scholarly journals A computational method for predicting nucleocapsid protein in retroviruses

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Manyun Guo ◽  
Yucheng Ma ◽  
Wanyuan Liu ◽  
Zuyi Yuan
Keyword(s):  
Nucleocapsid Protein ◽  
Gene Prediction ◽  
Specific Antigen ◽  
Prediction Method ◽  
Computational Method ◽  
Functional Study ◽  
Support Vector ◽  
Length Variation ◽  
Wide Range ◽  
Prediction Problems

AbstractNucleocapsid protein (NC) in the group-specific antigen (gag) of retrovirus is essential in the interactions of most retroviral gag proteins with RNAs. Computational method to predict NCs would benefit subsequent structure analysis and functional study on them. However, no computational method to predict the exact locations of NCs in retroviruses has been proposed yet. The wide range of length variation of NCs also increases the difficulties. In this paper, a computational method to identify NCs in retroviruses is proposed. All available retrovirus sequences with NC annotations were collected from NCBI. Models based on random forest (RF) and weighted support vector machine (WSVM) were built to predict initiation and termination sites of NCs. Factor analysis scales of generalized amino acid information along with position weight matrix were utilized to generate the feature space. Homology based gene prediction methods were also compared and integrated to bring out better predicting performance. Candidate initiation and termination sites predicted were then combined and screened according to their intervals, decision values and alignment scores. All available gag sequences without NC annotations were scanned with the model to detect putative NCs. Geometric means of sensitivity and specificity generated from prediction of initiation and termination sites under fivefold cross-validation are 0.9900 and 0.9548 respectively. 90.91% of all the collected retrovirus sequences with NC annotations could be predicted totally correct by the model combining WSVM, RF and simple alignment. The composite model performs better than the simplex ones. 235 putative NCs in unannotated gags were detected by the model. Our prediction method performs well on NC recognition and could also be expanded to solve other gene prediction problems, especially those whose training samples have large length variations.

scholarly journals HMMBinder: DNA-Binding Protein Prediction Using HMM Profile Based Features

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Rianon Zaman ◽  
Shahana Yasmin Chowdhury ◽  
Mahmood A. Rashid ◽  
Alok Sharma ◽  
Abdollah Dehzangi ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Protein ◽  
Prediction Method ◽  
Dna Binding Protein ◽  
Support Vector ◽  
Classification Technique ◽  
Protein Prediction ◽  
Wide Range ◽  
Vector Machines ◽  
Benchmark Datasets

DNA-binding proteins often play important role in various processes within the cell. Over the last decade, a wide range of classification algorithms and feature extraction techniques have been used to solve this problem. In this paper, we propose a novel DNA-binding protein prediction method called HMMBinder. HMMBinder uses monogram and bigram features extracted from the HMM profiles of the protein sequences. To the best of our knowledge, this is the first application of HMM profile based features for the DNA-binding protein prediction problem. We applied Support Vector Machines (SVM) as a classification technique in HMMBinder. Our method was tested on standard benchmark datasets. We experimentally show that our method outperforms the state-of-the-art methods found in the literature.

Evaluation of Machine Learning Approaches for Automated Diagnosis of COVID-19 using X-Ray images (Preprint)

2020 ◽  
Author(s):  
Mazin Mohammed ◽  
Karrar Hameed Abdulkareem ◽  
Mashael S. Maashi ◽  
Salama A. Mostafa A. Mostafa ◽  
Abdullah Baz ◽  
...  
Keyword(s):  
Machine Learning ◽  
Computational Method ◽  
Learning Performance ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Learning Approaches ◽  
Data Set ◽  
X Ray ◽  
Wide Range ◽  
Artificial Neural Network Ann

BACKGROUND In most recent times, global concern has been caused by a coronavirus (COVID19), which is considered a global health threat due to its rapid spread across the globe. Machine learning (ML) is a computational method that can be used to automatically learn from experience and improve the accuracy of predictions. OBJECTIVE In this study, the use of machine learning has been applied to Coronavirus dataset of 50 X-ray images to enable the development of directions and detection modalities with risk causes.The dataset contains a wide range of samples of COVID-19 cases alongside SARS, MERS, and ARDS. The experiment was carried out using a total of 50 X-ray images, out of which 25 images were that of positive COVIDE-19 cases, while the other 25 were normal cases. METHODS An orange tool has been used for data manipulation. To be able to classify patients as carriers of Coronavirus and non-Coronavirus carriers, this tool has been employed in developing and analysing seven types of predictive models. Models such as , artificial neural network (ANN), support vector machine (SVM), linear kernel and radial basis function (RBF), k-nearest neighbour (k-NN), Decision Tree (DT), and CN2 rule inducer were used in this study.Furthermore, the standard InceptionV3 model has been used for feature extraction target. RESULTS The various machine learning techniques that have been trained on coronavirus disease 2019 (COVID-19) dataset with improved ML techniques parameters. The data set was divided into two parts, which are training and testing. The model was trained using 70% of the dataset, while the remaining 30% was used to test the model. The results show that the improved SVM achieved a F1 of 97% and an accuracy of 98%. CONCLUSIONS :. In this study, seven models have been developed to aid the detection of coronavirus. In such cases, the learning performance can be improved through knowledge transfer, whereby time-consuming data labelling efforts are not required.the evaluations of all the models are done in terms of different parameters. it can be concluded that all the models performed well, but the SVM demonstrated the best result for accuracy metric. Future work will compare classical approaches with deep learning ones and try to obtain better results. CLINICALTRIAL None

A Computational Method for the Identification of Endolysins and Autolysins

2020 ◽  
Vol 27 (4) ◽  
pp. 329-336 ◽  
Author(s):  
Lei Xu ◽  
Guangmin Liang ◽  
Baowen Chen ◽  
Xu Tan ◽  
Huaikun Xiang ◽  
...  
Keyword(s):  
Support Vector Machine ◽  
Cell Wall ◽  
Experimental Results ◽  
Computational Method ◽  
Lytic Enzyme ◽  
Support Vector ◽  
Lytic Enzymes ◽  
Data Set ◽  
Optimal Feature ◽  
Better Than

Background: Cell lytic enzyme is a kind of highly evolved protein, which can destroy the cell structure and kill the bacteria. Compared with antibiotics, cell lytic enzyme will not cause serious problem of drug resistance of pathogenic bacteria. Thus, the study of cell wall lytic enzymes aims at finding an efficient way for curing bacteria infectious. Compared with using antibiotics, the problem of drug resistance becomes more serious. Therefore, it is a good choice for curing bacterial infections by using cell lytic enzymes. Cell lytic enzyme includes endolysin and autolysin and the difference between them is the purpose of the break of cell wall. The identification of the type of cell lytic enzymes is meaningful for the study of cell wall enzymes. Objective: In this article, our motivation is to predict the type of cell lytic enzyme. Cell lytic enzyme is helpful for killing bacteria, so it is meaningful for study the type of cell lytic enzyme. However, it is time consuming to detect the type of cell lytic enzyme by experimental methods. Thus, an efficient computational method for the type of cell lytic enzyme prediction is proposed in our work. Method: We propose a computational method for the prediction of endolysin and autolysin. First, a data set containing 27 endolysins and 41 autolysins is built. Then the protein is represented by tripeptides composition. The features are selected with larger confidence degree. At last, the classifier is trained by the labeled vectors based on support vector machine. The learned classifier is used to predict the type of cell lytic enzyme. Results: Following the proposed method, the experimental results show that the overall accuracy can attain 97.06%, when 44 features are selected. Compared with Ding's method, our method improves the overall accuracy by nearly 4.5% ((97.06-92.9)/92.9%). The performance of our proposed method is stable, when the selected feature number is from 40 to 70. The overall accuracy of tripeptides optimal feature set is 94.12%, and the overall accuracy of Chou's amphiphilic PseAAC method is 76.2%. The experimental results also demonstrate that the overall accuracy is improved by nearly 18% when using the tripeptides optimal feature set. Conclusion: The paper proposed an efficient method for identifying endolysin and autolysin. In this paper, support vector machine is used to predict the type of cell lytic enzyme. The experimental results show that the overall accuracy of the proposed method is 94.12%, which is better than some existing methods. In conclusion, the selected 44 features can improve the overall accuracy for identification of the type of cell lytic enzyme. Support vector machine performs better than other classifiers when using the selected feature set on the benchmark data set.

Prediction of Disease Comorbidity Using HeteSim Scores based on Multiple Heterogeneous Networks

2019 ◽  
Vol 19 (4) ◽  
pp. 232-241 ◽  
Author(s):  
Xuegong Chen ◽  
Wanwan Shi ◽  
Lei Deng
Keyword(s):  
Protein Interactions ◽  
Experimental Studies ◽  
Treatment Strategies ◽  
Computational Method ◽  
Biological Information ◽  
Support Vector ◽  
Protein Protein Interactions ◽  
Efficient Treatment ◽  
Disease Associations ◽  
Previous State

Background: Accumulating experimental studies have indicated that disease comorbidity causes additional pain to patients and leads to the failure of standard treatments compared to patients who have a single disease. Therefore, accurate prediction of potential comorbidity is essential to design more efficient treatment strategies. However, only a few disease comorbidities have been discovered in the clinic. Objective: In this work, we propose PCHS, an effective computational method for predicting disease comorbidity. Materials and Methods: We utilized the HeteSim measure to calculate the relatedness score for different disease pairs in the global heterogeneous network, which integrates six networks based on biological information, including disease-disease associations, drug-drug interactions, protein-protein interactions and associations among them. We built the prediction model using the Support Vector Machine (SVM) based on the HeteSim scores. Results and Conclusion: The results showed that PCHS performed significantly better than previous state-of-the-art approaches and achieved an AUC score of 0.90 in 10-fold cross-validation. Furthermore, some of our predictions have been verified in literatures, indicating the effectiveness of our method.

scholarly journals Grasp to See—Object Classification Using Flexion Glove with Support Vector Machine

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1461
Author(s):  
Shun-Hsin Yu ◽  
Jen-Shuo Chang ◽  
Chia-Hung Dylan Tsai
Keyword(s):  
Support Vector Machine ◽  
Daily Life ◽  
Object Classification ◽  
Target Object ◽  
The Other ◽  
Support Vector ◽  
Wide Range ◽  
Dark Space ◽  
Flex Sensors ◽  
Shape And Size

This paper proposes an object classification method using a flexion glove and machine learning. The classification is performed based on the information obtained from a single grasp on a target object. The flexion glove is developed with five flex sensors mounted on five finger sleeves, and is used for measuring the flexion of individual fingers while grasping an object. Flexion signals are divided into three phases, and they are the phases of picking, holding and releasing, respectively. Grasping features are extracted from the phase of holding for training the support vector machine. Two sets of objects are prepared for the classification test. One is printed-object set and the other is daily-life object set. The printed-object set is for investigating the patterns of grasping with specified shape and size, while the daily-life object set includes nine objects randomly chosen from daily life for demonstrating that the proposed method can be used to identify a wide range of objects. According to the results, the accuracy of the classifications are achieved 95.56% and 88.89% for the sets of printed objects and daily-life objects, respectively. A flexion glove which can perform object classification is successfully developed in this work and is aimed at potential grasp-to-see applications, such as visual impairment aid and recognition in dark space.

scholarly journals An information theoretic approach to link prediction in multiplex networks

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Seyed Hossein Jafari ◽  
Amir Mahdi Abdolhosseini-Qomi ◽  
Masoud Asadpour ◽  
Maseud Rahgozar ◽  
Naser Yazdani
Keyword(s):  
Real World ◽  
Link Prediction ◽  
Large Scale ◽  
Similarity Measures ◽  
Prediction Method ◽  
General Purpose ◽  
Fast Method ◽  
Theoretic Approach ◽  
Multiplex Networks ◽  
Wide Range

AbstractThe entities of real-world networks are connected via different types of connections (i.e., layers). The task of link prediction in multiplex networks is about finding missing connections based on both intra-layer and inter-layer correlations. Our observations confirm that in a wide range of real-world multiplex networks, from social to biological and technological, a positive correlation exists between connection probability in one layer and similarity in other layers. Accordingly, a similarity-based automatic general-purpose multiplex link prediction method—SimBins—is devised that quantifies the amount of connection uncertainty based on observed inter-layer correlations in a multiplex network. Moreover, SimBins enhances the prediction quality in the target layer by incorporating the effect of link overlap across layers. Applying SimBins to various datasets from diverse domains, our findings indicate that SimBins outperforms the compared methods (both baseline and state-of-the-art methods) in most instances when predicting links. Furthermore, it is discussed that SimBins imposes minor computational overhead to the base similarity measures making it a potentially fast method, suitable for large-scale multiplex networks.

scholarly journals An efficient computational method for predicting drug-target interactions using weighted extreme learning machine and speed up robot features

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ji-Yong An ◽  
Fan-Rong Meng ◽  
Zi-Ji Yan
Keyword(s):  
Ion Channel ◽  
Extreme Learning Machine ◽  
Nuclear Receptor ◽  
Drug Target ◽  
Computational Method ◽  
Evolutionary Information ◽  
Support Vector ◽  
Weighted Extreme Learning Machine ◽  
Speed Up ◽  
Learning Machine

Abstract Background Prediction of novel Drug–Target interactions (DTIs) plays an important role in discovering new drug candidates and finding new proteins to target. In consideration of the time-consuming and expensive of experimental methods. Therefore, it is a challenging task that how to develop efficient computational approaches for the accurate predicting potential associations between drug and target. Results In the paper, we proposed a novel computational method called WELM-SURF based on drug fingerprints and protein evolutionary information for identifying DTIs. More specifically, for exploiting protein sequence feature, Position Specific Scoring Matrix (PSSM) is applied to capturing protein evolutionary information and Speed up robot features (SURF) is employed to extract sequence key feature from PSSM. For drug fingerprints, the chemical structure of molecular substructure fingerprints was used to represent drug as feature vector. Take account of the advantage that the Weighted Extreme Learning Machine (WELM) has short training time, good generalization ability, and most importantly ability to efficiently execute classification by optimizing the loss function of weight matrix. Therefore, the WELM classifier is used to carry out classification based on extracted features for predicting DTIs. The performance of the WELM-SURF model was evaluated by experimental validations on enzyme, ion channel, GPCRs and nuclear receptor datasets by using fivefold cross-validation test. The WELM-SURF obtained average accuracies of 93.54, 90.58, 85.43 and 77.45% on enzyme, ion channels, GPCRs and nuclear receptor dataset respectively. We also compared our performance with the Extreme Learning Machine (ELM), the state-of-the-art Support Vector Machine (SVM) on enzyme and ion channels dataset and other exiting methods on four datasets. By comparing with experimental results, the performance of WELM-SURF is significantly better than that of ELM, SVM and other previous methods in the domain. Conclusion The results demonstrated that the proposed WELM-SURF model is competent for predicting DTIs with high accuracy and robustness. It is anticipated that the WELM-SURF method is a useful computational tool to facilitate widely bioinformatics studies related to DTIs prediction.

scholarly journals Deeply Learned Pose Invariant Image Analysis with Applications in 3D Face Recognition

2019 ◽  
Vol 2019 ◽  
pp. 1-21 ◽  
Author(s):  
Naeem Ratyal ◽  
Imtiaz Ahmad Taj ◽  
Muhammad Sajid ◽  
Anzar Mahmood ◽  
Sohail Razzaq ◽  
...  
Keyword(s):  
Face Recognition ◽  
Superior Performance ◽  
Support Vector ◽  
Complex Nature ◽  
Alignment Algorithm ◽  
3D Face Recognition ◽  
3D Face ◽  
Norm Minimization ◽  
Wide Range ◽  
The Face

Face recognition aims to establish the identity of a person based on facial characteristics and is a challenging problem due to complex nature of the facial manifold. A wide range of face recognition applications are based on classification techniques and a class label is assigned to the test image that belongs to the unknown class. In this paper, a pose invariant deeply learned multiview 3D face recognition approach is proposed and aims to address two problems: face alignment and face recognition through identification and verification setups. The proposed alignment algorithm is capable of handling frontal as well as profile face images. It employs a nose tip heuristic based pose learning approach to estimate acquisition pose of the face followed by coarse to fine nose tip alignment using L2 norm minimization. The whole face is then aligned through transformation using knowledge learned from nose tip alignment. Inspired by the intrinsic facial symmetry of the Left Half Face (LHF) and Right Half Face (RHF), Deeply learned (d) Multi-View Average Half Face (d-MVAHF) features are employed for face identification using deep convolutional neural network (dCNN). For face verification d-MVAHF-Support Vector Machine (d-MVAHF-SVM) approach is employed. The performance of the proposed methodology is demonstrated through extensive experiments performed on four databases: GavabDB, Bosphorus, UMB-DB, and FRGC v2.0. The results show that the proposed approach yields superior performance as compared to existing state-of-the-art methods.

scholarly journals Using the Relevance Vector Machine Model Combined with Local Phase Quantization to Predict Protein-Protein Interactions from Protein Sequences

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Ji-Yong An ◽  
Fan-Rong Meng ◽  
Zhu-Hong You ◽  
Yu-Hong Fang ◽  
Yu-Jun Zhao ◽  
...  
Keyword(s):  
Protein Sequences ◽  
Relevance Vector Machine ◽  
Experimental Results ◽  
Computational Method ◽  
Support Vector ◽  
Svm Classifier ◽  
Local Phase ◽  
Local Phase Quantization ◽  
Phase Quantization ◽  
Better Than

We propose a novel computational method known as RVM-LPQ that combines the Relevance Vector Machine (RVM) model and Local Phase Quantization (LPQ) to predict PPIs from protein sequences. The main improvements are the results of representing protein sequences using the LPQ feature representation on a Position Specific Scoring Matrix (PSSM), reducing the influence of noise using a Principal Component Analysis (PCA), and using a Relevance Vector Machine (RVM) based classifier. We perform 5-fold cross-validation experiments onYeastandHumandatasets, and we achieve very high accuracies of 92.65% and 97.62%, respectively, which is significantly better than previous works. To further evaluate the proposed method, we compare it with the state-of-the-art support vector machine (SVM) classifier on theYeastdataset. The experimental results demonstrate that our RVM-LPQ method is obviously better than the SVM-based method. The promising experimental results show the efficiency and simplicity of the proposed method, which can be an automatic decision support tool for future proteomics research.

Sign in / Sign up

Export Citation Format

Share Document