EGFAFS: A Novel Feature Selection Algorithm Based on Explosion Gravitation Field Algorithm
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ABSTRACT:
SUBMITTER: Huang L
PROVIDER: S-EPMC9322764 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:Searching optima is one of the most challenging tasks in clustering genes from available experimental data or given functions. SA, GA, PSO and other similar efficient global optimization methods are used by biotechnologists. All these algorithms are based on the imitation of natural phenomena. RESULTS:This paper proposes a novel searching optimization algorithm called Gravitation Field Algorithm (GFA) which is derived from the famous astronomy theory Solar Nebular Disk Model (SNDM) of planetary formation. GFA simulates the Gravitation field and outperforms GA and SA in some multimodal functions optimization problem. And GFA also can be used in the forms of unimodal functions. GFA clusters the dataset well from the Gene Expression Omnibus. CONCLUSIONS:The mathematical proof demonstrates that GFA could be convergent in the global optimum by probability 1 in three conditions for one independent variable mass functions. In addition to these results, the fundamental optimization concept in this paper is used to analyze how SA and GA affect the global search and the inherent defects in SA and GA. Some results and source code (in Matlab) are publicly available at http://ccst.jlu.edu.cn/CSBG/GFA.
| S-EPMC2949600 | biostudies-literature
Project description:Reconstruction of gene regulatory networks (GRNs) is of utmost interest and has become a challenge computational problem in system biology. However, every existing inference algorithm from gene expression profiles has its own advantages and disadvantages. In particular, the effectiveness and efficiency of every previous algorithm is not high enough. In this work, we proposed a novel inference algorithm from gene expression data based on differential equation model. In this algorithm, two methods were included for inferring GRNs. Before reconstructing GRNs, singular value decomposition method was used to decompose gene expression data, determine the algorithm solution space, and get all candidate solutions of GRNs. In these generated family of candidate solutions, gravitation field algorithm was modified to infer GRNs, used to optimize the criteria of differential equation model, and search the best network structure result. The proposed algorithm is validated on both the simulated scale-free network and real benchmark gene regulatory network in networks database. Both the Bayesian method and the traditional differential equation model were also used to infer GRNs, and the results were used to compare with the proposed algorithm in our work. And genetic algorithm and simulated annealing were also used to evaluate gravitation field algorithm. The cross-validation results confirmed the effectiveness of our algorithm, which outperforms significantly other previous algorithms.
| S-EPMC3514269 | biostudies-literature
Project description:Next-generation sequencing (NGS), which allows the simultaneous sequencing of billions of DNA fragments simultaneously, has revolutionized how we study genomics and molecular biology by generating genome-wide molecular maps of molecules of interest. However, the amount of information produced by NGS has made it difficult for researchers to choose the optimal set of genes. We have sought to resolve this issue by developing a neural network-based feature (gene) selection algorithm called Wx. The Wx algorithm ranks genes based on the discriminative index (DI) score that represents the classification power for distinguishing given groups. With a gene list ranked by DI score, researchers can institutively select the optimal set of genes from the highest-ranking ones. We applied the Wx algorithm to a TCGA pan-cancer gene-expression cohort to identify an optimal set of gene-expression biomarker candidates that can distinguish cancer samples from normal samples for 12 different types of cancer. The 14 gene-expression biomarker candidates identified by Wx were comparable to or outperformed previously reported universal gene expression biomarkers, highlighting the usefulness of the Wx algorithm for next-generation sequencing data. Thus, we anticipate that the Wx algorithm can complement current state-of-the-art analytical applications for the identification of biomarker candidates as an alternative method. The stand-alone and web versions of the Wx algorithm are available at https://github.com/deargen/DearWXpub and https://wx.deargendev.me/ , respectively.
| S-EPMC6642261 | biostudies-literature
Project description:Many scientific problems can be formulated as classification tasks. Data that harbor relevant information are usually described by a large number of features. Frequently, many of these features are irrelevant for the class prediction. The efficient implementation of classification models requires identification of suitable combinations of features. The smaller number of features reduces the problem's dimensionality and may result in higher classification performance. We developed DWFS, a web-based tool that allows for efficient selection of features for a variety of problems. DWFS follows the wrapper paradigm and applies a search strategy based on Genetic Algorithms (GAs). A parallel GA implementation examines and evaluates simultaneously large number of candidate collections of features. DWFS also integrates various filtering methods that may be applied as a pre-processing step in the feature selection process. Furthermore, weights and parameters in the fitness function of GA can be adjusted according to the application requirements. Experiments using heterogeneous datasets from different biomedical applications demonstrate that DWFS is fast and leads to a significant reduction of the number of features without sacrificing performance as compared to several widely used existing methods. DWFS can be accessed online at www.cbrc.kaust.edu.sa/dwfs.
| S-EPMC4342225 | biostudies-literature
Project description:BackgroundHigh-throughput bio-OMIC technologies are producing high-dimension data from bio-samples at an ever increasing rate, whereas the training sample number in a traditional experiment remains small due to various difficulties. This "large p, small n" paradigm in the area of biomedical "big data" may be at least partly solved by feature selection algorithms, which select only features significantly associated with phenotypes. Feature selection is an NP-hard problem. Due to the exponentially increased time requirement for finding the globally optimal solution, all the existing feature selection algorithms employ heuristic rules to find locally optimal solutions, and their solutions achieve different performances on different datasets.ResultsThis work describes a feature selection algorithm based on a recently published correlation measurement, Maximal Information Coefficient (MIC). The proposed algorithm, McTwo, aims to select features associated with phenotypes, independently of each other, and achieving high classification performance of the nearest neighbor algorithm. Based on the comparative study of 17 datasets, McTwo performs about as well as or better than existing algorithms, with significantly reduced numbers of selected features. The features selected by McTwo also appear to have particular biomedical relevance to the phenotypes from the literature.ConclusionMcTwo selects a feature subset with very good classification performance, as well as a small feature number. So McTwo may represent a complementary feature selection algorithm for the high-dimensional biomedical datasets.
| S-EPMC4804474 | biostudies-literature
Project description:Gene selection algorithm in micro-array data classification problem finds a small set of genes which are most informative and distinctive. A well-performed gene selection algorithm should pick a set of genes that achieve high performance and the size of this gene set should be as small as possible. Many of the existing gene selection algorithms suffer from either low performance or large size. In this study, we propose a wrapper gene selection approach, named WERFE, within a recursive feature elimination (RFE) framework to make the classification more efficient. This WERFE employs an ensemble strategy, takes advantages of a variety of gene selection methods and assembles the top selected genes in each approach as the final gene subset. By integrating multiple gene selection algorithms, the optimal gene subset is determined through prioritizing the more important genes selected by each gene selection method and a more discriminative and compact gene subset can be selected. Experimental results show that the proposed method can achieve state-of-the-art performance.
| S-EPMC7270206 | biostudies-literature
Project description:BackgroundSince the development of sequencing technology, an enormous amount of genetic information has been generated, and human cancer analysis using this information is drawing attention. As the effects of variants on human cancer become known, it is important to find cancer-associated variants among countless variants.ResultsWe propose a new filter-based feature selection method applicable for extracting cancer-associated somatic variants considering correlations of data. Both variants associated with the activation and deactivation of cancer's characteristics are analyzed using dual correlation filters. The multiobjective optimization is utilized to consider two types of variants simultaneously without redundancy. To overcome high computational complexity problem, we calculate the correlation-based weight to select significant variants instead of directly searching for the optimal subset of variants. The proposed algorithm is applied to the identification of melanoma metastasis or breast cancer stage, and the classification results of the proposed method are compared with those of conventional single correlation filter-based method.ConclusionsWe verified that the proposed dual correlation filter-based method can extract cancer-associated variants related to the characteristics of human cancer.
| S-EPMC7596964 | 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: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
Project description:Ozone is one of the most important air pollutants, with significant impacts on human health, regional air quality and ecosystems. In this study, we use geographic information and environmental information of the monitoring site of 5577 regions in the world from 2010 to 2014 as feature input to predict the long-term average ozone concentration of the site. A Bayesian optimization-based XGBoost-RFE feature selection model BO-XGBoost-RFE is proposed, and a variety of machine learning algorithms are used to predict ozone concentration based on the optimal feature subset. Since the selection of the underlying model hyperparameters is involved in the recursive feature selection process, different hyperparameter combinations will lead to differences in the feature subsets selected by the model, so that the feature subsets obtained by the model may not be optimal solutions. We combine the Bayesian optimization algorithm to adjust the parameters of recursive feature elimination based on XGBoost to obtain the optimal parameter combination and the optimal feature subset under the parameter combination. Experiments on long-term ozone concentration prediction on a global scale show that the prediction accuracy of the model after Bayesian optimized XGBoost-RFE feature selection is higher than that based on all features and on feature selection with Pearson correlation. Among the four prediction models, random forest obtained the highest prediction accuracy. The XGBoost prediction model achieved the greatest improvement in accuracy.
| S-EPMC9163069 | biostudies-literature