Hybrid Binary Dragonfly Algorithm with Simulated Annealing for Feature Selection.
Ontology highlight
ABSTRACT: Supplementary information
The online version contains supplementary material available at 10.1007/s42979-021-00687-5.
SUBMITTER: Chantar H
PROVIDER: S-EPMC8147911 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Feature selection is an independent technology for high-dimensional datasets that has been widely applied in a variety of fields. With the vast expansion of information, such as bioinformatics data, there has been an urgent need to investigate more effective and accurate methods involving feature selection in recent decades. Here, we proposed the hybrid MMPSO method, by combining the feature ranking method and the heuristic search method, to obtain an optimal subset that can be used for higher classification accuracy. In this study, ten datasets obtained from the UCI Machine Learning Repository were analyzed to demonstrate the superiority of our method. The MMPSO algorithm outperformed other algorithms in terms of classification accuracy while utilizing the same number of features. Then we applied the method to a biological dataset containing gene expression information about liver hepatocellular carcinoma (LIHC) samples obtained from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx). On the basis of the MMPSO algorithm, we identified a 18-gene signature that performed well in distinguishing normal samples from tumours. Nine of the 18 differentially expressed genes were significantly up-regulated in LIHC tumour samples, and the area under curves (AUC) of the combination seven genes (ADRA2B, ERAP2, NPC1L1, PLVAP, POMC, PYROXD2, TRIM29) in classifying tumours with normal samples was greater than 0.99. Six genes (ADRA2B, PYROXD2, CACHD1, FKBP1B, PRKD1 and RPL7AP6) were significantly correlated with survival time. The MMPSO algorithm can be used to effectively extract features from a high-dimensional dataset, which will provide new clues for identifying biomarkers or therapeutic targets from biological data and more perspectives in tumor research.
| S-EPMC9044222 | biostudies-literature
Project description:In this article, an improved slime mould algorithm (SMA-CSA) is proposed for solving global optimization and the capacitated vehicle routing problem (CVRP). This improvement is based on the mixed-strategy optimization of Cauchy mutation and simulated annealing to alleviate the lack of global optimization capability of the SMA. By introducing the Cauchy mutation strategy, the optimal solution is perturbed to increase the probability of escaping from the local extreme value; in addition, the annealing strategy is introduced, and the Metropolis sampling criterion is used as the acceptance criterion to expand the global search space to enhance the exploration phase to achieve optimal solutions. The performance of the proposed SMA-CSA algorithm is evaluated using the CEC 2013 benchmark functions and the capacitated vehicle routing problem. In all experiments, SMA-CSA is compared with ten other state-of-the-art metaheuristics. The results are also analyzed by Friedman and the Wilcoxon rank-sum test. The experimental results and statistical tests demonstrate that the SMA-CSA algorithm is very competitive and often superior compared to the algorithms used in the experiments. The results of the proposed algorithm on the capacitated vehicle routing problem demonstrate its efficiency and discrete solving ability.
| S-EPMC9876378 | biostudies-literature
Project description:It is necessary to ensure the ship's stability in container ship stowage and loading and unloading containers. This work aims to reduce the container dumping operation at the midway port and improve the efficiency of ship transportation. Firstly, the constraint problem of the traditional container ship stacking is introduced to realize the multi-condition mathematical model of the container ship, container, and wharf. Secondly, a Hybrid Genetic and Simulated Annealing Algorithm (HGSAA) model is proposed for the container stacking and loading stacking in the yard. The specific container space allocation and multi-yard crane adjustment scheme are studied. Finally, the effectiveness of the multi-condition container ship stowage model is verified by numerical experiments by changing the number of outbound containers, storage strategies, storage yards, and bridges. The experimental results show that the HGSAA mode converges to 106.1min at the 751st iteration. Of these, the non-loading and unloading time of yard bridge 1 is 3.43min. The number of operating boxes is 25. The non-loading and unloading time of yard bridge 2 is 3.2min, and the operating box volume is 25 boxes. The objective function of the genetic algorithm converges when it iterates to generation 903 and 107.9min. Among them, the non-loading and unloading time of yard bridge 1 is 4.1min. The non-loading and unloading time of yard bridge 2 is 3.1min. Therefore, the proposed HGSAA has a faster convergence speed than the genetic algorithm and can obtain relatively good results. The proposed container stacking strategy can effectively solve the specific container allocation and multi-yard crane scheduling problems. The finding provides a reference for optimizing container scheduling and improving shipping transportation efficiency.
| S-EPMC10081779 | biostudies-literature
Project description:BackgroundFor rehabilitation training systems, it is essential to automatically record and recognize exercises, especially when more than one type of exercise is performed without a predefined sequence. Most motion recognition methods are based on feature engineering and machine learning algorithms. Time-domain and frequency-domain features are extracted from original time series data collected by sensor nodes. For high-dimensional data, feature selection plays an important role in improving the performance of motion recognition. Existing feature selection methods can be categorized into filter and wrapper methods. Wrapper methods usually achieve better performance than filter methods; however, in most cases, they are computationally intensive, and the feature subset obtained is usually optimized only for the specific learning algorithm.ObjectiveThis study aimed to provide a feature selection method for motion recognition of upper-limb exercises and improve the recognition performance.MethodsMotion data from 5 types of upper-limb exercises performed by 21 participants were collected by a customized inertial measurement unit (IMU) node. A total of 60 time-domain and frequency-domain features were extracted from the original sensor data. A hybrid feature selection method by combining filter and wrapper methods (FESCOM) was proposed to eliminate irrelevant features for motion recognition of upper-limb exercises. In the filter stage, candidate features were first selected from the original feature set according to the significance for motion recognition. In the wrapper stage, k-nearest neighbors (kNN), Naïve Bayes (NB), and random forest (RF) were evaluated as the wrapping components to further refine the features from the candidate feature set. The performance of the proposed FESCOM method was verified using experiments on motion recognition of upper-limb exercises and compared with the traditional wrapper method.ResultsUsing kNN, NB, and RF as the wrapping components, the classification error rates of the proposed FESCOM method were 1.7%, 8.9%, and 7.4%, respectively, and the feature selection time in each iteration was 13 seconds, 71 seconds, and 541 seconds, respectively.ConclusionsThe experimental results demonstrated that, in the case of 5 motion types performed by 21 healthy participants, the proposed FESCOM method using kNN and NB as the wrapping components achieved better recognition performance than the traditional wrapper method. The FESCOM method dramatically reduces the search time in the feature selection process. The results also demonstrated that the optimal number of features depends on the classifier. This approach serves to improve feature selection and classification algorithm selection for upper-limb motion recognition based on wearable sensor data, which can be extended to motion recognition of more motion types and participants.
| S-EPMC8446846 | biostudies-literature
Project description:A comprehensive understanding of the linear/nonlinear dynamic behavior of wireless microresonators is essential for micro-electromechanical systems (MEMS) design optimization. This study investigates the dynamic behaviour of a magnetoelectric (ME) microresonator, using a finite element method (FEM) and machine learning algorithm. First, the linear/nonlinear behaviour of a fabricated thin-film ME microactuator is assessed in both the time domain and frequency spectrum. Next, a data driven system identification (DDSI) procedure and simulated annealing (SA) method are implemented to reconstruct differential equations from measured datasets. The Duffing equation is employed to replicate the dynamic behavior of the ME microactuator. The Duffing coefficients such as mass, stiffness, damping, force amplitude, and excitation frequency are considered as input parameters. Meanwhile, the microactuator displacement is taken as the output parameter, which is measured experimentally via a laser Doppler vibrometer (LDV) device. To determine the optimal range and step size for input parameters, the sensitivity analysis is conducted using Latin hypercube sampling (LHS). The peak index matching (PIM) and correlation coefficient (CC) are considered assessment criteria for the objective function. The data-driven developed models are subsequently employed to reconstruct/predict mode shapes and the vibration amplitude over the time domain. The effect of driving signal nonlinearity and total harmonic distortion (THD) is explored experimentally under resonance and sub-resonance conditions. The vibration measurements reveal that as excitation levels increase, hysteresis variations become more noticeable, which may result in a higher prediction error in the Duffing array model. The verification test indicates that the first bending mode reconstructs reasonably with a prediction accuracy of about 92 percent. This proof-of-concept study demonstrates that the simulated annealing approach is a promising tool for modeling the dynamic behavior of MEMS systems, making it a strong candidate for real-world applications.
| S-EPMC10608850 | biostudies-literature
Project description:Breast cancer is one of the most often diagnosed cancers in women, and identifying breast cancer histological images is an essential challenge in automated pathology analysis. According to research, the global BrC is around 12% of all cancer cases. Furthermore, around 25% of women suffer from BrC. Consequently, the prediction of BrC depends critically on the quick and precise processing of imaging data. The primary reason deep learning models are used in breast cancer detection is that they can produce findings more quickly and accurately than current machine learning-based techniques. Using a BreakHis dataset, we demonstrated in this work the viability of automatically identifying and classifying BrC. The first stage is pre-processing, which employs an Adaptive Switching Modified Decision Based Unsymmetrical Trimmed Median Filter (ASMDBUTMF) to remove high-density noise. After the image has been pre-processed, it is segmented using the Thresholding Level set approach. Next, we propose a hybrid chaotic sand cat optimization technique, together with the Remora Optimization Algorithm (ROA) for feature selection. The suggested strategy facilitates the acquisition of precise functionality attributes, hence simplifying the detection procedure. Additionally, it aids in resolving problems pertaining to global optimization. Following the selection, the best characteristics proceed to the categorization procedure. A DL classifier called the Conditional Variation Autoencoder is used to discriminate between cancerous and benign tumors while categorizing them. Consequently, a classification accuracy of 99.4%, Precision of 99.2%, Recall of 99.1%, F- score of 99%, Specificity of 99.14%, FDR of 0.54, FNR of 0.001, FPR of 0.002, MCC of 0.98 and NPV of 0.99 were obtained using the proposed approach. Furthermore, compared to other research using the current BreakHis dataset, the results of our research are more desirable.
| S-EPMC11008855 | biostudies-literature
Project description:The training machine learning algorithm from an imbalanced data set is an inherently challenging task. It becomes more demanding with limited samples but with a massive number of features (high dimensionality). The high dimensional and imbalanced data set has posed severe challenges in many real-world applications, such as biomedical data sets. Numerous researchers investigated either imbalanced class or high dimensional data sets and came up with various methods. Nonetheless, few approaches reported in the literature have addressed the intersection of the high dimensional and imbalanced class problem due to their complicated interactions. Lately, feature selection has become a well-known technique that has been used to overcome this problem by selecting discriminative features that represent minority and majority class. This paper proposes a new method called Robust Correlation Based Redundancy and Binary Grasshopper Optimization Algorithm (rCBR-BGOA); rCBR-BGOA has employed an ensemble of multi-filters coupled with the Correlation-Based Redundancy method to select optimal feature subsets. A binary Grasshopper optimisation algorithm (BGOA) is used to construct the feature selection process as an optimisation problem to select the best (near-optimal) combination of features from the majority and minority class. The obtained results, supported by the proper statistical analysis, indicate that rCBR-BGOA can improve the classification performance for high dimensional and imbalanced datasets in terms of G-mean and the Area Under the Curve (AUC) performance metrics.
| S-EPMC7397300 | biostudies-literature
Project description:In the process of solving the Traveling Salesman Problem (TSP), both Ant Colony Optimization and simulated annealing exhibit different limitations depending on the dataset. This article aims to address these limitations by improving and combining these two algorithms using the clustering method. The problems tackled include Ant Colony Optimization's susceptibility to stagnation, slow convergence, excessive computations, and local optima, as well as simulated annealing's slow convergence and limited local search capability. By conducting tests on various TSPLIB datasets, the algorithm proposed in this article demonstrates improved convergence speed and solution quality compared to traditional algorithms. Furthermore, it exhibits certain advantages over other existing improved algorithms. Finally, this article applies this algorithm to logistics transportation, yielding excellent results.
| S-EPMC10557949 | biostudies-literature
Project description:Feature selection is an important preprocessing method in machine learning and data mining. This process can be used not only to reduce the amount of data to be analyzed but also to build models with stronger interpretability based on fewer features. Traditional feature selection methods evaluate the dependency and redundancy of features separately, which leads to a lack of measurement of their combined effect. Moreover, a greedy search considers only the optimization of the current round and thus cannot be a global search. To evaluate the combined effect of different subsets in the entire feature space, an adaptive feature selection method based on V-shaped binary particle swarm optimization is proposed. In this method, the fitness function is constructed using the correlation information entropy. Feature subsets are regarded as individuals in a population, and the feature space is searched using V-shaped binary particle swarm optimization. The above procedure overcomes the hard constraint on the number of features, enables the combined evaluation of each subset as a whole, and improves the search ability of conventional binary particle swarm optimization. The proposed algorithm is an adaptive method with respect to the number of feature subsets. The experimental results show the advantages of optimizing the feature subsets using the V-shaped transfer function and confirm the effectiveness and efficiency of the feature subsets obtained under different classifiers.
| S-EPMC5373580 | biostudies-literature
Project description:The advent of big data era has imposed both running time and learning efficiency challenges for the machine learning researchers. Biomedical OMIC research is one of these big data areas and has changed the biomedical research drastically. But the high cost of data production and difficulty in participant recruitment introduce the paradigm of "large p small n" into the biomedical research. Feature selection is usually employed to reduce the high number of biomedical features, so that a stable data-independent classification or regression model may be achieved. This study randomly changes the first element of the widely-used incremental feature selection (IFS) strategy and selects the best feature subset that may be ranked low by the statistical association evaluation algorithms, e.g. t-test. The hypothesis is that two low-ranked features may be orchestrated to achieve a good classification performance. The proposed Randomly re-started Incremental Feature Selection (RIFS) algorithm demonstrates both higher classification accuracy and smaller feature number than the existing algorithms. RIFS also outperforms the existing methylomic diagnosis model for the prostate malignancy with a larger accuracy and a lower number of transcriptomic features.
| S-EPMC5638869 | biostudies-literature