Hybrid black widow optimization with iterated greedy algorithm for gene selection problems

Gene Selection (GS) is a strategy method targeted at reducing redundancy, limited expressiveness, and low informativeness in gene expression datasets obtained by DNA Microarray technology. These datasets contain a plethora of diverse and high-dimensional samples and genes, with a significant discrepancy in the number of samples and genes present. The complexities of GS are especially noticeable in the context of microarray expression data analysis, owing to the inherent data imbalance. The main goal of this study is to offer a simplified and computationally effective approach to dealing with the conundrum of attribute selection in microarray gene expression data. We use the Black Widow Optimization algorithm (BWO) in the context of GS to achieve this, using two unique methodologies: the unaltered BWO variation and the hybridized BWO variant combined with the Iterated Greedy algorithm (BWO-IG). By improving the local search capabilities of BWO, this hybridization attempts to promote more efficient gene selection. A series of tests was carried out using nine benchmark datasets that were obtained from the gene expression data repository in the pursuit of empirical validation. The results of these tests conclusively show that the BWO-IG technique performs better than the traditional BWO algorithm. Notably, the hybridized BWO-IG technique excels in the efficiency of local searches, making it easier to identify relevant genes and producing findings with higher levels of reliability in terms of accuracy and the degree of gene pruning. Additionally, a comparison analysis is done against five modern wrapper Feature Selection (FS) methodologies, namely BIMFOHHO, BMFO, BHHO, BCS, and BBA, in order to put the suggested BWO-IG method's effectiveness into context. The comparison that follows highlights BWO-IG's obvious superiority in reducing the number of selected genes while also obtaining remarkably high classification accuracy. The key findings were an average classification accuracy of 94.426, average fitness values of 0.061, and an average number of selected genes of 2933.767.

A survey on binary metaheuristic algorithms and their engineering applications

This article presents a comprehensively state-of-the-art investigation of the engineering applications utilized by binary metaheuristic algorithms. Surveyed work is categorized based on application scenarios and solution encoding, and describes these algorithms in detail to help researchers choose appropriate methods to solve related applications. It is seen that transfer function is the main binary coding of metaheuristic algorithms, which usually adopts Sigmoid function. Among the contributions presented, there were different implementations and applications of metaheuristic algorithms, or the study of engineering applications by different objective functions such as the single- and multi-objective problems of feature selection, scheduling, layout and engineering structure optimization. The article identifies current troubles and challenges by the conducted review, and discusses that novel binary algorithm, transfer function, benchmark function, time-consuming problem and application integration are need to be resolved in future.

Constructing Features Using a Hybrid Genetic Algorithm

A hybrid procedure that incorporates grammatical evolution and a weight decaying technique is proposed here for various classification and regression problems. The proposed method has two main phases: the creation of features and the evaluation of these features. During the first phase, using grammatical evolution, new features are created as non-linear combinations of the original features of the datasets. In the second phase, based on the characteristics of the first phase, the original dataset is modified and a neural network trained with a genetic algorithm is applied to this dataset. The proposed method was applied to an extremely wide set of datasets from the relevant literature and the experimental results were compared with four other techniques.

Modified BBO-Based Multivariate Time-Series Prediction System With Feature Subset Selection and Model Parameter Optimization

Multivariate time-series prediction is a challenging research topic in the field of time-series analysis and modeling, and is continually under research. The echo state network (ESN), a type of efficient recurrent neural network, has been widely used in time-series prediction, but when using ESN, two crucial problems have to be confronted: 1) how to select the optimal subset of input features and 2) how to set the suitable parameters of the model. To solve this problem, the modified biogeography-based optimization ESN (MBBO-ESN) system is proposed for system modeling and multivariate time-series prediction, which can simultaneously achieve feature subset selection and model parameter optimization. The proposed MBBO algorithm is an improved evolutionary algorithm based on biogeography-based optimization (BBO), which utilizes an S -type population migration rate model, a covariance matrix migration strategy, and a Lévy distribution mutation strategy to enhance the rotation invariance and exploration ability. Furthermore, the MBBO algorithm cannot only optimize the key parameters of the ESN model but also uses a hybrid-metric feature selection method to remove the redundancies and distinguish the importance of the input features. Compared with the traditional methods, the proposed MBBO-ESN system can discover the relationship between the input features and the model parameters automatically and make the prediction more accurate. The experimental results on the benchmark and real-world datasets demonstrate that MBBO outperforms the other traditional evolutionary algorithms, and the MBBO-ESN system is more competitive in multivariate time-series prediction than other classic machine-learning models.

Evolving Multiobjective Cancer Subtype Diagnosis From Cancer Gene Expression Data

Detection and diagnosis of cancer are especially essential for early prevention and effective treatments. Many studies have been proposed to tackle the subtype diagnosis problems with those data, which often suffer from low diagnostic ability and bad generalization. This article studies a multiobjective PSO-based hybrid algorithm (MOPSOHA) to optimize four objectives including the number of features, the accuracy, and two entropy-based measures: the relevance and the redundancy simultaneously, diagnosing the cancer data with high classification power and robustness. First, we propose a novel binary encoding strategy to choose informative gene subsets to optimize those objective functions. Second, a mutation operator is designed to enhance the exploration capability of the swarm. Finally, a local search method based on the "best/1" mutation operator of differential evolutionary algorithm (DE) is employed to exploit the neighborhood area with sparse high-quality solutions since the base vector always approaches to some good promising areas. In order to demonstrate the effectiveness of MOPSOHA, it is tested on 41 cancer datasets including thirty-five cancer gene expression datasets and six independent disease datasets. Compared MOPSOHA with other state-of-the-art algorithms, the performance of MOPSOHA is superior to other algorithms in most of the benchmark datasets.

Comparison Analysis of Gene Expression Profiles Proximity Metrics

The problems of gene regulatory network (GRN) reconstruction and the creation of disease diagnostic effective systems based on genes expression data are some of the current directions of modern bioinformatics. In this manuscript, we present the results of the research focused on the evaluation of the effectiveness of the most used metrics to estimate the gene expression profiles’ proximity, which can be used to extract the groups of informative gene expression profiles while taking into account the states of the investigated samples. Symmetry is very important in the field of both genes’ and/or proteins’ interaction since it undergirds essentially all interactions between molecular components in the GRN and extraction of gene expression profiles, which allows us to identify how the investigated biological objects (disease, state of patients, etc.) contribute to the further reconstruction of GRN in terms of both the symmetry and understanding the mechanism of molecular element interaction in a biological organism. Within the framework of our research, we have investigated the following metrics: Mutual information maximization (MIM) using various methods of Shannon entropy calculation, Pearson’s χ2 test and correlation distance. The accuracy of the investigated samples classification was used as the main quality criterion to evaluate the appropriate metric effectiveness. The random forest classifier (RF) was used during the simulation process. The research results have shown that results of the use of various methods of Shannon entropy within the framework of the MIM metric disagree with each other. As a result, we have proposed the modified mutual information maximization (MMIM) proximity metric based on the joint use of various methods of Shannon entropy calculation and the Harrington desirability function. The results of the simulation have also shown that the correlation proximity metric is less effective in comparison to both the MMIM metric and Pearson’s χ2 test. Finally, we propose the hybrid proximity metric (HPM) that considers both the MMIM metric and Pearson’s χ2 test. The proposed metric was investigated within the framework of one-cluster structure effectiveness evaluation. To our mind, the main benefit of the proposed HPM is in increasing the objectivity of mutually similar gene expression profiles extraction due to the joint use of the various effective proximity metrics that can contradict with each other when they are used alone.

A novel bio-inspired hybrid multi-filter wrapper gene selection method with ensemble classifier for microarray data

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 a small sample size, a significant number of genes, imbalanced data, etc., making classification models inefficient. Thus, a new hybrid solution based on a 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, a multi-filter model (i.e., ensemble filter) is proposed as preprocessing step to reduce the dataset's dimensions, using a combination of five filter methods to remove redundant and irrelevant genes. Accordingly, the results of the five filter methods are combined using a voting-based function. Additionally, the results of the proposed multi-filter indicate that it has good capability in reducing the gene subset size and selecting relevant 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, hypervolume indicator, and spacing metric with five hybrid multi-objective methods, and three hybrid single-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 the seven of nine microarray datasets compared to conventional ensemble methods. Moreover, the comparison results of the Ensemble Classifier model with three state-of-the-art ensemble generation methods indicate its competitive performance in which the proposed ensemble model achieved better results in the five of nine datasets.

Modified chemical reaction optimization and its application in engineering problems

Chemical Reaction Optimization (CRO) is a simple and efficient evolutionary optimization algorithm by simulating chemical reactions. As far as the current research is concerned, the algorithm has been successfully used for solving a number of real-world optimization tasks. In our paper, a new real encoded chemical reaction optimization algorithm is proposed to boost the efficiency of the optimization operations in standard chemical reactions optimization algorithm. Inspired by the evolutionary operation of the differential evolution algorithm, an improved search operation mechanism is proposed based on the underlying operation. It is modeled to further explore the search space of the algorithm under the best individuals. Afterwards, to control the perturbation frequency of the search strategy, the modification rate is increased to balance between the exploration ability and mining ability of the algorithm. Meanwhile, we also propose a new population initialization method that incorporates several models to produce high-quality initialized populations. To validate the effectiveness of the algorithm, nine unconstrained optimization algorithms are used as benchmark functions. As observed from the experimental results, it is evident that the proposed algorithm is significantly better than the standard chemical reaction algorithm and other evolutionary optimization algorithms. Then, we also apply the proposed model to address the synthesis problem of two antenna array synthesis. The results also reveal that the proposed algorithm is superior to other approaches from different perspectives.

CLGBO: An Algorithm for Constructing Highly Robust Coding Sets for DNA Storage

In the era of big data, new storage media are urgently needed because the storage capacity for global data cannot meet the exponential growth of information. Deoxyribonucleic acid (DNA) storage, where primer and address sequences play a crucial role, is one of the most promising storage media because of its high density, large capacity and durability. In this study, we describe an enhanced gradient-based optimizer that includes the Cauchy and Levy mutation strategy (CLGBO) to construct DNA coding sets, which are used as primer and address libraries. Our experimental results show that the lower bounds of DNA storage coding sets obtained using the CLGBO algorithm are increased by 4.3–13.5% compared with previous work. The non-adjacent subsequence constraint was introduced to reduce the error rate in the storage process. This helps to resolve the problem that arises when consecutive repetitive subsequences in the sequence cause errors in DNA storage. We made use of the CLGBO algorithm and the non-adjacent subsequence constraint to construct larger and more highly robust coding sets.

Deep embedded clustering with multiple objectives on scRNA-seq data

In recent years, single-cell RNA sequencing (scRNA-seq) technologies have been widely adopted to interrogate gene expression of individual cells; it brings opportunities to understand the underlying processes in a high-throughput manner. Deep embedded clustering (DEC) was demonstrated successful in high-dimensional sparse scRNA-seq data by joint feature learning and cluster assignment for identifying cell types simultaneously. However, the deep network architecture for embedding clustering is not trivial to optimize. Therefore, we propose an evolutionary multiobjective DEC by synergizing the multiobjective evolutionary optimization to simultaneously evolve the hyperparameters and architectures of DEC in an automatic manner. Firstly, a denoising autoencoder is integrated into the DEC to project the high-dimensional sparse scRNA-seq data into a low-dimensional space. After that, to guide the evolution, three objective functions are formulated to balance the model's generality and clustering performance for robustness. Meanwhile, migration and mutation operators are proposed to optimize the objective functions to select the suitable hyperparameters and architectures of DEC in the multiobjective framework. Multiple comparison analyses are conducted on twenty synthetic data and eight real data from different representative single-cell sequencing platforms to validate the effectiveness. The experimental results reveal that the proposed algorithm outperforms other state-of-the-art clustering methods under different metrics. Meanwhile, marker genes identification, gene ontology enrichment and pathology analysis are conducted to reveal novel insights into the cell type identification and characterization mechanisms.

Multi-variant differential evolution algorithm for feature selection

This work introduces a new population-based stochastic search technique, named multi-variant differential evolution (MVDE) algorithm for solving fifteen well-known real world problems from UCI repository and compared to four popular optimization methods. The MVDE proposes a new self-adaptive scaling factor based on cosine and logistic distributions as an almost factor-free optimization technique. For more updated chances, this factor is binary-mapped by incorporating an adaptive crossover operator. During the evolution, both greedy and less-greedy variants are managed by adjusting and incorporating the binary scaling factor and elite identification mechanism into a new multi-mutation crossover process through a number of sequentially evolutionary phases. Feature selection decreases the number of features by eliminating irrelevant or misleading, noisy and redundant data which can accelerate the process of classification. In this paper, a new feature selection algorithm based on the MVDE method and artificial neural network is presented which enabled MVDE to get a combination features’ set, accelerate the accuracy of the classification, and optimize both the structure and weights of Artificial Neural Network (ANN) simultaneously. The experimental results show the encouraging behavior of the proposed algorithm in terms of the classification accuracies and optimal number of feature selection.

A Distributed Feature Selection Algorithm Based on Distance Correlation with an Application to Microarrays

DNA microarray datasets are characterized by a large number of features with very few samples, which is a typical cause of overfitting and poor generalization in the classification task. Here, we introduce a novel feature selection (FS) approach which employs the distance correlation (dCor) as a criterion for evaluating the dependence of the class on a given feature subset. The dCor index provides a reliable dependence measure among random vectors of arbitrary dimension, without any assumption on their distribution. Moreover, it is sensitive to the presence of redundant terms. The proposed FS method is based on a probabilistic representation of the feature subset model, which is progressively refined by a repeated process of model extraction and evaluation. A key element of the approach is a distributed optimization scheme based on a vertical partitioning of the dataset, which alleviates the negative effects of its unbalanced dimensions. The proposed method has been tested on several microarray datasets, resulting in quite compact and accurate models obtained at a reasonable computational cost.

A New Hybrid Feature Subset Selection Framework Based on Binary Genetic Algorithm and Information Theory

The explosion of the high-dimensional dataset in the scientific repository has been encouraging interdisciplinary research on data mining, pattern recognition and bioinformatics. The fundamental problem of the individual Feature Selection (FS) method is extracting informative features for classification model and to seek for the malignant disease at low computational cost. In addition, existing FS approaches overlook the fact that for a given cardinality, there can be several subsets with similar information. This paper introduces a novel hybrid FS algorithm, called Filter-Wrapper Feature Selection (FWFS) for a classification problem and also addresses the limitations of existing methods. In the proposed model, the front-end filter ranking method as Conditional Mutual Information Maximization (CMIM) selects the high ranked feature subset while the succeeding method as Binary Genetic Algorithm (BGA) accelerates the search in identifying the significant feature subsets. One of the merits of the proposed method is that, unlike an exhaustive method, it speeds up the FS procedure without lancing of classification accuracy on reduced dataset when a learning model is applied to the selected subsets of features. The efficacy of the proposed (FWFS) method is examined by Naive Bayes (NB) classifier which works as a fitness function. The effectiveness of the selected feature subset is evaluated using numerous classifiers on five biological datasets and five UCI datasets of a varied dimensionality and number of instances. The experimental results emphasize that the proposed method provides additional support to the significant reduction of the features and outperforms the existing methods. For microarray data-sets, we found the lowest classification accuracy is 61.24% on SRBCT dataset and highest accuracy is 99.32% on Diffuse large B-cell lymphoma (DLBCL). In UCI datasets, the lowest classification accuracy is 40.04% on the Lymphography using k-nearest neighbor (k-NN) and highest classification accuracy is 99.05% on the ionosphere using support vector machine (SVM).

Classification of high dimensional biomedical data based on feature selection using redundant removal

High dimensional biomedical data contain tens of thousands of features, accurate and effective identification of the core features in these data can be used to assist diagnose related diseases. However, there are often a large number of irrelevant or redundant features in biomedical data, which seriously affect subsequent classification accuracy and machine learning efficiency. To solve this problem, a novel filter feature selection algorithm based on redundant removal (FSBRR) is proposed to classify high dimensional biomedical data in this paper. First of all, two redundant criteria are determined by vertical relevance (the relationship between feature and class attribute) and horizontal relevance (the relationship between feature and feature). Secondly, to quantify redundant criteria, an approximate redundancy feature framework based on mutual information (MI) is defined to remove redundant and irrelevant features. To evaluate the effectiveness of our proposed algorithm, controlled trials based on typical feature selection algorithm are conducted using three different classifiers, and the experimental results indicate that the FSBRR algorithm can effectively reduce the feature dimension and improve the classification accuracy. In addition, an experiment of small sample dataset is designed and conducted in the section of discussion and analysis to clarify the specific implementation process of FSBRR algorithm more clearly.

Nature-Inspired Multiobjective Cancer Subtype Diagnosis

Cancer gene expression data is of great importance in cancer subtype diagnosis and drug discovery. Many computational methods have been proposed to classify subtypes using those data. However, most of the previous computational methods suffer from poor interpretability, experimental noises, and low diagnostic quality. To address those problems, multiobjective ensemble cuckoo search based on decomposition (MOECSA) is proposed to optimize those four objectives simultaneously including the number of features, the accuracy, and two entropy-based measures: the relevance and the redundancy, classifying the cancer gene expression data with high predictive power for different cardinality levels under multiple objectives. A novel binary encoding is proposed to choose gene subsets from the cancer gene expression data for calculating four objective functions. Furthermore, an effective ensemble mechanism blended in the cuckoo search algorithm framework is applied to balance the convergence speed and population diversity in MOECSA. To demonstrate the effectiveness and efficiency of the proposed algorithm, experiments on thirty-five benchmark cancer gene expression datasets, four independent disease datasets, and one sequencing-based dataset are carried out to compare MOECSA with the six state-of-the-art multiobjective evolutionary algorithms and seven traditional classification algorithms. The experimental results in different perspectives demonstrate that MOECSA has better diagnosis performance than others at multiple levels.

An Improved Binary Differential Evolution Algorithm for Feature Selection in Molecular Signatures

The discovery of biomarkers from high-dimensional data is a very challenging task in cancer diagnoses. On the one hand, biomarker discovery is the so-called high-dimensional small-sample problem. On the other hand, these data are redundant and noisy. In recent years, biomarker discovery from high-throughput biological data has become an increasingly important emerging topic in the field of bioinformatics. In this study, we propose a binary differential evolution algorithm for feature selection. Firstly, we suggest using a two-stage approach, where three filter methods including the Fisher score, T-statistics, and Information gain are used to generate the feature pool for input to differential evolution (DE). Secondly, in order to improve the performance of differential evolution algorithm for feature selection, a new variant of binary DE called BDE is proposed. Three optimization strategies are incorporated into the BDE. The first strategy is the heuristic method in initial stage, the second one is the self-adaptive parameter control, and the third one is the minimum change value to improve the exploration behaviour thus enhance the diversity. Finally, Support vector machine (SVM) is used as the classifier in 10 fold cross-validation method. The experimental results of our proposed algorithm on some benchmark datasets demonstrate the effectiveness of our algorithm. In addition, the BDE forged in this study will be of great potential in feature selection problems.

Supervised, Unsupervised, and Semi-Supervised Feature Selection: A Review on Gene Selection

Recently, feature selection and dimensionality reduction have become fundamental tools for many data mining tasks, especially for processing high-dimensional data such as gene expression microarray data. Gene expression microarray data comprises up to hundreds of thousands of features with relatively small sample size. Because learning algorithms usually do not work well with this kind of data, a challenge to reduce the data dimensionality arises. A huge number of gene selection are applied to select a subset of relevant features for model construction and to seek for better cancer classification performance. This paper presents the basic taxonomy of feature selection, and also reviews the state-of-the-art gene selection methods by grouping the literatures into three categories: supervised, unsupervised, and semi-supervised. The comparison of experimental results on top 5 representative gene expression datasets indicates that the classification accuracy of unsupervised and semi-supervised feature selection is competitive with supervised feature selection.

Feature selection methods for big data bioinformatics: A survey from the search perspective

This paper surveys main principles of feature selection and their recent applications in big data bioinformatics. Instead of the commonly used categorization into filter, wrapper, and embedded approaches to feature selection, we formulate feature selection as a combinatorial optimization or search problem and categorize feature selection methods into exhaustive search, heuristic search, and hybrid methods, where heuristic search methods may further be categorized into those with or without data-distilled feature ranking measures.

Parameters Identification of Fluxgate Magnetic Core Adopting the Biogeography-Based Optimization Algorithm

The main part of the magnetic fluxgate sensor is the magnetic core, the hysteresis characteristic of which affects the performance of the sensor. When the fluxgate sensors are modelled for design purposes, an accurate model of hysteresis characteristic of the cores is necessary to achieve good agreement between modelled and experimental data. The Jiles-Atherton model is simple and can reflect the hysteresis properties of the magnetic material precisely, which makes it widely used in hysteresis modelling and simulation of ferromagnetic materials. However, in practice, it is difficult to determine the parameters accurately owing to the sensitivity of the parameters. In this paper, the Biogeography-Based Optimization (BBO) algorithm is applied to identify the Jiles-Atherton model parameters. To enhance the performances of the BBO algorithm such as global search capability, search accuracy and convergence rate, an improved Biogeography-Based Optimization (IBBO) algorithm is put forward by using Arnold map and mutation strategy of Differential Evolution (DE) algorithm. Simulation results show that IBBO algorithm is superior to Genetic Algorithm (GA), Particle Swarm Optimization (PSO) algorithm, Differential Evolution algorithm and BBO algorithm in identification accuracy and convergence rate. The IBBO algorithm is applied to identify Jiles-Atherton model parameters of selected permalloy. The simulation hysteresis loop is in high agreement with experimental data. Using permalloy as core of fluxgate probe, the simulation output is consistent with experimental output. The IBBO algorithm can identify the parameters of Jiles-Atherton model accurately, which provides a basis for the precise analysis and design of instruments and equipment with magnetic core.

A Multi-Stage Krill Herd Algorithm for Global Numerical Optimization

A multi-stage krill herd (MSKH) algorithm is presented to fully exploit the global and local search abilities of the standard krill herd (KH) optimization method. The proposed method involves exploration and exploitation stages. The exploration stage uses the basic KH algorithm to select a good candidate solution set. This phase is followed by fine-tuning a good candidate solution in the exploitation stage with a focused local mutation and crossover (LMC) operator in order to enhance the reliability of the method for solving global numerical optimization problems. Moreover, the elitism scheme is introduced into the MSKH method to guarantee the best solution. The performance of MSKH is verified using twenty-five standard and rotated and shifted benchmark problems. The results show the superiority of the proposed algorithm to the standard KH and other well-known optimization methods.

A Hybrid Meta-Heuristic Method Based on Firefly Algorithm and Krill Herd

This study proposes a new firefly-inspired krill herd (FKH) optimization method based on integration of firefly and krill herd algorithms. FKH introduces an attractiveness and light intensity updating (ALIU) operator originally used in firefly algorithm into the krill herd method. This is basically done to improve local search technique and promote the diversity of the population to avoid a premature convergence. Moreover, an elitism strategy is adopted to maintain the optimal krill with the best fitness when updating the krill. The performance of the FKH method is verified using fifteen different benchmark functions. The results indicate that FKH performs more accurate and effective than the basic krill herd and other optimization algorithms.