The ability to accurately classify disease subtypes is of vital importance, especially in oncology where this capability could have a life saving impact. Here we report a classification between two subtypes of non-small cell lung cancer, namely Adeno- carcinoma vs Squamous cell carcinoma. The data consists of approximately 20,000 gene expression values for each of 104 patients. The data was curated from [1] [2]. We used an amalgamation of classical and and quantum machine learning models to successfully classify these patients. We utilized feature selection methods based on univariate statistics in addition to XGBoost [3]. A novel and proprietary data representation method developed by one of the authors called QCrush was also used as it was designed to incorporate a maximal amount of information under the size constraints of the D-Wave quantum annealing computer. The machine learning was performed by a Quantum Boltzmann Machine. This paper will report our results, the various classical methods, and the quantum machine learning approach we utilized.
The ability to accurately classify disease subtypes is of vital importance, especially in oncology where this capability could have a life saving impact. Here we report a classification between two subtypes of non-small cell lung cancer, namely Adeno- carcinoma vs Squamous cell carcinoma. The data consists of approximately 20,000 gene expression values for each of 104 patients. The data was curated from [1] [2]. We used an amalgamation of classical and and quantum machine learning models to successfully classify these patients. We utilized feature selection methods based on univariate statistics in addition to XGBoost [3]. A novel and proprietary data representation method developed by one of the authors called QCrush was also used as it was designed to incorporate a maximal amount of information under the size constraints of the D-Wave quantum annealing computer. The machine learning was performed by a Quantum Boltzmann Machine. This paper will report our results, the various classical methods, and the quantum machine learning approach we utilized.
Quantum machine learning offers a promising new paradigm for computational biology by leveraging quantum mechanical principles to enhance cancer classification, biomarker discovery, and bioinformatics diagnostics. In this study, we apply QML to identify subtype specific biomarkers for lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), the two predominant forms of non-small cell lung cancer. Our methodology involves a two-phase process: in Phase 1, differential expression analysis and methylation analysis between tumor and normal samples allows us to identify LUAD-specific and LUSC-specific genes, revealing potential prognostic biomarkers for cancer subtypes. Phase 2 focuses on developing a quantum classifier capable of distinguishing between LUAD and LUSC tumors, as well as between tumor and normal samples. This classifier not only enhances diagnostic precision but also demonstrates the quantum advantage in processing large-scale multiomic datasets. Our results consistently demonstrated that Sample3, representing the combined gene set, achieved the highest overall predictive performance in all metrics. These results demonstrate that QML provides an effective and scalable approach for biomarker discovery and subtype specific cancer classification. GO enrichment analysis highlighted the significant involvement of genes in synaptic signaling, ion channel regulation, and neuronal development. In the quantum phase, KEGG analysis further identified enrichment in cancer-associated pathways, including neurotrophin, MAPK, Ras, and PI3KAkt signaling, with key genes such as NGFR, NTRK2, and NTF3 suggesting a central role in neurotrophinmediated oncogenic processes. Our findings highlight the growing potential of quantum computing to advance precision oncology and next-generation biomedical analytics.
Subtyping of lung cancer is crucial for individualized treatment and optimizing outcomes. Computational modeling allows data analysis over large scales, which helps in making precision classification in large datasets or high-dimensional datasets. Conventional machine learning methods perform well, but integration of multi-omic data (DNA, RNA, miRNA) is challenging in cancer subtyping because of high dimensionality and complex inter-omic relationships. To bypass this Quantum machine learning (QML) provides better ability to navigate high-dimensional biological data with many variables using quantum computational concepts that can identify fine patterns or small-scale patterns beyond the capability of classical approaches. Through the integration of quantum computing principles with the machine learning framework, the study highlights the improvement of computer technology. The framework shows how the system is optimized with the help of quantum principles, how it can improve accuracy, parallel processing and reducing latency. In this work, we have combined data on miRNA, RNA expression, and DNA methylation to create a complete workflow for classifying cancer. This method uses a wide variety of feature selection techniques, such as random forest-based selection, chi-square, mutual information(MI), and principal component analysis(PCA).In order to illustrate the notion of quantum advantage, we carefully compare the performance metrics of the Quantum Support Vector Classifier (QSVC) to the classical Support Vector Machine (SVM), using a ZZ feature map quantum kernel as our baseline for analysis. Using five-fold crossvalidation, we have also verified that the quantum has an advantage with consistently lower variance and higher accuracy.
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.
Abstract Quantum machine learning algorithms using the power of quantum computing provide fast- developing approaches for solving complicated problems and speeding-up calculations for big data. As such, they could effectively operate better than the classical algorithms. Herein, we demonstrate for the first time the classification of eleven cancers based on the gene expression values with 4495 samples using quantum machine learning. In addition, we compare the obtained quantum classification results with the classical outcomes. By implementing a dimensional reduction method, we introduce significant biomarkers for each cancer. In this research, we express that some of the identified gene biomarkers are consistent with DNA promotor methylation, and some other ones can be applied for the survival determination of patients.
Early diagnosis of lung cancer and reliable decision support are crucial steps since this is a leading cause of cancer-related mortality worldwide. This research aims to build an approach using quantum-assisted capacity that can infer lung cancer from a limited amount of patient data. To do so, this research starts with a dataset containing 309 patient records, which is augmented and balanced to 540 patient records. This dataset has 16 attributes of symptom and risk-based lung cancer factors. Following preprocessing on the dataset, this study uses a quantum method named quadratic unconstrained binary optimization (QUBO) to select the relevant features of the dataset. Three classifiers, quantum support vector machine (QSVM), quantum k-nearest neighbor (QKNN), and quantum boosting (QBoost), are then trained and tested on the processed dataset to identify lung cancer. These classifiers are examined using different frameworks of circuit and annealing-based quantum techniques. Only 108 balance samples are used during training the classifiers to ensure the learning capability of the quantum method from limited data. To safeguard against overfitting and underfitting due to a lack of data, the remaining 432 samples are evaluated to estimate prediction error. All experiments are done using cross-validation. The final results demonstrate that the QSVM by D-Wave framework achieves the best performance with an accuracy of 94.31% in simulation and 91.90% in a real D-Wave quantum computer. The findings of this work show a path for applying quantum computing to support healthcare decision-making when data availability is often limited.
Quantum machine learning (QML) combines quantum computing with machine learning, offering potential for solving intricate problems. Our research delves into QML's application in identifying gene expression biomarkers for clear cell renal cell carcinoma (ccRCC) metastasis. ccRCC, the primary renal cancer subtype, poses significant challenges due to its high lethality and complex metastasis process. Despite extensive research, understanding the mechanisms of cancer cell dissemination and establishment in distant sites remains elusive. Identifying metastasis biomarkers is a daunting task in machine learning. Our study addresses the need for improved execution time and accuracy in QSVC and QNN algorithms compared to SVC and NN for binary classification. Drawing inspiration from the Neural Quantum Embedding (NQE) method, we propose a two-stage approach for the binary classification problem. We aim to assess if integrating NQE with QSVC/QNN enhances performance compared to NQE with SVC/NN across diverse biomedical datasets, demonstrating the effectiveness and generalizability of the approach.