Feature selection is a machine learning technique for identifying relevant variables in classification and regression models. In single-cell RNA sequencing (scRNA-seq) data analysis, feature selection is used to identify relevant genes that are crucial for understanding cellular processes. Traditional feature selection methods often struggle with the complexity of scRNA-seq data and suffer from interpretation difficulties. Quantum annealing presents a promising alternative approach. In this study, we implement quantum annealing-empowered quadratic unconstrained binary optimization (QUBO) for feature selection in scRNA-seq data. Using data from a human cell differentiation system and an anticancer drug resistance study, we demonstrate that QUBO feature selection effectively identifies genes whose expression patterns reflect critical cell state transitions associated with differentiation and drug resistance development. Our findings indicate that quantum annealing-powered QUBO reveals complex gene expression patterns potentially missed by traditional methods, thereby enhancing scRNA-seq data analysis and interpretation.
Feature selection is a machine learning technique for identifying relevant variables in classification and regression models. In single-cell RNA sequencing (scRNA-seq) data analysis, feature selection is used to identify relevant genes that are crucial for understanding cellular processes. Traditional feature selection methods often struggle with the complexity of scRNA-seq data and suffer from interpretation difficulties. Quantum annealing presents a promising alternative approach. In this study, we implement quantum annealing-empowered quadratic unconstrained binary optimization (QUBO) for feature selection in scRNA-seq data. Using data from a human cell differentiation system and an anticancer drug resistance study, we demonstrate that QUBO feature selection effectively identifies genes whose expression patterns reflect critical cell state transitions associated with differentiation and drug resistance development. Our findings indicate that quantum annealing-powered QUBO reveals complex gene expression patterns potentially missed by traditional methods, thereby enhancing scRNA-seq data analysis and interpretation.
Cluster analysis is a crucial stage in the analysis and interpretation of single-cell gene expression (scRNA-seq) data. It is an inherently ill-posed problem whose solutions depend heavily on hyper-parameter and algorithmic choice. The popular approach of K-means clustering, for example, depends heavily on the choice of K and the convergence of the expectation-maximization algorithm to local minima of the objective. Exhaustive search of the space for multiple good quality solutions is known to be a complex problem. Here, we show that quantum computing offers a solution to exploring the cost function of clustering by quantum annealing, implemented on a quantum computing facility offered by D-Wave [1]. Out formulation extracts minimum vertex cover of an affinity graph to sub-sample the cell population and quantum annealing to optimise the cost function. A distribution of low-energy solutions can thus be extracted, offering alternate hypotheses about how genes group together in their space of expressions.
Feature selection is crucial for enhancing the accuracy and efficiency of machine learning (ML) models. This work investigates the utility of quantum annealing for the feature selection process in an ML-pipeline, used for maximizing the mutual information (MI) or conditional mutual information (CMI) of the underlying feature space. Calculating the optimal set of features that maximize the MI or CMI is computationally intractable for large datasets on classical computers, even with approximative methods. This study employs a Mutual Information Quadratic Unconstrained Binary Optimization (MIQUBO) formulation, enabling its solution on a quantum annealer. We demonstrate the capability of this approach to identify the best feature combinations that maximize the MI or CMI. To showcase its real-world applicability, we solve the MIQUBO problem to forecast the prices of used excavators. Our results demonstrate that for datasets with a small MI concentration the MIQUBO approach can provide a significant improvement over MI-only based approaches, dependent on the dimension of the selected feature space.
This paper explores the applications of quantum annealing (QA) and classical simulated annealing (SA) to a suite of combinatorial optimization problems in machine learning, namely feature selection, instance selection, and clustering. We formulate each task as a Quadratic Unconstrained Binary Optimization (QUBO) problem and implement both quantum and classical solvers to compare their effectiveness. For feature selection, we propose several QUBO configurations that balance feature importance and redundancy, showing that quantum annealing (QA) produces solutions that are computationally more efficient. In instance selection, we propose a few novel heuristics for instance-level importance measures that extend existing methods. For clustering, we embed a classical-to-quantum pipeline, using classical clustering followed by QUBO-based medoid refinement, and demonstrate consistent improvements in cluster compactness and retrieval metrics. Our results suggest that QA can be a competitive and efficient tool for discrete machine learning optimization, even within the constraints of current quantum hardware.
Feature selection is crucial for enhancing the accuracy and efficiency of machine learning models. This work investigates the possibility of the usefulness of a quantum annealer to tackle the challenge of selecting features based on maximizing mutual information (MI) and conditional mutual information (CMI). Calculating the optimal feature set for maximum MI and CMI remains computationally intractable for large datasets on classical computers, even with approximation methods. This study employs a Mutual Information Quadratic Unconstrained Binary Optimization (MIQUBO) formulation, enabling its solution on a quantum annealer. Importantly, the study demonstrates the relevancy of this approach in identifying the best feature combinations that maximizes the MI and CMI. To showcase its real-world applicability, we apply MIQUBO to forecasting the price of used excavators. Our results demonstrate that using the MIQUBO approach there is an improvement in the prediction of machine learning models for datasets, with a smaller MI concentration on a subset of all features. • Problem Addressed: We tackle the computationally difficult problem of feature selection for machine learning models, specifically by maximizing mutual information (MI) and conditional mutual information (CMI) between features and the target variable. • Proposed Solution: We employ the adiabatic quantum computation paradigm to tackle this problem. The study utilizes a hybrid annealing approach, specifically the D-Wave Kerberos framework, which combines classical and quantum algorithms to solve the complex optimization problem. The feature selection task is reformulated as a Mutual Information Quadratic Unconstrained Binary Optimization (MIQUBO) problem, which can be solved on a quantum annealer. • Real-World Application: The MIQUBO method is applied to a practical, real-world scenario: forecasting the prices of used excavators. • Key Findings: The research demonstrates that using the MIQUBO approach leads to an improvement in the prediction performance of machine learning models. This is particularly true for datasets where the mutual information is less concentrated on a small subset of features.
The rapid explosion of medical image data poses a significant challenge to reliable disease Classification with high-dimensional feature spaces and intricate inter-feature correlations. In this paper, a new quantum annealing-inspired framework for optimal feature subset selection, specifically tailored to improve medical image Classification. In contrast to traditional filter, wrapper, or embedded techniques that tend to ignore redundancy and feature interactions, our solution poses feature selection as a Quadratic Unconstrained Binary Optimization (QUBO) problem and solves it effectively using D-Wave quantum annealer hardware. The presented approach makes three primary contributions: (i) a QUBO formulation that captures feature importance, redundancy suppression, and interaction synergy simultaneously, (ii) a hybrid quantum-classical pipeline with embedding, decomposition, and chain strength optimization for efficient execution on existing quantum hardware, and (iii) a comprehensive evaluation on three heterogeneous medical imaging datasets—diabetic retinopathy, breast cancer histopathology, and chest X-ray pneumonia. Experimental findings exhibit uniform improvements in Classification performance (up to 12.1%), drastic feature reduction (65–80%), and much reduced computational time over six state-of-the-art classical approaches. With the exposure of clinically relevant features and robust statistical significance across benchmarks, our approach places quantum annealing as an influential and scalable tool for future medical AI applications.
Abstract In machine learning, fewer features reduce model complexity. Carefully assessing the influence of each input feature on the model quality is therefore a crucial preprocessing step. We propose a novel feature selection algorithm based on a quadratic unconstrained binary optimization (QUBO) problem, which allows to select a specified number of features based on their importance and redundancy. In contrast to iterative or greedy methods, our direct approach yields higher-quality solutions. QUBO problems are particularly interesting because they can be solved on quantum hardware. To evaluate our proposed algorithm, we conduct a series of numerical experiments using a classical computer, a quantum gate computer, and a quantum annealer. Our evaluation compares our method to a range of standard methods on various benchmark data sets. We observe competitive performance.