Dataset Information

2lpiRNApred: a two-layered integrated algorithm for identifying piRNAs and their functions based on LFE-GM feature selection.

ABSTRACT: Piwi-interacting RNAs (piRNAs) are indispensable in the transposon silencing, including in germ cell formation, germline stem cell maintenance, spermatogenesis, and oogenesis. piRNA pathways are amongst the major genome defence mechanisms, which maintain genome integrity. They also have important functions in tumorigenesis, as indicated by aberrantly expressed piRNAs being recently shown to play roles in the process of cancer development. A number of computational methods for this have recently been proposed, but they still have not yielded satisfactory predictive performance. Moreover, only one computational method that identifies whether piRNAs function in inducting target mRNA deadenylation been reported in the literature. In this study, we developed a two-layered integrated classifier algorithm, 2lpiRNApred. It identifies piRNAs in the first layer and determines whether they function in inducting target mRNA deadenylation in the second layer. A new feature selection algorithm, which was based on Luca fuzzy entropy and Gaussian membership function (LFE-GM), was proposed to reduce the dimensionality of the features. Five feature extraction strategies, namely, Kmer, General parallel correlation pseudo-dinucleotide composition, General series correlation pseudo-dinucleotide composition, Normalized Moreau-Broto autocorrelation, and Geary autocorrelation, and two types of classifier, Sparse Representation Classifier (SRC) and support vector machine with Mahalanobis distance-based radial basis function (SVMMDRBF), were used to construct a two-layered integrated classifier algorithm, 2lpiRNApred. The results indicate that 2lpiRNApred performs significantly better than six other existing prediction tools.

SUBMITTER: Zuo Y

PROVIDER: S-EPMC7549647 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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2lpiRNApred: a two-layered integrated algorithm for identifying piRNAs and their functions based on LFE-GM feature selection.

Zuo Yun Y Zou Quan Q Lin Jianyuan J Jiang Min M Liu Xiangrong X

RNA biology 20200305 6

Piwi-interacting RNAs (piRNAs) are indispensable in the transposon silencing, including in germ cell formation, germline stem cell maintenance, spermatogenesis, and oogenesis. piRNA pathways are amongst the major genome defence mechanisms, which maintain genome integrity. They also have important functions in tumorigenesis, as indicated by aberrantly expressed piRNAs being recently shown to play roles in the process of cancer development. A number of computational methods for this have recently ...[more]

PMID: 32138598

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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

2lpiRNApred: a two-layered integrated algorithm for identifying piRNAs and their functions based on LFE-GM feature selection.

Publications

2lpiRNApred: a two-layered integrated algorithm for identifying piRNAs and their functions based on LFE-GM feature selection.

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