Gene selection for microarray data classification via adaptive hypergraph embedded dictionary learning

A New Filter Approach Based on Effective Ranges for Classification of Gene Expression Data

Over the years, many studies have been carried out to reduce and eliminate the effects of diseases on human health. Gene expression data sets play a critical role in diagnosing and treating diseases. These data sets consist of thousands of genes and a small number of sample sizes. This situation creates the curse of dimensionality and it becomes problematic to analyze such data sets. One of the most effective strategies to solve this problem is feature selection methods. Feature selection is a preprocessing step to improve classification performance by selecting the most relevant and informative features while increasing the accuracy of classification. In this article, we propose a new statistically based filter method for the feature selection approach named Effective Range-based Feature Selection Algorithm (FSAER). As an extension of the previous Effective Range based Gene Selection (ERGS) and Improved Feature Selection based on Effective Range (IFSER) algorithms, our novel method includes the advantages of both methods while taking into account the disjoint area. To illustrate the efficacy of the proposed algorithm, the experiments have been conducted on six benchmark gene expression data sets. The results of the FSAER and the other filter methods have been compared in terms of classification accuracies to demonstrate the effectiveness of the proposed method. For classification methods, support vector machines, naive Bayes classifier, and k-nearest neighbor algorithms have been used.

Diagnosis of Alzheimer's disease using hypergraph p-Laplacian regularized multi-task feature learning

Multimodal data-based classification methods have been widely used in the diagnosis of Alzheimer's disease (AD) and have achieved better performance than single-modal-based methods. However, most classification methods based on multimodal data tend to consider only the correlation between different modal data and ignore the inherent non-linear higher-order relationships between similar data, which can improve the robustness of the model. Therefore, this study proposes a hypergraph p-Laplacian regularized multi-task feature selection (HpMTFS) method for AD classification. Specifically, feature selection for each modal data is considered as a distinct task and the common features of multimodal data are extracted jointly by group-sparsity regularizer. In particular, two regularization terms are introduced in this study, namely (1) a hypergraph p-Laplacian regularization term to retain higher-order structural information for similar data, and (2) a Frobenius norm regularization term to improve the noise immunity of the model. Finally, using a multi-kernel support vector machine to fuse multimodal features and perform the final classification. We used baseline sMRI, FDG-PET, and AV-45 PET imaging data from 528 subjects in the Alzheimer's Disease Neuroimaging Initiative (ADNI) to evaluate our approach. Experimental results show that our HpMTFS method outperforms existing multimodal-based classification methods.

Graph-based relevancy-redundancy gene selection method for cancer diagnosis

Nowadays, microarray data processing is one of the most important applications in molecular biology for cancer diagnosis. A major task in microarray data processing is gene selection, which aims to find a subset of genes with the least inner similarity and most relevant to the target class. Removing unnecessary, redundant, or noisy data reduces the data dimensionality. This research advocates a graph theoretic-based gene selection method for cancer diagnosis. Both unsupervised and supervised modes use well-known and successful social network approaches such as the maximum weighted clique criterion and edge centrality to rank genes. The suggested technique has two goals: (i) to maximize the relevancy of the chosen genes with the target class and (ii) to reduce their inner redundancy. A maximum weighted clique is chosen in a repetitive way in each iteration of this procedure. The appropriate genes are then chosen from among the existing features in this maximum clique using edge centrality and gene relevance. In the experiment, several datasets consisting of Colon, Leukemia, SRBCT, Prostate Tumor, and Lung Cancer, with different properties, are used to demonstrate the efficacy of the developed model. Our performance is compared to that of renowned filter-based gene selection approaches for cancer diagnosis whose results demonstrate a clear superiority.

Hypergraph Learning: Methods and Practices

Hypergraph learning is a technique for conducting learning on a hypergraph structure. In recent years, hypergraph learning has attracted increasing attention due to its flexibility and capability in modeling complex data correlation. In this paper, we first systematically review existing literature regarding hypergraph generation, including distance-based, representation-based, attribute-based, and network-based approaches. Then, we introduce the existing learning methods on a hypergraph, including transductive hypergraph learning, inductive hypergraph learning, hypergraph structure updating, and multi-modal hypergraph learning. After that, we present a tensor-based dynamic hypergraph representation and learning framework that can effectively describe high-order correlation in a hypergraph. To study the effectiveness and efficiency of hypergraph generation and learning methods, we conduct comprehensive evaluations on several typical applications, including object and action recognition, Microblog sentiment prediction, and clustering. In addition, we contribute a hypergraph learning development toolkit called THU-HyperG.

Gene selection for microarray data classification via multi-objective graph theoretic-based method

In recent decades, the improvement of computer technology has increased the growth of high-dimensional microarray data. Thus, data mining methods for DNA microarray data classification usually involve samples consisting of thousands of genes. One of the efficient strategies to solve this problem is gene selection, which improves the accuracy of microarray data classification and also decreases computational complexity. In this paper, a novel social network analysis-based gene selection approach is proposed. The proposed method has two main objectives of the relevance maximization and redundancy minimization of the selected genes. In this method, on each iteration, a maximum community is selected repetitively. Then among the existing genes in this community, the appropriate genes are selected by using the node centrality-based criterion. The reported results indicate that the developed gene selection algorithm while increasing the classification accuracy of microarray data, will also decrease the time complexity.

A novel explainable COVID-19 diagnosis method by integration of feature selection with random forest

Several Artificial Intelligence-based models have been developed for COVID-19 disease diagnosis. In spite of the promise of artificial intelligence, there are very few models which bridge the gap between traditional human-centered diagnosis and the potential future of machine-centered disease diagnosis. Under the concept of human-computer interaction design, this study proposes a new explainable artificial intelligence method that exploits graph analysis for feature visualization and optimization for the purpose of COVID-19 diagnosis from blood test samples. In this developed model, an explainable decision forest classifier is employed to COVID-19 classification based on routinely available patient blood test data. The approach enables the clinician to use the decision tree and feature visualization to guide the explainability and interpretability of the prediction model. By utilizing this novel feature selection phase, the proposed diagnosis model will not only improve diagnosis accuracy but decrease the execution time as well.

Gene Correlation Guided Gene Selection for Microarray Data Classification

The microarray cancer data obtained by DNA microarray technology play an important role for cancer prevention, diagnosis, and treatment. However, predicting the different types of tumors is a challenging task since the sample size in microarray data is often small but the dimensionality is very high. Gene selection, which is an effective means, is aimed at mitigating the curse of dimensionality problem and can boost the classification accuracy of microarray data. However, many of previous gene selection methods focus on model design, but neglect the correlation between different genes. In this paper, we introduce a novel unsupervised gene selection method by taking the gene correlation into consideration, named gene correlation guided gene selection (G³CS). Specifically, we calculate the covariance of different gene dimension pairs and embed it into our unsupervised gene selection model to regularize the gene selection coefficient matrix. In such a manner, redundant genes can be effectively excluded. In addition, we utilize a matrix factorization term to exploit the cluster structure of original microarray data to assist the learning process. We design an iterative updating algorithm with convergence guarantee to solve the resultant optimization problem. Experimental results on six publicly available microarray datasets are conducted to validate the efficacy of our proposed method.

CLASSIFICATION OF HEALTHY PEOPLE AND PD PATIENTS USING TAKAGI–SUGENO FUZZY MODEL-BASED INSTANCE SELECTION AND WAVELET TRANSFORMS

In this study, a new instance selection method that combines the neural network with weighted fuzzy memberships (NEWFM) and Takagi–Sugeno (T–S) fuzzy model was proposed to improve the classification accuracy of healthy people and Parkinson’s disease (PD) patients. In order to evaluate the proposed instance selection for the classification accuracy of healthy people and PD patients, foot pressure data were collected from healthy people and PD patients as experimental data. This study uses wavelet transforms (WTs) to remove the noise from the foot pressure data in preprocessing step. The proposed instance selection method is an algorithm that selects instances using both weighted mean defuzzification (WMD) in the T–S fuzzy model and the confidence interval of a normal distribution used in statistics. The classification accuracy was compared before and after instance selection was applied to prove the superiority of instance selection. Classification accuracy before and after instance selection was 77.33% and 78.19%, respectively. The classification accuracy after instance selection exhibited a higher classification accuracy than that before instance selection by 0.86%. Further, McNemar’s test, which is used in statistics, was employed to show the difference in classification accuracy before and after instance selection was applied. The results of the McNemar’s test revealed that the probability of significance was smaller than 0.05, which reaffirmed that the classification accuracy was better when instance selection was applied than when instance selection was not applied. NEWFM includes the bounded sum of weighted fuzzy memberships (BSWFMs) that can easily show the differences in the graphically distinct characteristics between healthy people and PD patients. This study proposes new technique that NEWFM can detect PD patients from foot pressure data by the BSWFMs embedded in devices or systems.