scholarly journals PhD7Faster 2.0: predicting clones propagating faster from the Ph.D.-7 phage display library by coupling PseAAC and tripeptide composition

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7131 ◽  
Author(s):  
Bifang He ◽  
Heng Chen ◽  
Jian Huang
Keyword(s):  
Feature Selection ◽  
Phage Display ◽  
Large Scale ◽  
Permutation Test ◽  
Feature Selection Method ◽  
Phage Display Library ◽  
Support Vector ◽  
Affinity Ligands ◽  
Phage Display Libraries ◽  
Fold Cross Validation

Selection from phage display libraries empowers isolation of high-affinity ligands for various targets. However, this method also identifies propagation-related target-unrelated peptides (PrTUPs). These false positive hits appear because of their amplification advantages. In this report, we present PhD7Faster 2.0 for predicting fast-propagating clones from the Ph.D.-7 phage display library, which was developed based on the support vector machine. Feature selection was performed against PseAAC and tripeptide composition using the incremental feature selection method. Ten-fold cross-validation results show that PhD7Faster 2.0 succeeds a decent performance with the accuracy of 81.84%, the Matthews correlation coefficient of 0.64 and the area under the ROC curve of 0.90. The permutation test with 1,000 shuffles resulted in p < 0.001. We implemented PhD7Faster 2.0 into a publicly accessible web tool (http://i.uestc.edu.cn/sarotup3/cgi-bin/PhD7Faster.pl) and constructed standalone graphical user interface and command-line versions for different systems. The standalone PhD7Faster 2.0 is able to detect PrTUPs within small datasets as well as large-scale datasets. This makes PhD7Faster 2.0 an enhanced and powerful tool for scanning and reporting faster-growing clones from the Ph.D.-7 phage display library.

PhD7FASTER: PREDICTING CLONES PROPAGATING FASTER FROM THE Ph.D.-7 PHAGE DISPLAY PEPTIDE LIBRARY

2014 ◽  
Vol 12 (01) ◽  
pp. 1450005 ◽  
Author(s):  
BEIBEI RU ◽  
PETER A. C. 'T HOEN ◽  
FULEI NIE ◽  
HAO LIN ◽  
FENG-BIAO GUO ◽  
...  
Keyword(s):  
Phage Display ◽  
Peptide Library ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Phage Display Peptide Library ◽  
Phage Display Libraries ◽  
Specific Affinity ◽  
Basic And Applied Research ◽  
Fold Cross Validation ◽  
Better Than

Phage display can rapidly discover peptides binding to any given target; thus, it has been widely used in basic and applied research. Each round of panning consists of two basic processes: Selection and amplification. However, recent studies have showed that the amplification step would decrease the diversity of phage display libraries due to different propagation capacity of phage clones. This may induce phages with growth advantage rather than specific affinity to appear in the final experimental results. The peptides displayed by such phages are termed as propagation-related target-unrelated peptides (PrTUPs). They would mislead further analysis and research if not removed. In this paper, we describe PhD7Faster, an ensemble predictor based on support vector machine (SVM) for predicting clones with growth advantage from the Ph.D.-7 phage display peptide library. By using reduced dipeptide composition (ReDPC) as features, an accuracy (Acc) of 79.67% and a Matthews correlation coefficient (MCC) of 0.595 were achieved in 5-fold cross-validation. In addition, the SVM-based model was demonstrated to perform better than several representative machine learning algorithms. We anticipate that PhD7Faster can assist biologists to exclude potential PrTUPs and accelerate the finding of specific binders from the popular Ph.D.-7 library. The web server of PhD7Faster can be freely accessed at http://immunet.cn/sarotup/cgi-bin/PhD7Faster.pl .

A fuzzy gaussian rank aggregation ensemble feature selection method for microarray data

2021 ◽  
Vol 24 (4) ◽  
pp. 289-301
Author(s):  
B. Venkatesh ◽  
J. Anuradha
Keyword(s):  
Feature Selection ◽  
Microarray Data ◽  
Classification Accuracy ◽  
Performance Metrics ◽  
Feature Selection Method ◽  
Selection Method ◽  
Support Vector ◽  
Svm Classifier ◽  
Binary Particle Swarm Optimization ◽  
Selection Methods

In Microarray Data, it is complicated to achieve more classification accuracy due to the presence of high dimensions, irrelevant and noisy data. And also It had more gene expression data and fewer samples. To increase the classification accuracy and the processing speed of the model, an optimal number of features need to extract, this can be achieved by applying the feature selection method. In this paper, we propose a hybrid ensemble feature selection method. The proposed method has two phases, filter and wrapper phase in filter phase ensemble technique is used for aggregating the feature ranks of the Relief, minimum redundancy Maximum Relevance (mRMR), and Feature Correlation (FC) filter feature selection methods. This paper uses the Fuzzy Gaussian membership function ordering for aggregating the ranks. In wrapper phase, Improved Binary Particle Swarm Optimization (IBPSO) is used for selecting the optimal features, and the RBF Kernel-based Support Vector Machine (SVM) classifier is used as an evaluator. The performance of the proposed model are compared with state of art feature selection methods using five benchmark datasets. For evaluation various performance metrics such as Accuracy, Recall, Precision, and F1-Score are used. Furthermore, the experimental results show that the performance of the proposed method outperforms the other feature selection methods.

Design of Text Categorization System Based on SVM

2012 ◽  
Vol 532-533 ◽  
pp. 1191-1195 ◽  
Author(s):  
Zhen Yan Liu ◽  
Wei Ping Wang ◽  
Yong Wang
Keyword(s):  
Feature Extraction ◽  
Feature Selection ◽  
Text Categorization ◽  
Feature Selection Method ◽  
Extraction Methods ◽  
Support Vector ◽  
Text Representation ◽  
Text Feature ◽  
Categorization System ◽  
Classifier Training

This paper introduces the design of a text categorization system based on Support Vector Machine (SVM). It analyzes the high dimensional characteristic of text data, the reason why SVM is suitable for text categorization. According to system data flow this system is constructed. This system consists of three subsystems which are text representation, classifier training and text classification. The core of this system is the classifier training, but text representation directly influences the currency of classifier and the performance of the system. Text feature vector space can be built by different kinds of feature selection and feature extraction methods. No research can indicate which one is the best method, so many feature selection and feature extraction methods are all developed in this system. For a specific classification task every feature selection method and every feature extraction method will be tested, and then a set of the best methods will be adopted.

Feature Selection Method Based on Mutual Information and Support Vector Machine

2021 ◽  
pp. 2150021
Author(s):  
Gang Liu ◽  
Chunlei Yang ◽  
Sen Liu ◽  
Chunbao Xiao ◽  
Bin Song
Keyword(s):  
Support Vector Machine ◽  
Feature Selection ◽  
Mutual Information ◽  
Classification Accuracy ◽  
Feature Selection Method ◽  
Selection Method ◽  
Support Vector ◽  
Svm Classifier ◽  
Standard Data ◽  
Feature Dimension

A feature selection method based on mutual information and support vector machine (SVM) is proposed in order to eliminate redundant feature and improve classification accuracy. First, local correlation between features and overall correlation is calculated by mutual information. The correlation reflects the information inclusion relationship between features, so the features are evaluated and redundant features are eliminated with analyzing the correlation. Subsequently, the concept of mean impact value (MIV) is defined and the influence degree of input variables on output variables for SVM network based on MIV is calculated. The importance weights of the features described with MIV are sorted by descending order. Finally, the SVM classifier is used to implement feature selection according to the classification accuracy of feature combination which takes MIV order of feature as a reference. The simulation experiments are carried out with three standard data sets of UCI, and the results show that this method can not only effectively reduce the feature dimension and high classification accuracy, but also ensure good robustness.

scholarly journals A Machine Learning Approach to EEG-based Prediction of Human Affective States Using Recursive Feature Elimination Method

2021 ◽  
Vol 335 ◽  
pp. 04001
Author(s):  
Didar Dadebayev ◽  
Goh Wei Wei ◽  
Tan Ee Xion
Keyword(s):  
Feature Selection ◽  
Fractal Dimension ◽  
Emotion Recognition ◽  
Affective Computing ◽  
Feature Selection Method ◽  
Recursive Feature Elimination ◽  
Support Vector ◽  
Emotional States ◽  
Affective States ◽  
Emotion Classification

Emotion recognition, as a branch of affective computing, has attracted great attention in the last decades as it can enable more natural brain-computer interface systems. Electroencephalography (EEG) has proven to be an effective modality for emotion recognition, with which user affective states can be tracked and recorded, especially for primitive emotional events such as arousal and valence. Although brain signals have been shown to correlate with emotional states, the effectiveness of proposed models is somewhat limited. The challenge is improving accuracy, while appropriate extraction of valuable features might be a key to success. This study proposes a framework based on incorporating fractal dimension features and recursive feature elimination approach to enhance the accuracy of EEG-based emotion recognition. The fractal dimension and spectrum-based features to be extracted and used for more accurate emotional state recognition. Recursive Feature Elimination will be used as a feature selection method, whereas the classification of emotions will be performed by the Support Vector Machine (SVM) algorithm. The proposed framework will be tested with a widely used public database, and results are expected to demonstrate higher accuracy and robustness compared to other studies. The contributions of this study are primarily about the improvement of the EEG-based emotion classification accuracy. There is a potential restriction of how generic the results can be as different EEG dataset might yield different results for the same framework. Therefore, experimenting with different EEG dataset and testing alternative feature selection schemes can be very interesting for future work.

Computer-Aided Detection of Polyps in CT Colonography by Means of Feature Selection and Massive-Training Support Vector Regression

2012 ◽  
pp. 178-201
Author(s):  
Jian-Wu Xu ◽  
Kenji Suzuki
Keyword(s):  
Feature Selection ◽  
Support Vector Regression ◽  
Ct Colonography ◽  
Feature Selection Method ◽  
Selection Method ◽  
Support Vector ◽  
Computer Aided Detection ◽  
Training Time ◽  
Computer Aided ◽  
Wilks Lambda

One of the major challenges in current Computer-Aided Detection (CADe) of polyps in CT Colonography (CTC) is to improve the specificity without sacrificing the sensitivity. If a large number of False Positive (FP) detections of polyps are produced by the scheme, radiologists might lose their confidence in the use of CADe. In this chapter, the authors used a nonlinear regression model operating on image voxels and a nonlinear classification model with extracted image features based on Support Vector Machines (SVMs). They investigated the feasibility of a Support Vector Regression (SVR) in the massive-training framework, and the authors developed a Massive-Training SVR (MTSVR) in order to reduce the long training time associated with the Massive-Training Artificial Neural Network (MTANN) for reduction of FPs in CADe of polyps in CTC. In addition, the authors proposed a feature selection method directly coupled with an SVM classifier to maximize the CADe system performance. They compared the proposed feature selection method with the conventional stepwise feature selection based on Wilks’ lambda with a linear discriminant analysis classifier. The FP reduction system based on the proposed feature selection method was able to achieve a 96.0% by-polyp sensitivity with an FP rate of 4.1 per patient. The performance is better than that of the stepwise feature selection based on Wilks’ lambda (which yielded the same sensitivity with 18.0 FPs/patient). To test the performance of the proposed MTSVR, the authors compared it with the original MTANN in the distinction between actual polyps and various types of FPs in terms of the training time reduction and FP reduction performance. The authors’ CTC database consisted of 240 CTC datasets obtained from 120 patients in the supine and prone positions. With MTSVR, they reduced the training time by a factor of 190, while achieving a performance (by-polyp sensitivity of 94.7% with 2.5 FPs/patient) comparable to that of the original MTANN (which has the same sensitivity with 2.6 FPs/patient).

scholarly journals Predictor Selection for Bacterial Vaginosis Diagnosis Using Decision Tree and Relief Algorithms

2020 ◽  
Vol 10 (9) ◽  
pp. 3291
Author(s):  
Jesús F. Pérez-Gómez ◽  
Juana Canul-Reich ◽  
José Hernández-Torruco ◽  
Betania Hernández-Ocaña
Keyword(s):  
Feature Selection ◽  
Decision Tree ◽  
Bacterial Vaginosis ◽  
Cross Validation ◽  
Performance Comparison ◽  
Support Vector ◽  
Ongoing Research ◽  
Selection For ◽  
Comparison Of The Results ◽  
Fold Cross Validation

Requiring only a few relevant characteristics from patients when diagnosing bacterial vaginosis is highly useful for physicians as it makes it less time consuming to collect these data. This would result in having a dataset of patients that can be more accurately diagnosed using only a subset of informative or relevant features in contrast to using the entire set of features. As such, this is a feature selection (FS) problem. In this work, decision tree and Relief algorithms were used as feature selectors. Experiments were conducted on a real dataset for bacterial vaginosis with 396 instances and 252 features/attributes. The dataset was obtained from universities located in Baltimore and Atlanta. The FS algorithms utilized feature rankings, from which the top fifteen features formed a new dataset that was used as input for both support vector machine (SVM) and logistic regression (LR) algorithms for classification. For performance evaluation, averages of 30 runs of 10-fold cross-validation were reported, along with balanced accuracy, sensitivity, and specificity as performance measures. A performance comparison of the results was made between using the total number of features against using the top fifteen. These results found similar attributes from our rankings compared to those reported in the literature. This study is part of ongoing research that is investigating a range of feature selection and classification methods.

Discriminative Feature Selection Based on Imbalance SVDD for Fault Detection of Semiconductor Manufacturing Processes

2016 ◽  
Vol 25 (11) ◽  
pp. 1650143 ◽  
Author(s):  
Jian Wang ◽  
Jian Feng ◽  
Zhiyan Han
Keyword(s):  
Feature Selection ◽  
Fault Detection ◽  
Semiconductor Industry ◽  
Feature Selection Method ◽  
Class Imbalance ◽  
Support Vector ◽  
Support Vector Data Description ◽  
The Real ◽  
Discriminative Feature ◽  
New Feature

Feature selection has become a key step of fault detection. Unfortunately, the class imbalance in the modern semiconductor industry makes feature selection quite challenging. This paper analyzes the challenges and indicates the limitations of the traditional supervised and unsupervised feature selection methods. To cope with the limitations, a new feature selection method named imbalanced support vector data description-radius-recursive feature selection (ISVDD-radius-RFE) is proposed. When selecting features, the ISVDD-radius-RFE has three advantages: (1) ISVDD-radius-RFE is designed to find the most representative feature by finding the real shape of normal samples. (2) ISVDD-radius-RFE can represent the real shape of normal samples more correctly by introducing the discriminant information from fault samples. (3) ISVDD-radius-RFE is optimized for fault detection where the imbalance data is common. The kernel ISVDD-radius-RFE is also described in this paper. The proposed method is demonstrated through its application in the banana set and SECOM dataset. The experimental results confirm ISVDD-radius-RFE and kernel ISVDD-radius-RFE improve the performance of fault detection.

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