Dataset Information

DWFS: a wrapper feature selection tool based on a parallel genetic algorithm.

ABSTRACT: 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.

SUBMITTER: Soufan O

PROVIDER: S-EPMC4342225 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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DWFS: a wrapper feature selection tool based on a parallel genetic algorithm.

Soufan Othman O Kleftogiannis Dimitrios D Kalnis Panos P Bajic Vladimir B VB

PloS one 20150226 2

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-bas ...[more]

PMID: 25719748

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Project description:BACKGROUND:Through the wealth of information contained within them, genome-wide association studies (GWAS) have the potential to provide researchers with a systematic means of associating genetic variants with a wide variety of disease phenotypes. Due to the limitations of approaches that have analyzed single variants one at a time, it has been proposed that the genetic basis of these disorders could be determined through detailed analysis of the genetic variants themselves and in conjunction with one another. The construction of models that account for these subsets of variants requires methodologies that generate predictions based on the total risk of a particular group of polymorphisms. However, due to the excessive number of variants, constructing these types of models has so far been computationally infeasible. RESULTS:We have implemented an algorithm, known as greedy RLS, that we use to perform the first known wrapper-based feature selection on the genome-wide level. The running time of greedy RLS grows linearly in the number of training examples, the number of features in the original data set, and the number of selected features. This speed is achieved through computational short-cuts based on matrix calculus. Since the memory consumption in present-day computers can form an even tighter bottleneck than running time, we also developed a space efficient variation of greedy RLS which trades running time for memory. These approaches are then compared to traditional wrapper-based feature selection implementations based on support vector machines (SVM) to reveal the relative speed-up and to assess the feasibility of the new algorithm. As a proof of concept, we apply greedy RLS to the Hypertension - UK National Blood Service WTCCC dataset and select the most predictive variants using 3-fold external cross-validation in less than 26 minutes on a high-end desktop. On this dataset, we also show that greedy RLS has a better classification performance on independent test data than a classifier trained using features selected by a statistical p-value-based filter, which is currently the most popular approach for constructing predictive models in GWAS. CONCLUSIONS:Greedy RLS is the first known implementation of a machine learning based method with the capability to conduct a wrapper-based feature selection on an entire GWAS containing several thousand examples and over 400,000 variants. In our experiments, greedy RLS selected a highly predictive subset of genetic variants in a fraction of the time spent by wrapper-based selection methods used together with SVM classifiers. The proposed algorithms are freely available as part of the RLScore software library at http://users.utu.fi/aatapa/RLScore/.

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.

Dataset Information

DWFS: a wrapper feature selection tool based on a parallel genetic algorithm.

Publications

DWFS: a wrapper feature selection tool based on a parallel genetic algorithm.

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