scholarly journals Computational prediction of species-specific yeast DNA replication origin via iterative feature representation

2020 ◽  
Author(s):  
Balachandran Manavalan ◽  
Shaherin Basith ◽  
Tae Hwan Shin ◽  
Gwang Lee
Keyword(s):  
Regulation Of Gene Expression ◽  
Feature Learning ◽  
Computational Prediction ◽  
Feature Representation ◽  
Support Vector ◽  
Systematic Analysis ◽  
Accurate Performance ◽  
Dna Replication Origin ◽  
Stable Performance ◽  
Species Specific

Abstract Deoxyribonucleic acid replication is one of the most crucial tasks taking place in the cell, and it has to be precisely regulated. This process is initiated in the replication origins (ORIs), and thus it is essential to identify such sites for a deeper understanding of the cellular processes and functions related to the regulation of gene expression. Considering the important tasks performed by ORIs, several experimental and computational approaches have been developed in the prediction of such sites. However, existing computational predictors for ORIs have certain curbs, such as building only single-feature encoding models, limited systematic feature engineering efforts and failure to validate model robustness. Hence, we developed a novel species-specific yeast predictor called yORIpred that accurately identify ORIs in the yeast genomes. To develop yORIpred, we first constructed optimal 40 baseline models by exploring eight different sequence-based encodings and five different machine learning classifiers. Subsequently, the predicted probability of 40 models was considered as the novel feature vector and carried out iterative feature learning approach independently using five different classifiers. Our systematic analysis revealed that the feature representation learned by the support vector machine algorithm (yORIpred) could well discriminate the distribution characteristics between ORIs and non-ORIs when compared with the other four algorithms. Comprehensive benchmarking experiments showed that yORIpred achieved superior and stable performance when compared with the existing predictors on the same training datasets. Furthermore, independent evaluation showcased the best and accurate performance of yORIpred thus underscoring the significance of iterative feature representation. To facilitate the users in obtaining their desired results without undergoing any mathematical, statistical or computational hassles, we developed a web server for the yORIpred predictor, which is available at: http://thegleelab.org/yORIpred.

scholarly journals Recognition of EEG Signal Motor Imagery Intention Based on Deep Multi-View Feature Learning

Sensors ◽  
2020 ◽  
Vol 20 (12) ◽  
pp. 3496
Author(s):  
Jiacan Xu ◽  
Hao Zheng ◽  
Jianhui Wang ◽  
Donglin Li ◽  
Xiaoke Fang
Keyword(s):  
Frequency Domain ◽  
Motor Imagery ◽  
Recognition Performance ◽  
Feature Learning ◽  
Feature Representation ◽  
Support Vector ◽  
Imagery Task ◽  
Learning Method ◽  
Eeg Signals ◽  
Time Frequency

Recognition of motor imagery intention is one of the hot current research focuses of brain-computer interface (BCI) studies. It can help patients with physical dyskinesia to convey their movement intentions. In recent years, breakthroughs have been made in the research on recognition of motor imagery task using deep learning, but if the important features related to motor imagery are ignored, it may lead to a decline in the recognition performance of the algorithm. This paper proposes a new deep multi-view feature learning method for the classification task of motor imagery electroencephalogram (EEG) signals. In order to obtain more representative motor imagery features in EEG signals, we introduced a multi-view feature representation based on the characteristics of EEG signals and the differences between different features. Different feature extraction methods were used to respectively extract the time domain, frequency domain, time-frequency domain and spatial features of EEG signals, so as to made them cooperate and complement. Then, the deep restricted Boltzmann machine (RBM) network improved by t-distributed stochastic neighbor embedding(t-SNE) was adopted to learn the multi-view features of EEG signals, so that the algorithm removed the feature redundancy while took into account the global characteristics in the multi-view feature sequence, reduced the dimension of the multi-visual features and enhanced the recognizability of the features. Finally, support vector machine (SVM) was chosen to classify deep multi-view features. Applying our proposed method to the BCI competition IV 2a dataset we obtained excellent classification results. The results show that the deep multi-view feature learning method further improved the classification accuracy of motor imagery tasks.

scholarly journals Meta Learning for Few-Shot One-Class Classification

AI ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 195-208
Author(s):  
Gabriel Dahia ◽  
Maurício Pamplona Segundo
Keyword(s):  
Feature Representation ◽  
Support Vector ◽  
Support Vector Data Description ◽  
Target Class ◽  
Feature Representations ◽  
Shot Classification ◽  
Training Stage ◽  
Comparable Performance ◽  
Meta Learning ◽  
One Class Classification

We propose a method that can perform one-class classification given only a small number of examples from the target class and none from the others. We formulate the learning of meaningful features for one-class classification as a meta-learning problem in which the meta-training stage repeatedly simulates one-class classification, using the classification loss of the chosen algorithm to learn a feature representation. To learn these representations, we require only multiclass data from similar tasks. We show how the Support Vector Data Description method can be used with our method, and also propose a simpler variant based on Prototypical Networks that obtains comparable performance, indicating that learning feature representations directly from data may be more important than which one-class algorithm we choose. We validate our approach by adapting few-shot classification datasets to the few-shot one-class classification scenario, obtaining similar results to the state-of-the-art of traditional one-class classification, and that improves upon that of one-class classification baselines employed in the few-shot setting.

mAHTPred: a sequence-based meta-predictor for improving the prediction of anti-hypertensive peptides using effective feature representation

2018 ◽  
Vol 35 (16) ◽  
pp. 2757-2765 ◽  
Author(s):  
Balachandran Manavalan ◽  
Shaherin Basith ◽  
Tae Hwan Shin ◽  
Leyi Wei ◽  
Gwang Lee
Keyword(s):  
Nearest Neighbor ◽  
Feature Representation ◽  
Superior Performance ◽  
Supplementary Information ◽  
Gradient Boosting ◽  
Support Vector ◽  
Pharmaceutical Drugs ◽  
K Nearest Neighbor ◽  
Feature Descriptors ◽  
Predicted Probability

AbstractMotivationCardiovascular disease is the primary cause of death globally accounting for approximately 17.7 million deaths per year. One of the stakes linked with cardiovascular diseases and other complications is hypertension. Naturally derived bioactive peptides with antihypertensive activities serve as promising alternatives to pharmaceutical drugs. So far, there is no comprehensive analysis, assessment of diverse features and implementation of various machine-learning (ML) algorithms applied for antihypertensive peptide (AHTP) model construction.ResultsIn this study, we utilized six different ML algorithms, namely, Adaboost, extremely randomized tree (ERT), gradient boosting (GB), k-nearest neighbor, random forest (RF) and support vector machine (SVM) using 51 feature descriptors derived from eight different feature encodings for the prediction of AHTPs. While ERT-based trained models performed consistently better than other algorithms regardless of various feature descriptors, we treated them as baseline predictors, whose predicted probability of AHTPs was further used as input features separately for four different ML-algorithms (ERT, GB, RF and SVM) and developed their corresponding meta-predictors using a two-step feature selection protocol. Subsequently, the integration of four meta-predictors through an ensemble learning approach improved the balanced prediction performance and model robustness on the independent dataset. Upon comparison with existing methods, mAHTPred showed superior performance with an overall improvement of approximately 6–7% in both benchmarking and independent datasets.Availability and implementationThe user-friendly online prediction tool, mAHTPred is freely accessible at http://thegleelab.org/mAHTPred.Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals Computational QSAR model combined molecular descriptors and fingerprints to predict HDAC1 inhibitors

2018 ◽  
Vol 34 ◽  
pp. 52-58 ◽  
Author(s):  
Jingsheng Shi ◽  
Guanglei Zhao ◽  
Yibing Wei
Keyword(s):  
Histone Deacetylases ◽  
Computational Models ◽  
Nearest Neighbor ◽  
Dynamic Balance ◽  
Regulation Of Gene Expression ◽  
Hdac Inhibitors ◽  
Qsar Model ◽  
Support Vector ◽  
C4.5 Decision Tree ◽  
Fold Cross Validation

The dynamic balance between acetylation and deacetylation of histones plays a crucial role in the epigenetic regulation of gene expression. It is equilibrated by two families of enzymes: histone acetyltransferases and histone deacetylases (HDACs). HDACs repress transcription by regulating the conformation of the higher-order chromatin structure. HDAC inhibitors have recently become a class of chemical agents for potential treatment of the abnormal chromatin remodeling process involved in certain cancers. In this study, we constructed a large dataset to predict the activity value of HDAC1 inhibitors. Each compound was represented with seven fingerprints, and computational models were subsequently developed to predict HDAC1 inhibitors via five machine learning methods. These methods include naïve Bayes, κ-nearest neighbor, C4.5 decision tree, random forest, and support vector machine (SVM) algorithms. The best predicting model was CDK fingerprint with SVM, which exhibited an accuracy of 0.89. This model also performed best in five-fold cross-validation. Some representative substructure alerts responsible for HDAC1 inhibitors were identified by using MoSS in KNIME, which could facilitate the identification of HDAC1 inhibitors.

scholarly journals Machine learning for identification of surgeries with high risks of cancellation

2018 ◽  
Vol 26 (1) ◽  
pp. 141-155 ◽  
Author(s):  
Li Luo ◽  
Fengyi Zhang ◽  
Yao Yao ◽  
RenRong Gong ◽  
Martina Fu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Predictive Value ◽  
Operating Characteristic ◽  
Sampling Methods ◽  
Characteristic Curve ◽  
Support Vector ◽  
Chi Square ◽  
Stable Performance ◽  
Operating Characteristic Curve

Surgery cancellations waste scarce operative resources and hinder patients’ access to operative services. In this study, the Wilcoxon and chi-square tests were used for predictor selection, and three machine learning models – random forest, support vector machine, and XGBoost – were used for the identification of surgeries with high risks of cancellation. The optimal performances of the identification models were as follows: sensitivity − 0.615; specificity − 0.957; positive predictive value − 0.454; negative predictive value − 0.904; accuracy − 0.647; and area under the receiver operating characteristic curve − 0.682. Of the three models, the random forest model achieved the best performance. Thus, the effective identification of surgeries with high risks of cancellation is feasible with stable performance. Models and sampling methods significantly affect the performance of identification. This study is a new application of machine learning for the identification of surgeries with high risks of cancellation and facilitation of surgery resource management.

scholarly journals Disentangled Feature Learning Network for Vehicle Re-Identification

2020 ◽  
Author(s):  
Yan Bai ◽  
Yihang Lou ◽  
Yongxing Dai ◽  
Jun Liu ◽  
Ziqian Chen ◽  
...  
Keyword(s):  
State Of The Art ◽  
Feature Learning ◽  
Feature Representation ◽  
Public Security ◽  
The Public ◽  
Common Features ◽  
Learning Network ◽  
Single Feature ◽  
Art Performance

Vehicle Re-Identification (ReID) has attracted lots of research efforts due to its great significance to the public security. In vehicle ReID, we aim to learn features that are powerful in discriminating subtle differences between vehicles which are visually similar, and also robust against different orientations of the same vehicle. However, these two characteristics are hard to be encapsulated into a single feature representation simultaneously with unified supervision. Here we propose a Disentangled Feature Learning Network (DFLNet) to learn orientation specific and common features concurrently, which are discriminative at details and invariant to orientations, respectively. Moreover, to effectively use these two types of features for ReID, we further design a feature metric alignment scheme to ensure the consistency of the metric scales. The experiments show the effectiveness of our method that achieves state-of-the-art performance on three challenging datasets.

scholarly journals iBitter-Fuse: A Novel Sequence-Based Bitter Peptide Predictor by Fusing Multi-View Features

2021 ◽  
Vol 22 (16) ◽  
pp. 8958
Author(s):  
Phasit Charoenkwan ◽  
Chanin Nantasenamat ◽  
Md. Mehedi Hasan ◽  
Mohammad Ali Moni ◽  
Pietro Lio’ ◽  
...  
Keyword(s):  
Machine Learning ◽  
Large Scale ◽  
De Novo ◽  
Predictive Performance ◽  
Support Vector ◽  
Sufficient Information ◽  
Self Assessment ◽  
Accurate Identification ◽  
Bitter Peptides ◽  
Accurate Performance

Accurate identification of bitter peptides is of great importance for better understanding their biochemical and biophysical properties. To date, machine learning-based methods have become effective approaches for providing a good avenue for identifying potential bitter peptides from large-scale protein datasets. Although few machine learning-based predictors have been developed for identifying the bitterness of peptides, their prediction performances could be improved. In this study, we developed a new predictor (named iBitter-Fuse) for achieving more accurate identification of bitter peptides. In the proposed iBitter-Fuse, we have integrated a variety of feature encoding schemes for providing sufficient information from different aspects, namely consisting of compositional information and physicochemical properties. To enhance the predictive performance, the customized genetic algorithm utilizing self-assessment-report (GA-SAR) was employed for identifying informative features followed by inputting optimal ones into a support vector machine (SVM)-based classifier for developing the final model (iBitter-Fuse). Benchmarking experiments based on both 10-fold cross-validation and independent tests indicated that the iBitter-Fuse was able to achieve more accurate performance as compared to state-of-the-art methods. To facilitate the high-throughput identification of bitter peptides, the iBitter-Fuse web server was established and made freely available online. It is anticipated that the iBitter-Fuse will be a useful tool for aiding the discovery and de novo design of bitter peptides

scholarly journals Wheel fault diagnosis model based on multichannel attention and supervised contrastive learning

2021 ◽  
Vol 13 (12) ◽  
pp. 168781402110670
Author(s):  
Yanxiang Chen ◽  
Zuxing Zhao ◽  
Euiyoul Kim ◽  
Haiyang Liu ◽  
Juan Xu ◽  
...  
Keyword(s):  
Network Architecture ◽  
Feature Learning ◽  
Feature Representation ◽  
Diagnostic Methods ◽  
Learning Ability ◽  
Noise Interference ◽  
Backbone Network ◽  
Mechanical Methods ◽  
Wheel Flat ◽  
Wheel Radius

As wheels are important components of train operation, diagnosing and predicting wheel faults are essential to ensure the reliability of rail transit. Currently, the existing studies always separately deal with two main types of wheel faults, namely wheel radius difference and wheel flat, even though they are both reflected by wheel radius changes. Moreover, traditional diagnostic methods, such as mechanical methods or a combination of data analysis methods, have limited abilities to efficiently extract data features. Deep learning models have become useful tools to automatically learn features from raw vibration signals. However, research on improving the feature-learning capabilities of models under noise interference to yield higher wheel diagnostic accuracies has not yet been conducted. In this paper, a unified training framework with the same model architecture and loss function is established for two homologous wheel faults. After selecting deep residual networks (ResNets) as the backbone network to build the model, we add the squeeze and excitation (SE) module based on a multichannel attention mechanism to the backbone network to learn the global relationships among feature channels. Then the influence of noise interference features is reduced while the extraction of useful information features is enhanced, leading to the improved feature-learning ability of ResNet. To further obtain effective feature representation using the model, we introduce supervised contrastive loss (SCL) on the basis of ResNet + SE to enlarge the feature distances of different fault classes through a comparison between positive and negative examples under label supervision to obtain a better class differentiation and higher diagnostic accuracy. We also complete a regression task to predict the fault degrees of wheel radius difference and wheel flat without changing the network architecture. The extensive experimental results show that the proposed model has a high accuracy in diagnosing and predicting two types of wheel faults.

scholarly journals sPepFinder expedites genome-wide identification of small proteins in bacteria

2020 ◽  
Author(s):  
Lei Li ◽  
Yanjie Chao
Keyword(s):  
De Novo ◽  
Bacterial Species ◽  
Computational Prediction ◽  
Ribosome Profiling ◽  
Support Vector ◽  
Initiation Rate ◽  
E Coli ◽  
Small Proteins ◽  
Genome Wide ◽  
A Genome

ABSTRACTSmall proteins shorter than 50 amino acids have been long overlooked. A number of small proteins have been identified in several model bacteria using experimental approaches and assigned important functions in diverse cellular processes. The recent development of ribosome profiling technologies has allowed a genome-wide identification of small proteins and small ORFs (smORFs), but our incomplete understanding of small proteins hinders de novo computational prediction of smORFs in non-model bacterial species. Here, we have identified several sequence features for smORFs by a systematic analysis of all the known small proteins in E. coli, among which the translation initiation rate is the strongest determinant. By integrating these features into a support vector machine learning model, we have developed a novel sPepFinder algorithm that can predict conserved smORFs in bacterial genomes with a high accuracy of 92.8%. De novo prediction in E. coli has revealed several novel smORFs with evidence of translation supported by ribosome profiling. Further application of sPepFinder in 549 bacterial species has led to the identification of > 100,000 novel smORFs, many of which are conserved at the amino acid and nucleotide levels under purifying selection. Overall, we have established sPepFinder as a valuable tool to identify novel smORFs in both model and non-model bacterial organisms, and provided a large resource of small proteins for functional characterizations.

scholarly journals Deep Learning for Person Reidentification Using Support Vector Machines

2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Mengyu Xu ◽  
Zhenmin Tang ◽  
Yazhou Yao ◽  
Lingxiang Yao ◽  
Huafeng Liu ◽  
...  
Keyword(s):  
Data Augmentation ◽  
Metric Learning ◽  
Representation Learning ◽  
Activation Function ◽  
Feature Representation ◽  
Support Vector ◽  
Similarity Learning ◽  
Vector Machines ◽  
Augmentation Techniques ◽  
Suboptimal Solution

Due to the variations of viewpoint, pose, and illumination, a given individual may appear considerably different across different camera views. Tracking individuals across camera networks with no overlapping fields is still a challenging problem. Previous works mainly focus on feature representation and metric learning individually which tend to have a suboptimal solution. To address this issue, in this work, we propose a novel framework to do the feature representation learning and metric learning jointly. Different from previous works, we represent the pairs of pedestrian images as new resized input and use linear Support Vector Machine to replace softmax activation function for similarity learning. Particularly, dropout and data augmentation techniques are also employed in this model to prevent the network from overfitting. Extensive experiments on two publically available datasets VIPeR and CUHK01 demonstrate the effectiveness of our proposed approach.

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