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Int. J. Bioinform. Res. Appl.最新文献

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BiETopti: biclustering ensemble technique using optimisation BiETopti:使用优化的双聚类集成技术
Int. J. Bioinform. Res. Appl. Pub Date : 2017-03-24 DOI: 10.1504/IJBRA.2017.10003485
Geeta Aggarwal, Neelima Gupta
{"title":"BiETopti: biclustering ensemble technique using optimisation","authors":"Geeta Aggarwal, Neelima Gupta","doi":"10.1504/IJBRA.2017.10003485","DOIUrl":"https://doi.org/10.1504/IJBRA.2017.10003485","url":null,"abstract":"Ensemble methods have been known to improve the quality of clusters/biclusters. We present in this paper an ensemble method for the biclustering problem using optimisation techniques. Extensive experiments performed on synthetic datasets and gene expression data have shown that the proposed method provides superior biclusters than the existing biclustering solutions most of the times.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"73 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125459639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A new and efficient method based on syntactic dependency relations features for ad hoc clinical question classification 基于句法依赖关系特征的特殊临床问题分类新方法
Int. J. Bioinform. Res. Appl. Pub Date : 2017-03-24 DOI: 10.1504/IJBRA.2017.10003490
Mourad Sarrouti, Abdelmonaime Lachkar
{"title":"A new and efficient method based on syntactic dependency relations features for ad hoc clinical question classification","authors":"Mourad Sarrouti, Abdelmonaime Lachkar","doi":"10.1504/IJBRA.2017.10003490","DOIUrl":"https://doi.org/10.1504/IJBRA.2017.10003490","url":null,"abstract":"Clinical question classification is an important and a challenging task for any clinical Question Answering (QA) system. It classifies questions into different semantic categories, which indicate the expected semantic type of answers. Indeed, the semantic category allows filtering out irrelevant answer candidates. Existing methods dealing with the problem of clinical question classification don't take into account the syntactic dependency relations in questions. Therefore, this may impact negatively the performance of the clinical question classification system. To overcome this drawback, we propose to incorporate the syntactic dependency relations as discriminative features for machine learning. To evaluate and illustrate the interest of our contribution, we conduct a comparative study using nine methods and two machine-learning algorithms: Naive Bayes and Support Vector Machine (SVM). The obtained results using 4654 clinical questions maintained by the National Library of Medicine (NLM) show that our proposed method is very efficient and outperforms greatly the others by the average F-score of 4.5% for Naive Bayes and 4.73% for SVM.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"187 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115425809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
Evaluating a hierarchical approach for heartbeat classification from ECG 评价一种基于ECG的分层心跳分类方法
Int. J. Bioinform. Res. Appl. Pub Date : 2017-03-24 DOI: 10.1504/IJBRA.2017.10003488
Eduardo José da S. Luz, L. Merschmann, D. Menotti, G. Moreira
{"title":"Evaluating a hierarchical approach for heartbeat classification from ECG","authors":"Eduardo José da S. Luz, L. Merschmann, D. Menotti, G. Moreira","doi":"10.1504/IJBRA.2017.10003488","DOIUrl":"https://doi.org/10.1504/IJBRA.2017.10003488","url":null,"abstract":"Several types of arrhythmias that can be rare and harmless, but may result in serious cardiac issues, and several ECG analysis methods have been proposed in the literature to automatically classify the various classes of arrhythmias. Following the Association for the Advancement of Medical Instrumentation (AAMI) standard, 15 classes of heartbeats can be hierarchically grouped into five superclasses. In this work, we propose to employ the hierarchical classification paradigm to five ECG analysis methods in the literature, and compare their performance with flat classification paradigm. In our experiments, we use the MIT-BIH Arrhythmia Database and analyse the use of the hierarchical classification following AAMI standard and a well-known and established evaluation protocol using five superclasses. The experimental results showed that the hierarchical classification provided the highest gross accuracy for most of the methods used in this work and provided an improvement in classification performance of N and SVEB superclasses.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134021753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Using conditional inference forest to identify variable importance 利用条件推理林识别变量重要性
Int. J. Bioinform. Res. Appl. Pub Date : 2017-03-24 DOI: 10.1504/IJBRA.2017.10003483
N. Settouti, Mostafa EL HABIB DAHO, Amine Chikh
{"title":"Using conditional inference forest to identify variable importance","authors":"N. Settouti, Mostafa EL HABIB DAHO, Amine Chikh","doi":"10.1504/IJBRA.2017.10003483","DOIUrl":"https://doi.org/10.1504/IJBRA.2017.10003483","url":null,"abstract":"Variable importance measure with Random Forests (RF) have received increased attention as a means of variable selection in classification tasks. The measure of variable importance in Random Forests is a smart way of variable selection in many applications, but is not reliable in situations where potential predictor variables vary in their scale of measurement or their number of categories. In this paper, we have implemented Random Forest built from Conditional Inference Trees (CIT) that is called Conditional Inference Forest (CIF). In each tree in the forest of conditional inference, the division of the nodes is based on the way to have a good associativity. The chi-square test statistics is used to measure the association. In addition to identifying variables that improve the classification accuracy, the methodology also clearly identifies the variables that are neutral to the accuracy, and also those who interfere in the right classification. In this paper, we are particularly interested in the overall algorithm Conditional Inference Forest (CIF) for the classification of large biological data. The algorithm is evaluated on its ability to select a reduced number of features while preserving a very satisfactory classification rate.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125583854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A new neural unsupervised classification approach using amended competitive Hebbian learning: PET image segmentation insights 利用改进的竞争性Hebbian学习的一种新的神经无监督分类方法:PET图像分割洞察
Int. J. Bioinform. Res. Appl. Pub Date : 2017-02-09 DOI: 10.1504/IJBRA.2017.10002820
M. Timouyas, S. Eddarouich, A. Hammouch
{"title":"A new neural unsupervised classification approach using amended competitive Hebbian learning: PET image segmentation insights","authors":"M. Timouyas, S. Eddarouich, A. Hammouch","doi":"10.1504/IJBRA.2017.10002820","DOIUrl":"https://doi.org/10.1504/IJBRA.2017.10002820","url":null,"abstract":"This paper proposes a new classification procedure based on the competitive concept, divided into three processing stages. It begins by the estimation of the Probability Density Function (pdf), followed by a competitive training neural network with the Mahalanobis distance as an activation function. This stage allows detecting the local maxima of the pdf. Then, we use the competitive Hebbian learning to analyse the connectivity between the detected maxima of the pdf upon the Mahalanobis distance. The so detected groups of maxima are then used for the classification process. Compared to the K-means clustering or the clustering approaches based on the different competitive learning schemes, the proposed approach has proven, under a number of real (positron emission tomography image) and synthetic data samples, that it does not pass by any thresholding and does not require any prior information on the number of classes or on the structure of their distributions in the data set.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"41 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123976999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
An empirical study of self-training and data balancing techniques for splice site prediction 剪接位置预测的自我训练和数据平衡技术的实证研究
Int. J. Bioinform. Res. Appl. Pub Date : 2017-02-09 DOI: 10.1504/IJBRA.2017.10002831
A. Stanescu, Doina Caragea
{"title":"An empirical study of self-training and data balancing techniques for splice site prediction","authors":"A. Stanescu, Doina Caragea","doi":"10.1504/IJBRA.2017.10002831","DOIUrl":"https://doi.org/10.1504/IJBRA.2017.10002831","url":null,"abstract":"Thanks to Next Generation Sequencing technologies, unlabelled data is now generated easily, while the annotation process remains expensive. Semi-supervised learning represents a cost-effective alternative to supervised learning, as it can improve supervised classifiers by making use of unlabelled data. However, semi-supervised learning has not been studied much for problems with highly skewed class distributions, which are prevalent in bioinformatics. To address this limitation, we carry out a study of a semi-supervised learning algorithm, specifically self-training based on Naive Bayes, with focus on data-level approaches for handling imbalanced class distributions. Our study is conducted on the problem of predicting splice sites and it is based on datasets for which the ratio of positive to negative examples is 1-to-99. Our results show that under certain conditions semi-supervised learning algorithms are a better choice than purely supervised classification algorithms.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"90 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126235628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
In silico pathway analysis of MAPKs and computational investigation of bipyrazole analogues as novel p38alpha MAPK inhibitors MAPK的硅通路分析和双吡唑类似物作为新型p38 α MAPK抑制剂的计算研究
Int. J. Bioinform. Res. Appl. Pub Date : 2016-03-01 DOI: 10.1504/IJBRA.2016.075395
Deepak Nedunuri, Y. Adimulam, K. Reddi
{"title":"In silico pathway analysis of MAPKs and computational investigation of bipyrazole analogues as novel p38alpha MAPK inhibitors","authors":"Deepak Nedunuri, Y. Adimulam, K. Reddi","doi":"10.1504/IJBRA.2016.075395","DOIUrl":"https://doi.org/10.1504/IJBRA.2016.075395","url":null,"abstract":"Mitogen-Activated Protein Kinase MAPK belongs to one of the largest super-families of proteins. The activity of most MAPKs is stimulated by a large variety of signals, including mitogens, growth factors, cytokines, T-cell antigens, pheromones, UV and ionising radiations, osmotic stress, heat shock, oxidative stress and others. The present work determines the participation of particular MAPK to one specific pathway in the MAPKinase signalling MAPK 1-14. Various computational analyses involving Clustal omega, phylogenetic tree reconstruction and ProDom have been utilised in the study. Based on evolutionary relationships, domain detections and comparison of active site residues, the specificity of MAPKs in defined pathways is emphasised. MAPKs have been shown to play a pivotal role in diverse diseases, including cancer. Majority of studies have focused on targeting p38 MAPK isoform alpha MAPK14. Hence, in this paper we elucidate a computational mechanism of inhibition by bipyrazole analogues, for the first time, as promising inhibitors of p38alpha MAPK.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"135 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116669748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
An improved gSVM-SCADL2 with firefly algorithm for identification of informative genes and pathways 基于萤火虫算法的改进gSVM-SCADL2信息基因和路径识别
Int. J. Bioinform. Res. Appl. Pub Date : 2016-03-01 DOI: 10.1504/IJBRA.2016.075404
Weng Howe Chan, M. S. Mohamad, S. Deris, J. Corchado, S. Omatu, Z. Ibrahim, S. Kasim
{"title":"An improved gSVM-SCADL2 with firefly algorithm for identification of informative genes and pathways","authors":"Weng Howe Chan, M. S. Mohamad, S. Deris, J. Corchado, S. Omatu, Z. Ibrahim, S. Kasim","doi":"10.1504/IJBRA.2016.075404","DOIUrl":"https://doi.org/10.1504/IJBRA.2016.075404","url":null,"abstract":"Incorporation of pathway knowledge into microarray analysis has been favoured by researchers owing to the improved biological interpretation of the analysis outcome. However, most of the pathway data are manually curated without specific biological context. Inclusion of non-informative genes in the analysis of context specific microarray data could lead to classifier with poor discriminative power. Thus, one of the main challenges is how to effectively identify informative genes from the pathway data. This paper proposes a firefly optimised penalised support vector machine with SCADL2 penalty function SVM-SCADL2-FFA in optimising tuning parameters for each pathway for efficient identification of informative genes and pathways. Experiments are done on lung cancer and gender data sets. Tenfold CV is used to evaluate the performance in terms of accuracy, specificity, sensitivity and F-score. The identified informative genes are validated through online databases. Our proposed method shows consistent improvements compared to previous works.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126866104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Wireless monitoring and analysis of PPG signal for assessment of cardiovascular system in real time 无线监测和分析PPG信号，实时评估心血管系统
Int. J. Bioinform. Res. Appl. Pub Date : 2016-03-01 DOI: 10.1504/IJBRA.2016.075397
B. Jayadevappa, M. Holi
{"title":"Wireless monitoring and analysis of PPG signal for assessment of cardiovascular system in real time","authors":"B. Jayadevappa, M. Holi","doi":"10.1504/IJBRA.2016.075397","DOIUrl":"https://doi.org/10.1504/IJBRA.2016.075397","url":null,"abstract":"In the present work a simple, non-invasive and portable electro-optical based wireless real-time PPG monitoring system has been developed. The system can be used for monitoring of patient's health status specially those of disabled and suffering from cardiovascular diseases. It records variations in the volume of blood with each heart beat resulting in the form of signal called photoplethysmogram PPG. System consists of light source and photo-detector packed in the form of probe, fitted to patient's index finger. For remote monitoring of PPG signals, a ZigBee wireless technology is used. The PPG contain rich information about cardiovascular and respiratory systems. From PPG, parameters like pulse rate PR, average pulse rate APR, pulse rate variability PRV and frequency spectrum were determined for diagnostic purpose. System monitors the patient's health conditions without restricting their movements, hence can be extended beyond hospital limits. Thus, physician can monitor the patient's health status remotely.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128746309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
A complete review of computational methods for human and HIV-1 protein interaction prediction 人类和HIV-1蛋白相互作用预测计算方法的完整回顾
Int. J. Bioinform. Res. Appl. Pub Date : 2016-03-01 DOI: 10.1504/IJBRA.2016.075396
Debasmita Pal, K. Mondal
{"title":"A complete review of computational methods for human and HIV-1 protein interaction prediction","authors":"Debasmita Pal, K. Mondal","doi":"10.1504/IJBRA.2016.075396","DOIUrl":"https://doi.org/10.1504/IJBRA.2016.075396","url":null,"abstract":"Human Immunodeficiency Virus Type 1 HIV-1 has grabbed the attention of virologists in recent times owing to its life-threatening nature and epidemic spread throughout the globe. The virus exploits a complex interaction network of HIV-1 and human proteins for replication, and causes destruction to the human immunity power. Antiviral drugs are designed to utilise the information on viral-host Protein-Protein Interactions PPIs, so that the viral replication and infection can be prevented. Therefore, the prediction of novel interactions based on experimentally validated interactions, curated in the public PPI database, could help in discovering new therapeutic targets. This article gives an overview of HIV-1 proteins and their role in virus-replication followed by a discussion on different types of antiretroviral drugs and HIV-1-human PPI database. Thereafter, we have presented a brief explanation of different computational approaches adopted to predict new HIV-1-human PPIs along with a comparative study among them.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"146 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123076518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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