery. By leveraging quantum-enhanced algorithms, researchers can rapidly model molecular interactions, analyze drug-receptor binding affinities, and predict pharmacokinetics with unprecedented precision. Additionally, we examine quantum-assisted deep learning models for deciphering intricate biological mechanisms such as protein folding, epigenetic modifications, and metabolic pathway interactions, enabling more accurate predictions of disease progression and therapeutic targets. Furthermore, the integration of AI-quantum hybrid models in clinical diagnostics and imaging analytics is redefining personalized medicine. Quantum-enhanced deep learning facilitates high-resolution medical imaging, real-time anomaly detection, and optimized radiomic feature extraction, leading to early and more accurate disease diagnosis. In genomics, quantum computing significantly accelerates whole-genome sequencing and mutation analysis, paving the way for tailored treatment strategies based on an individual's genetic profile. Despite its promise, challenges such as quantum hardware limitations, data coherence issues, and ethical considerations must be addressed to ensure the practical implementation of quantum-AI healthcare solutions. This paper provides a comprehensive analysis of the potential, challenges, and future directions of quantum-AI synergy in transforming modern healthcare.
With the growing complexity of biomedical data, molecular interactions and genomic architectures, there are significant challenges in adapting traditional healthcare analytics and drug discovery systems to meet computational demands. The paradigm of quantum computing has recently come into the spotlight as a potential method to solve multidimensional optimization, molecular simulation and genomic inference problems using concepts like superposition, entanglement, and quantum parallelism. This chapter examines quantum algorithms and hybrid quantum-classical architectures in the drug discovery, protein folding, genomic analysis, and precision medicine applications. It also explores quantum machine learning algorithms such as VQE, QAOA, QSVM, and QNN, which are used for intelligent biomedical analytics. In addition, the conversation also covers cloud-edge quantum healthcare infrastructures, post-quantum security, and real-world healthcare applications, further demonstrating the potential impact of quantum-enhanced healthcare systems.
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.