DeepCPP: a deep neural network based on nucleotide bias information and minimum distribution similarity feature selection for RNA coding potential prediction

2020 ◽  
Author(s):  
Yu Zhang ◽  
Cangzhi Jia ◽  
Melissa Jane Fullwood ◽  
Chee Keong Kwoh
Keyword(s):  
Neural Network ◽  
Feature Selection ◽  
Deep Neural Network ◽  
Feature Selection Method ◽  
Classification Problem ◽  
Open Reading Frames ◽  
Nucleotide Bias ◽  
Sequencing Technologies ◽  
Type Data ◽  
Coding Potential

Abstract The development of deep sequencing technologies has led to the discovery of novel transcripts. Many in silico methods have been developed to assess the coding potential of these transcripts to further investigate their functions. Existing methods perform well on distinguishing majority long noncoding RNAs (lncRNAs) and coding RNAs (mRNAs) but poorly on RNAs with small open reading frames (sORFs). Here, we present DeepCPP (deep neural network for coding potential prediction), a deep learning method for RNA coding potential prediction. Extensive evaluations on four previous datasets and six new datasets constructed in different species show that DeepCPP outperforms other state-of-the-art methods, especially on sORF type data, which overcomes the bottleneck of sORF mRNA identification by improving more than 4.31, 37.24 and 5.89% on its accuracy for newly discovered human, vertebrate and insect data, respectively. Additionally, we also revealed that discontinuous k-mer, and our newly proposed nucleotide bias and minimal distribution similarity feature selection method play crucial roles in this classification problem. Taken together, DeepCPP is an effective method for RNA coding potential prediction.

scholarly journals Effect on speech emotion classification of a feature selection approach using a convolutional neural network

2021 ◽  
Vol 7 ◽  
pp. e766
Author(s):  
Ammar Amjad ◽  
Lal Khan ◽  
Hsien-Tsung Chang
Keyword(s):  
Neural Network ◽  
Feature Selection ◽  
Convolutional Neural Network ◽  
Feature Selection Method ◽  
Classification Problem ◽  
Speech Emotion Recognition ◽  
Support Vector ◽  
Emotion Classification ◽  
K Nearest Neighbors ◽  
Feature Selection Technique

Speech emotion recognition (SER) is a challenging issue because it is not clear which features are effective for classification. Emotionally related features are always extracted from speech signals for emotional classification. Handcrafted features are mainly used for emotional identification from audio signals. However, these features are not sufficient to correctly identify the emotional state of the speaker. The advantages of a deep convolutional neural network (DCNN) are investigated in the proposed work. A pretrained framework is used to extract the features from speech emotion databases. In this work, we adopt the feature selection (FS) approach to find the discriminative and most important features for SER. Many algorithms are used for the emotion classification problem. We use the random forest (RF), decision tree (DT), support vector machine (SVM), multilayer perceptron classifier (MLP), and k-nearest neighbors (KNN) to classify seven emotions. All experiments are performed by utilizing four different publicly accessible databases. Our method obtains accuracies of 92.02%, 88.77%, 93.61%, and 77.23% for Emo-DB, SAVEE, RAVDESS, and IEMOCAP, respectively, for speaker-dependent (SD) recognition with the feature selection method. Furthermore, compared to current handcrafted feature-based SER methods, the proposed method shows the best results for speaker-independent SER. For EMO-DB, all classifiers attain an accuracy of more than 80% with or without the feature selection technique.

scholarly journals Heart Disease Prediction Based on the Embedded Feature Selection Method and Deep Neural Network

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Dengqing Zhang ◽  
Yunyi Chen ◽  
Yuxuan Chen ◽  
Shengyi Ye ◽  
Wenyu Cai ◽  
...  
Keyword(s):  
Neural Network ◽  
Feature Selection ◽  
Heart Disease ◽  
Deep Neural Network ◽  
Feature Selection Method ◽  
Selection Method ◽  
The Body ◽  
Prediction Algorithm ◽  
Disease Prediction ◽  
Risk Of Death

In recent decades, heart disease threatens people’s health seriously because of its prevalence and high risk of death. Therefore, predicting heart disease through some simple physical indicators obtained from the regular physical examination at an early stage has become a valuable subject. Clinically, it is essential to be sensitive to these indicators related to heart disease to make predictions and provide a reliable basis for further diagnosis. However, the large amount of data makes manual analysis and prediction taxing and arduous. Our research aims to predict heart disease both accurately and quickly through various indicators of the body. In this paper, a novel heart disease prediction model is given. We propose a heart disease prediction algorithm that combines the embedded feature selection method and deep neural networks. This embedded feature selection method is based on the LinearSVC algorithm, using the L1 norm as a penalty item to choose a subset of features significantly associated with heart disease. These features are fed into the deep neural network we built. The weight of the network is initialized with the He initializer to prevent gradient varnishing or explosion so that the predictor can have a better performance. Our model is tested on the heart disease dataset obtained from Kaggle. Some indicators including accuracy, recall, precision, and F1-score are calculated to evaluate the predictor, and the results show that our model achieves 98.56%, 99.35%, 97.84%, and 0.983, respectively, and the average AUC score of the model reaches 0.983, confirming that the method we proposed is efficient and reliable for predicting heart disease.

scholarly journals Network-based drug sensitivity prediction

2020 ◽  
Vol 13 (S11) ◽  
Author(s):  
Khandakar Tanvir Ahmed ◽  
Sunho Park ◽  
Qibing Jiang ◽  
Yunku Yeu ◽  
TaeHyun Hwang ◽  
...  
Keyword(s):  
Neural Network ◽  
Feature Selection ◽  
Drug Response ◽  
Deep Neural Network ◽  
Drug Sensitivity ◽  
Feature Selection Method ◽  
Network Models ◽  
Prediction Performance ◽  
Neural Network Models ◽  
Drug Sensitivity Prediction

Abstract Background Drug sensitivity prediction and drug responsive biomarker selection on high-throughput genomic data is a critical step in drug discovery. Many computational methods have been developed to serve this purpose including several deep neural network models. However, the modular relations among genomic features have been largely ignored in these methods. To overcome this limitation, the role of the gene co-expression network on drug sensitivity prediction is investigated in this study. Methods In this paper, we first introduce a network-based method to identify representative features for drug response prediction by using the gene co-expression network. Then, two graph-based neural network models are proposed and both models integrate gene network information directly into neural network for outcome prediction. Next, we present a large-scale comparative study among the proposed network-based methods, canonical prediction algorithms (i.e., Elastic Net, Random Forest, Partial Least Squares Regression, and Support Vector Regression), and deep neural network models for drug sensitivity prediction. All the source code and processed datasets in this study are available at https://github.com/compbiolabucf/drug-sensitivity-prediction. Results In the comparison of different feature selection methods and prediction methods on a non-small cell lung cancer (NSCLC) cell line RNA-seq gene expression dataset with 50 different drug treatments, we found that (1) the network-based feature selection method improves the prediction performance compared to Pearson correlation coefficients; (2) Random Forest outperforms all the other canonical prediction algorithms and deep neural network models; (3) the proposed graph-based neural network models show better prediction performance compared to deep neural network model; (4) the prediction performance is drug dependent and it may relate to the drug’s mechanism of action. Conclusions Network-based feature selection method and prediction models improve the performance of the drug response prediction. The relations between the genomic features are more robust and stable compared to the correlation between each individual genomic feature and the drug response in high dimension and low sample size genomic datasets.

scholarly journals Integrating ensemble systems biology feature selection and bimodal deep neural network for breast cancer prognosis prediction

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Li-Hsin Cheng ◽  
Te-Cheng Hsu ◽  
Che Lin
Keyword(s):  
Breast Cancer ◽  
Neural Network ◽  
Feature Selection ◽  
Systems Biology ◽  
Ensemble Learning ◽  
Microarray Data ◽  
Deep Neural Network ◽  
Prediction Models ◽  
Biological Knowledge ◽  
Prognosis Prediction

AbstractBreast cancer is a heterogeneous disease. To guide proper treatment decisions for each patient, robust prognostic biomarkers, which allow reliable prognosis prediction, are necessary. Gene feature selection based on microarray data is an approach to discover potential biomarkers systematically. However, standard pure-statistical feature selection approaches often fail to incorporate prior biological knowledge and select genes that lack biological insights. Besides, due to the high dimensionality and low sample size properties of microarray data, selecting robust gene features is an intrinsically challenging problem. We hence combined systems biology feature selection with ensemble learning in this study, aiming to select genes with biological insights and robust prognostic predictive power. Moreover, to capture breast cancer's complex molecular processes, we adopted a multi-gene approach to predict the prognosis status using deep learning classifiers. We found that all ensemble approaches could improve feature selection robustness, wherein the hybrid ensemble approach led to the most robust result. Among all prognosis prediction models, the bimodal deep neural network (DNN) achieved the highest test performance, further verified by survival analysis. In summary, this study demonstrated the potential of combining ensemble learning and bimodal DNN in guiding precision medicine.

scholarly journals USE OF GENETIC ALGORITHM IN DEEP NEURAL NETWORKS CONFIGURATION FOR THE PURPOSES OF COMPUTER ATTACKS CLASSIFICATION

2020 ◽  
pp. 104-117
Author(s):  
O.S. Amosov ◽  
◽  
S.G. Amosova ◽  
D.S. Magola ◽  
◽  
...  
Keyword(s):  
Neural Network ◽  
Genetic Algorithm ◽  
Network Architecture ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Classification Problem ◽  
Neural Network Architecture ◽  
Computer Attacks ◽  
Neural Network Technology

The task of multiclass network classification of computer attacks is given. The applicability of deep neural network technology in problem solving has been considered. Deep neural network architecture was chosen based on the strategy of combining a set of convolution and recurrence LSTM layers. Op-timization of neural network parameters based on genetic algorithm is proposed. The presented results of modeling show the possibility of solving the network classification problem in real time.

Speech Emotion Feature Selection Method Based on Contribution Analysis Algorithm of Neural Network

2008 ◽  
Author(s):  
Xiaojia Wang ◽  
Qirong Mao ◽  
Yongzhao Zhan ◽  
Theodore E. Simos ◽  
George Psihoyios
Keyword(s):  
Neural Network ◽  
Feature Selection ◽  
Feature Selection Method ◽  
Selection Method ◽  
Analysis Algorithm ◽  
Contribution Analysis
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