DNA microarray technology enables the simultaneous measurement of expression levels of thousands of genes, thereby facilitating the understanding of the molecular mechanisms underlying complex diseases such as brain tumors and the identification of diagnostic genetic signatures. To derive meaningful biological insights from the high-dimensional and complex gene features obtained through this technology and to analyze gene properties in detail, classical AI-based approaches such as machine learning and deep learning are widely employed. However, these methods face various limitations in managing high-dimensional vector spaces and modeling the intricate relationships among genes. In particular, challenges such as hyperparameter tuning, computational costs, and high processing power requirements can hinder their efficiency. To overcome these limitations, quantum computing and quantum AI approaches are gaining increasing attention. Leveraging quantum properties such as superposition and entanglement, quantum methods enable more efficient parallel processing of high-dimensional data and offer faster and more effective solutions to problems that are computationally demanding for classical methods. In this study, a novel model called "Deep VQC" is proposed, based on the Variational Quantum Classifier approach. Developed using microarray data containing 54,676 gene features, the model successfully classified four different types of brain tumors-ependymoma, glioblastoma, medulloblastoma, and pilocytic astrocytoma-alongside healthy samples with high accuracy. Furthermore, compared to classical ML algorithms, our model demonstrated either superior or comparable classification performance. These results highlight the potential of quantum AI methods as an effective and promising approach for the analysis and classification of complex structures such as brain tumors based on gene expression features.

This article focuses on the supervised classification of datasets with a large number of variables and a small number of instances. This is the case, for example, for microarray data sets commonly used in bioinformatics. Complex classifiers that require estimating statistics over many variables are not suitable for this type of data. Probabilistic classifiers with low-order probability tables, e.g. NB and AODE, are good alternatives for dealing with this type of data. AODE usually improves NB in accuracy, but suffers from high spatial complexity since $k$ models, each with $n+1$ variables, are included in the AODE ensemble. In this paper, we propose MiniAnDE, an algorithm that includes only a small number of heterogeneous base classifiers in the ensemble, i.e., each model only includes a different subset of the $k$ predictive variables. Experimental evaluation shows that using MiniAnDE classifiers on microarray data is feasible and outperforms NB and other ensembles such as bagging and random forest.

Subject clustering (i.e., the use of measured features to cluster subjects, such as patients or cells, into multiple groups) is a problem of great interest. In recent years, many approaches were proposed, among which unsupervised deep learning (UDL) has received a great deal of attention. Two interesting questions are (a) how to combine the strengths of UDL and other approaches, and (b) how these approaches compare to one other. We combine Variational Auto-Encoder (VAE), a popular UDL approach, with the recent idea of Influential Feature PCA (IF-PCA), and propose IF-VAE as a new method for subject clustering. We study IF-VAE and compare it with several other methods (including IF-PCA, VAE, Seurat, and SC3) on $10$ gene microarray data sets and $8$ single-cell RNA-seq data sets. We find that IF-VAE significantly improves over VAE, but still underperforms IF-PCA. We also find that IF-PCA is quite competitive, which slightly outperforms Seurat and SC3 over the $8$ single-cell data sets. IF-PCA is conceptually simple and permits delicate analysis. We demonstrate that IF-PCA is capable of achieving the phase transition in a Rare/Weak model. Comparatively, Seurat and SC3 are more complex and theoretically difficult to analyze (for these reasons, their optimality remains unclear).

The most effective dimensionality reduction procedures produce interpretable features from the raw input space while also providing good performance for downstream supervised learning tasks. For many methods, this requires optimizing one or more hyperparameters for a specific task, which can limit generalizability. In this study we propose sparse compressed agglomeration (SparCA), a novel dimensionality reduction procedure that involves a multistep hierarchical feature grouping, compression, and feature selection process. We demonstrate the characteristics and performance of the SparCA method across heterogenous synthetic and real-world datasets, including images, natural language, and single cell gene expression data. Our results show that SparCA is applicable to a wide range of data types, produces highly interpretable features, and shows compelling performance on downstream supervised learning tasks without the need for hyperparameter tuning.

Microarray experiments are capable of measuring the expression level of thousands of genes simultaneously. Dealing with this enormous amount of information requires complex computation. Support Vector Machines (SVM) have been widely used with great efficiency to solve classification problems that have high dimension. In this sense, it is plausible to develop new feature selection strategies for microarray data that are associated with this type of classifier. Therefore, we propose, in this paper, a new method for feature selection based on an ordered search process to explore the space of possible subsets.

Microarray technology is known as one of the most important tools for collecting DNA expression data. This technology allows researchers to investigate and examine types of diseases and their origins. However, microarray data are often associated with challenges such as small sample size, a significant number of genes, imbalanced data, etc. that make classification models inefficient. Thus, a new hybrid solution based on multi-filter and adaptive chaotic multi-objective forest optimization algorithm (AC-MOFOA) is presented to solve the gene selection problem and construct the Ensemble Classifier. In the proposed solution, to reduce the dataset's dimensions, a multi-filter model uses a combination of five filter methods to remove redundant and irrelevant genes. Then, an AC-MOFOA based on the concepts of non-dominated sorting, crowding distance, chaos theory, and adaptive operators is presented. AC-MOFOA as a wrapper method aimed at reducing dataset dimensions, optimizing KELM, and increasing the accuracy of the classification, simultaneously. Next, in this method, an ensemble classifier model is presented using AC-MOFOA results to classify microarray data. The performance of the proposed algorithm was evaluated on nine public microarray datasets, and its results were compared in terms of the number of selected genes, classification efficiency, execution time, time complexity, and hypervolume indicator criterion with five hybrid multi-objective methods. According to the results, the proposed hybrid method could increase the accuracy of the KELM in most datasets by reducing the dataset's dimensions and achieve similar or superior performance compared to other multi-objective methods. Furthermore, the proposed Ensemble Classifier model could provide better classification accuracy and generalizability in microarray data compared to conventional ensemble methods.

Over the past few years, there has been a considerable spread of microarray technology in many biological patterns, particularly in those pertaining to cancer diseases like leukemia, prostate, colon cancer, etc. The primary bottleneck that one experiences in the proper understanding of such datasets lies in their dimensionality, and thus for an efficient and effective means of studying the same, a reduction in their dimension to a large extent is deemed necessary. This study is a bid to suggesting different algorithms and approaches for the reduction of dimensionality of such microarray datasets. This study exploits the matrix-like structure of such microarray data and uses a popular technique called Non-Negative Matrix Factorization (NMF) to reduce the dimensionality, primarily in the field of biological data. Classification accuracies are then compared for these algorithms. This technique gives an accuracy of 98%.

We consider classifiers for high-dimensional data under the strongly spiked eigenvalue (SSE) model. We first show that high-dimensional data often have the SSE model. We consider a distance-based classifier using eigenstructures for the SSE model. We apply the noise reduction methodology to estimation of the eigenvalues and eigenvectors in the SSE model. We create a new distance-based classifier by transforming data from the SSE model to the non-SSE model. We give simulation studies and discuss the performance of the new classifier. Finally, we demonstrate the new classifier by using microarray data sets.

Traditional medicine typically applies one-size-fits-all treatment for the entire patient population whereas precision medicine develops tailored treatment schemes for different patient subgroups. The fact that some factors may be more significant for a specific patient subgroup motivates clinicians and medical researchers to develop new approaches to subgroup detection and analysis, which is an effective strategy to personalize treatment. In this study, we propose a novel patient subgroup detection method, called Supervised Biclustring (SUBIC) using convex optimization and apply our approach to detect patient subgroups and prioritize risk factors for hypertension (HTN) in a vulnerable demographic subgroup (African-American). Our approach not only finds patient subgroups with guidance of a clinically relevant target variable but also identifies and prioritizes risk factors by pursuing sparsity of the input variables and encouraging similarity among the input variables and between the input and target variables

The bioinformatics is an interdisciplinary area of study where one of the objectives is to deal with the analysis and interpretation of large sets of data generated from various large-scale biological experiments. The example of one such large-scale biological experiment is measuring the expression levels of tens of thousands of genes simultaneously under some environmental condition. Microarray is one of the essential technologies used by the biologist to measure genome-wide expression levels of genes in a particular organism. As microarrays technologies have become more prevalent, the challenges 1 associated with collecting, managing, and analyzing the data from each experiment have essentially increased. Robust laboratory protocols, improved understanding of the complex experimental design and falling prices of commercial platforms, all these have combined to drive the field to more complex experiments, generating huge amounts of data (Brazma and Vilo, 2000).