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Prediction of transposable elements evolution using tabu search 基于禁忌搜索的转座因子演化预测
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2018-12-01 DOI: 10.1109/BIBM.2018.8621478
Lingling Jin, Ian McQuillan
{"title":"Prediction of transposable elements evolution using tabu search","authors":"Lingling Jin, Ian McQuillan","doi":"10.1109/BIBM.2018.8621478","DOIUrl":"https://doi.org/10.1109/BIBM.2018.8621478","url":null,"abstract":"Transposable elements (TEs) are DNA sequences that can move or copy to new positions within a genome. Due to their abundance in many species, predicting the evolution of these TEs within a genome is a major component of understanding the evolution of the genome generally. The sequential interruption model is defined between TEs that occur in a single genome, which has been shown to be useful in previous literature in predicting TE ages and periods of activity throughout evolution. This model is closely related to a classic matrix optimization problem: the linear ordering problem (LOP). By applying a well-studied method of solving the LOP, tabu search, to the sequential interruption model, a relative age order of all TEs in the human genome is predicted in only 38 seconds. A comparison of the TE ordering between tabu search and the previously existing method shows that tabu search solves the TE problem exceedingly more efficiently, while it still achieves a more accurate result. The speed improvements allow a complete prediction of human TEs to be made, whereas previously, ordering of only a small portion of human TEs could be predicted. A simulation of TE transpositions throughout evolution is then developed and used as a form of in silico verification to the sequential interruption model. By feeding the simulated TE remnants and activity data into the model, a relative age order is predicted using the sequential interruption model, and a quantified correlation between this predicted order and the input (true) age order in the simulation can be calculated. An average correlation over ten simulations is calculated as 0.738 with the correct simulated answer.","PeriodicalId":108667,"journal":{"name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128782400","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
Reconstructing and Decomposing Protein Energy Landscapes to Organize Structure Spaces and Reveal Biologically-active States 重构与分解蛋白质能量景观，组织结构空间，揭示生物活性状态
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2018-12-01 DOI: 10.1109/BIBM.2018.8621411
N. Akhter, Jing Lei, Wanli Qiao, Amarda Shehu
{"title":"Reconstructing and Decomposing Protein Energy Landscapes to Organize Structure Spaces and Reveal Biologically-active States","authors":"N. Akhter, Jing Lei, Wanli Qiao, Amarda Shehu","doi":"10.1109/BIBM.2018.8621411","DOIUrl":"https://doi.org/10.1109/BIBM.2018.8621411","url":null,"abstract":"The concept of energy landscape has become a useful construction in protein modeling due to its ability to relate structures and structural dynamics to function. While great progress is being made in probing energy landscapes, it remains unclear how to reconstruct the landscape from computed structures. Recently, our laboratories have made headway in this direction via concepts from topological and statistical analysis of spatial data. In this paper, we propose a novel approach to reconstruct the underlying energy landscape populated by computed/sampled energy-evaluated structures of a molecule and decompose it into basins of attraction. We demonstrate that such a construction not only allows deep analysis of the efficacy of a structure computation algorithm and the energy function it employs in the first place, but, more importantly, makes important steps toward addressing the open decoy selection problem in template-free protein structure prediction.","PeriodicalId":108667,"journal":{"name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124589951","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
GPU-accelerated CellProfiler GPU-accelerated CellProfiler
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2018-12-01 DOI: 10.1109/BIBM.2018.8621271
Imen Chakroun, Nick Michiels, Roel Wuyts
{"title":"GPU-accelerated CellProfiler","authors":"Imen Chakroun, Nick Michiels, Roel Wuyts","doi":"10.1109/BIBM.2018.8621271","DOIUrl":"https://doi.org/10.1109/BIBM.2018.8621271","url":null,"abstract":"CellProfiler excels at bridging the gap between advanced image analysis algorithms and scientists who lack computational expertise. It lacks however high performance capabilities needed for High Throughput Imaging experiments where workloads reach hundreds of TB of data and are computationally very demanding. In this work, we introduce a GPU-accelerated CellProfiler where the most time-consuming algorithmic steps are executed on Graphics Processing Units. Experiments on a benchmark dataset showed significant speedup over both single and multi-core CPU versions. The overall execution time was reduced from 9.83 Days to 31.64 Hours.","PeriodicalId":108667,"journal":{"name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124752132","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
ImmunoAdept – bringing blood microbiome profiling to the clinical practice 将血液微生物组分析带入临床实践
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2018-12-01 DOI: 10.1109/BIBM.2018.8621354
P. Walsh, B. Andrade, C. Palu, Jason Wu, B. Lawlor, B. Kelly, M. Hemmje, Michael Kramer
{"title":"ImmunoAdept – bringing blood microbiome profiling to the clinical practice","authors":"P. Walsh, B. Andrade, C. Palu, Jason Wu, B. Lawlor, B. Kelly, M. Hemmje, Michael Kramer","doi":"10.1109/BIBM.2018.8621354","DOIUrl":"https://doi.org/10.1109/BIBM.2018.8621354","url":null,"abstract":"Microbiome research aims to understand environmental features, relationships and microorganisms’ composition and their genomes. In the context of healthcare, microbiomics has unveiled that health status of the patient is more dependent on the microbiota than ever before thought. Here we present a pipeline designed to bring microbiome analysis to clinical practitioners in order to offer it as a service for diagnostic support. The Immunology Assay Development Platform (ImmunoAdept) enables the analysis of the whole-metagenome, therefore it can identify viruses, bacteria and archaea at species level. With the objective of making the ImmunoAdept platform broadly available, a cloud-based infrastructure was used, combined with an easy to use input and results interface. This was achieved by implementing it as part of Simplicity, TM a bespoke bioinformatics platform.","PeriodicalId":108667,"journal":{"name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"58 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126701964","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
Multiscale Computing in Systems Medicine: a Brief Reflection 系统医学中的多尺度计算:一个简短的反思
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2018-12-01 DOI: 10.1109/BIBM.2018.8621361
Huiru Zheng, Jyotsna Talreja Wassan, M. Moisescu, L. Stoicu-Tivadar, J. Miranda, Mihaela Crișan-Vida, I. Sacala, A. Badnjević, I. Chorbev, B. Jakimovski
{"title":"Multiscale Computing in Systems Medicine: a Brief Reflection","authors":"Huiru Zheng, Jyotsna Talreja Wassan, M. Moisescu, L. Stoicu-Tivadar, J. Miranda, Mihaela Crișan-Vida, I. Sacala, A. Badnjević, I. Chorbev, B. Jakimovski","doi":"10.1109/BIBM.2018.8621361","DOIUrl":"https://doi.org/10.1109/BIBM.2018.8621361","url":null,"abstract":"Today’s modelling approaches in Systems Medicine are increasingly multiscale, containing two or more submodels, where each operates on different temporal and/or spatial scales. In addition, as these models become increasingly sophisticated, they tend to be run as multiscale computing applications using computational infrastructures such as clusters, supercomputers, grids or clouds. Constructing, validating and deploying such applications is far from trivial, and communities in different scientific disciplines have chosen very diverse approaches to address these challenges. Within this paper we reflect on the use of Multiscale Computing within the context of Systems Medicine. Multiscale Computing is widely applied within this area, and instead of summarizing the field as a whole we will highlight a set of challenges that we believe are of key relevance to the Systems Medicine community.","PeriodicalId":108667,"journal":{"name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124017968","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 new type of wavelet de-noising algorithm for lung sound signals 一种新的肺声信号小波去噪算法
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2018-12-01 DOI: 10.1109/BIBM.2018.8621442
Fei Meng, Yixuan Wang, Yan Shi, M. Cai, Liman Yang, Dongkai Shen
{"title":"A new type of wavelet de-noising algorithm for lung sound signals","authors":"Fei Meng, Yixuan Wang, Yan Shi, M. Cai, Liman Yang, Dongkai Shen","doi":"10.1109/BIBM.2018.8621442","DOIUrl":"https://doi.org/10.1109/BIBM.2018.8621442","url":null,"abstract":"With the development of digital auscultation, the computer-based intelligent auscultation of respiratory sounds has drawn attention of researchers. However, the noises of acquired signals influence the further analysis of lung sound, so there is necessity to develop the noise reduction algorithm of lung sound signals. In this paper, a new type of noise reduction is proposed. The original signals are decomposed into 7 layers by wavelet transform. The locations of lung sound part are obtained in the sub-signals by the mean values of autocorrelation coefficients. The noises between lung sound parts are reduced by setting zero directly. The noises in the lung sound parts are filtered by a Chebyshev type I band-pass filter. The de-noising results are judged by two means. One is the subjective judgement of internal physicians and the de-noising effect is accepted by doctors without distortion. The other is the classification result of sound types in the further research by BP neural network and the classification accuracy can reach 85%.","PeriodicalId":108667,"journal":{"name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"50 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123634248","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
Acupoint Stimulation in Treatment of Obstructive Sleep Apnea Hypopnea Syndrome (OSAHS): A Systematic Review and Meta-analysis 穴位刺激治疗阻塞性睡眠呼吸暂停低通气综合征(OSAHS):系统综述和荟萃分析
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2018-12-01 DOI: 10.1109/BIBM.2018.8621491
Jiayou Zhao, L. Hu, Jinlan Feng, Xinxin Yun, Shan Wu
{"title":"Acupoint Stimulation in Treatment of Obstructive Sleep Apnea Hypopnea Syndrome (OSAHS): A Systematic Review and Meta-analysis","authors":"Jiayou Zhao, L. Hu, Jinlan Feng, Xinxin Yun, Shan Wu","doi":"10.1109/BIBM.2018.8621491","DOIUrl":"https://doi.org/10.1109/BIBM.2018.8621491","url":null,"abstract":"This study aimed to evaluate the clinical effects of acupoint stimulation therapy on patients with obstructive sleep apnea hypopnea syndrome (OSAHS). Methods: A systematic literature search of electronic databases (PubMed, Embase, CENTRAL and Chinese database) was conducted for randomized controlled trials comparing acupoint stimulation with other treatments in OSAHS patients. Literature collected in this paper was published up to May 2016, and random effects meta-analyses were performed by RevMen 5.3 software. Results: 703 patients from 10 trials were included. Comparison between acupoint stimulation and conventional treatment to OSAHS patients, showed significant differences in AHI ([WMD=-9.71, 95% CI (-11.63, -7.78), P<0.00001]), SaO2min ([WMD=4.20, 95% CI (2.26, 6.14), P<0.00001]), and Epworth Sleepiness Scale (ESS) scores ([WMD=- 3.99, 95%CI (-5.83,-2.15), p<0.0001]). However, significant difference between acupoint stimulation and CPAP treatment to OSAHS was not observed. Conclusion: Evidence from this study suggests that stimulate acupoints therapy is effective in improving AHI, SaO2min and ESS in patients with OSAHS.","PeriodicalId":108667,"journal":{"name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121323202","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
An Overview of Machine Learning and HPC in Open Sources for Bioinformatics* 生物信息学开源中的机器学习和高性能计算概述*
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2018-12-01 DOI: 10.1109/BIBM.2018.8621078
Yin-Te Tsai
{"title":"An Overview of Machine Learning and HPC in Open Sources for Bioinformatics*","authors":"Yin-Te Tsai","doi":"10.1109/BIBM.2018.8621078","DOIUrl":"https://doi.org/10.1109/BIBM.2018.8621078","url":null,"abstract":"With development of recent open source software in HPC, such as Hadoop project, bioinformatics applications with large scale biological data can be solved more efficiently. The emerging machine learning algorithms are widely adapted for analysis, recognition and prediction. This paper will survey recent literatures about open source software of machine learning and HPC for bioinformatics applications. The commonly used machine learning algorithms for bioinformatics applications will be summarized here, and the situations of HPC adaption are also provided. Finally, the issues of future usages of machine learning for bioinformatics applications will be included.","PeriodicalId":108667,"journal":{"name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"842 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121389572","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 Extracting Method of Symmetry Plane from Head CT images for Surgery Based on OBB and Image Mutual Information 基于OBB和互信息的外科头部CT图像对称面提取方法
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2018-12-01 DOI: 10.1109/BIBM.2018.8621221
Wenjun Tan, Ying Kang, Zhiwei Dong, Jinzhu Yang, Yingfei Su, Li Zhang, Lisheng Xu, Dazhe Zhao
{"title":"An Extracting Method of Symmetry Plane from Head CT images for Surgery Based on OBB and Image Mutual Information","authors":"Wenjun Tan, Ying Kang, Zhiwei Dong, Jinzhu Yang, Yingfei Su, Li Zhang, Lisheng Xu, Dazhe Zhao","doi":"10.1109/BIBM.2018.8621221","DOIUrl":"https://doi.org/10.1109/BIBM.2018.8621221","url":null,"abstract":"In the field of oral and maxillofacial of surgery, in order to recover the facial symmetry of patients, head symmetry plane is calculated with points chosen manually by doctors. It is great clinical significance to find automatically the symmetry plane of the head before surgery. Aimed at this challenge, an extraction method for head symmetry plane extracting is proposed in this paper. First, region growing method is applied to extract brain tissues from head CT images. Then OBB bounding box method is used to surround the brain tissues to build an initial symmetry plane. Finally, the initial plane is shifted to the best position by mathematical translation and rotation operation with the mutual information. Furthermore, asymmetric index was used to evaluate the accuracy of the extracting symmetry plane. Experimental results showed that the method proposed can achieve the accuracy of manual extracted, but the stable level of this method significantly higher than the manual method.","PeriodicalId":108667,"journal":{"name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114115978","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
Artifact Detection in Multichannel Sleep EEG using Random Forest Classifier 基于随机森林分类器的多通道睡眠脑电图伪影检测
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2018-12-01 DOI: 10.1109/BIBM.2018.8621374
E. Saifutdinova, D. Dudysova, L. Lhotská, V. Gerla, M. Macas
{"title":"Artifact Detection in Multichannel Sleep EEG using Random Forest Classifier","authors":"E. Saifutdinova, D. Dudysova, L. Lhotská, V. Gerla, M. Macas","doi":"10.1109/BIBM.2018.8621374","DOIUrl":"https://doi.org/10.1109/BIBM.2018.8621374","url":null,"abstract":"Detection of artifacts in sleep electroencephalography (EEG) is one of the important tasks on the preprocessing step. Despite many algorithms of artifact detection developed through years, many of them lose their benefits in sleep EEG application. This study proposes a method of artifact detection based on a classification of quasi-stationary EEG epochs with random forest classifier. The method was tested on data of three sleep stages and pre-sleep wake EEG. Results showed 16% increase in $F_{1,} $for the wake and 9%, 5% and 16% for different sleep stages in comparison to a baseline. All false detection at every presented sleep stage is investigated.","PeriodicalId":108667,"journal":{"name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114196447","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
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