Deep learning model for protein disease classification

2021 ◽  
Vol 16 ◽  
Author(s):  
Farida Alaaeldin Mostafa ◽  
Yasmine Mohamed Afify ◽  
Rasha Mohamed Ismail ◽  
Nagwa Lotfy Badr
Keyword(s):  
Neural Network ◽  
Support Vector Machine ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Protein Analysis ◽  
Kernel Functions ◽  
Support Vector ◽  
Feature Descriptors

Background: Protein sequence analysis helps in the prediction of protein functions. As the number of proteins increases, it gives the bioinformaticians a challenge to analyze and study the similarity between them. Most of the existing protein analysis methods use Support Vector Machine. Deep learning did not receive much attention regarding protein analysis as it is noted that little work focused on studying the protein diseases classification. Objective: The contribution of this paper is to present a deep learning approach that classifies protein diseases based on protein descriptors. Methods: Different protein descriptors are used and decomposed into modified feature descriptors. Uniquely, we introduce using Convolutional Neural Network model to learn and classify protein diseases. The modified feature descriptors are fed to the Convolutional Neural Network model on a dataset of 1563 protein sequences classified into 3 different disease classes: Aids, Tumor suppressor, and Proto oncogene. Results: The usage of the modified feature descriptors shows a significant increase in the performance of the Convolutional Neural Network model over Support Vector Machine using different kernel functions. One modified feature descriptor improved by 19.8%, 27.9%, 17.6%, 21.5%, 17.3%, and 22% for evaluation metrics: Area Under the Curve, Matthews Correlation Coefficient, Accuracy, F1-score, Recall, and Precision, respectively. Conclusion: Results show that the prediction of the proposed modified feature descriptors significantly surpasses that of Support Vector Machine model.

scholarly journals Malware Classification with Improved Convolutional Neural Network Model

2020 ◽  
Vol 12 (6) ◽  
pp. 30-43
Author(s):  
Sumit S. Lad ◽  
◽  
Amol C. Adamuthe
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Personal Information ◽  
Support Vector ◽  
Svm Classifier ◽  
Gray Scale ◽  
Malware Classification

Malware is a threat to people in the cyber world. It steals personal information and harms computer systems. Various developers and information security specialists around the globe continuously work on strategies for detecting malware. From the last few years, machine learning has been investigated by many researchers for malware classification. The existing solutions require more computing resources and are not efficient for datasets with large numbers of samples. Using existing feature extractors for extracting features of images consumes more resources. This paper presents a Convolutional Neural Network model with pre-processing and augmentation techniques for the classification of malware gray-scale images. An investigation is conducted on the Malimg dataset, which contains 9339 gray-scale images. The dataset created from binaries of malware belongs to 25 different families. To create a precise approach and considering the success of deep learning techniques for the classification of raising the volume of newly created malware, we proposed CNN and Hybrid CNN+SVM model. The CNN is used as an automatic feature extractor that uses less resource and time as compared to the existing methods. Proposed CNN model shows (98.03%) accuracy which is better than other existing CNN models namely VGG16 (96.96%), ResNet50 (97.11%) InceptionV3 (97.22%), Xception (97.56%). The execution time of the proposed CNN model is significantly reduced than other existing CNN models. The proposed CNN model is hybridized with a support vector machine. Instead of using Softmax as activation function, SVM performs the task of classifying the malware based on features extracted by the CNN model. The proposed fine-tuned model of CNN produces a well-selected features vector of 256 Neurons with the FC layer, which is input to SVM. Linear SVC kernel transforms the binary SVM classifier into multi-class SVM, which classifies the malware samples using the one-against-one method and delivers the accuracy of 99.59%.

scholarly journals Deep Learning Assisted Neonatal Cry Classification via Support Vector Machine Models

2021 ◽  
Vol 9 ◽  
Author(s):  
Ashwini K ◽  
P. M. Durai Raj Vincent ◽  
Kathiravan Srinivasan ◽  
Chuan-Yu Chang
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Support Vector Machine ◽  
Feature Extraction ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Support Vector ◽  
Svm Classifier ◽  
Infant Cry ◽  
Learning Techniques

Neonatal infants communicate with us through cries. The infant cry signals have distinct patterns depending on the purpose of the cries. Preprocessing, feature extraction, and feature selection need expert attention and take much effort in audio signals in recent days. In deep learning techniques, it automatically extracts and selects the most important features. For this, it requires an enormous amount of data for effective classification. This work mainly discriminates the neonatal cries into pain, hunger, and sleepiness. The neonatal cry auditory signals are transformed into a spectrogram image by utilizing the short-time Fourier transform (STFT) technique. The deep convolutional neural network (DCNN) technique takes the spectrogram images for input. The features are obtained from the convolutional neural network and are passed to the support vector machine (SVM) classifier. Machine learning technique classifies neonatal cries. This work combines the advantages of machine learning and deep learning techniques to get the best results even with a moderate number of data samples. The experimental result shows that CNN-based feature extraction and SVM classifier provides promising results. While comparing the SVM-based kernel techniques, namely radial basis function (RBF), linear and polynomial, it is found that SVM-RBF provides the highest accuracy of kernel-based infant cry classification system provides 88.89% accuracy.

scholarly journals Comparisons of different deep learning-based methods on fault diagnosis for geared system

2019 ◽  
Vol 15 (11) ◽  
pp. 155014771988816 ◽  
Author(s):  
Bing Han ◽  
Xiaohui Yang ◽  
Yafeng Ren ◽  
Wanggui Lan
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Fault Diagnosis ◽  
Convolutional Neural Network ◽  
Mechanical System ◽  
Network Model ◽  
Learning Theory ◽  
Neural Network Model ◽  
Deep Neural Network ◽  
Gear Fault

The running state of a geared transmission system affects the stability and reliability of the whole mechanical system. It will greatly reduce the maintenance cost of a mechanical system to identify the faulty state of the geared transmission system. Based on the measured gear fault vibration signals and the deep learning theory, four fault diagnosis neural network models including fast Fourier transform–deep belief network model, wavelet transform–convolutional neural network model, Hilbert-Huang transform–convolutional neural network model, and comprehensive deep neural network model are developed and trained respectively. The results show that the gear fault diagnosis method based on deep learning theory can effectively identify various gear faults under real test conditions. The comprehensive deep neural network model is the most effective one in gear fault recognition.

scholarly journals An Efficient Deep Learning Approach to Pneumonia Classification in Healthcare

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Okeke Stephen ◽  
Mangal Sain ◽  
Uchenna Joseph Maduh ◽  
Do-Un Jeong
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Data Augmentation ◽  
Classification Performance ◽  
Learning Approaches ◽  
X Ray ◽  
Chest X Ray

This study proposes a convolutional neural network model trained from scratch to classify and detect the presence of pneumonia from a collection of chest X-ray image samples. Unlike other methods that rely solely on transfer learning approaches or traditional handcrafted techniques to achieve a remarkable classification performance, we constructed a convolutional neural network model from scratch to extract features from a given chest X-ray image and classify it to determine if a person is infected with pneumonia. This model could help mitigate the reliability and interpretability challenges often faced when dealing with medical imagery. Unlike other deep learning classification tasks with sufficient image repository, it is difficult to obtain a large amount of pneumonia dataset for this classification task; therefore, we deployed several data augmentation algorithms to improve the validation and classification accuracy of the CNN model and achieved remarkable validation accuracy.

scholarly journals A robust and interpretable, end-to-end deep learning model for cytometry data

2020 ◽  
Author(s):  
Zicheng Hu ◽  
Alice Tang ◽  
Jaiveer Singh ◽  
Sanchita Bhattacharya ◽  
Atul J. Butte
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Learning Model ◽  
Deep Convolutional Neural Network ◽  
Significant Information ◽  
End To End ◽  
Deep Learning Model

AbstractCytometry technologies are essential tools for immunology research, providing high-throughput measurements of the immune cells at the single-cell level. Traditional approaches in interpreting and using cytometry measurements include manual or automated gating to identify cell subsets from the cytometry data, providing highly intuitive results but may lead to significant information loss, in that additional details in measured or correlated cell signals might be missed. In this study, we propose and test a deep convolutional neural network for analyzing cytometry data in an end-to-end fashion, allowing a direct association between raw cytometry data and the clinical outcome of interest. Using nine large CyTOF studies from the open-access ImmPort database, we demonstrated that the deep convolutional neural network model can accurately diagnose the latent cytomegalovirus (CMV) in healthy individuals, even when using highly heterogeneous data from different studies. In addition, we developed a permutation-based method for interpreting the deep convolutional neural network model and identified a CD27-CD94+ CD8+ T cell population significantly associated with latent CMV infection. Finally, we provide a tutorial for creating, training and interpreting the tailored deep learning model for cytometry data using Keras and TensorFlow (github.com/hzc363/DeepLearningCyTOF).

Sign in / Sign up

Export Citation Format

Share Document