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18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05)最新文献

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ProGenGrid: a workflow service infrastructure for composing and executing bioinformatics grid services ProGenGrid:用于组合和执行生物信息学网格服务的工作流服务基础设施
18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05) Pub Date : 2005-06-23 DOI: 10.1109/CBMS.2005.90
G. Aloisio, M. Cafaro, S. Fiore, M. Mirto
{"title":"ProGenGrid: a workflow service infrastructure for composing and executing bioinformatics grid services","authors":"G. Aloisio, M. Cafaro, S. Fiore, M. Mirto","doi":"10.1109/CBMS.2005.90","DOIUrl":"https://doi.org/10.1109/CBMS.2005.90","url":null,"abstract":"We describe the ProGenGrid (Proteomics and Genomics Grid) Workflow system, developed by the CACT/ISUFI at the University of Lecce which aims at providing a tool that e-scientists can utilize to simulate biological experiments, compose existing analysis and visualization tools, monitor their execution, store the intermediate and final output and finally, if needed, save the model of the experiment for updating or reproducing it. The tools that we are considering are software components wrapped as Web services and composed through a workflow. Since bioinformatics applications need to use high performance machines or many workstations to reduce the computational time, we are exploiting a Grid infrastructure for interconnecting wide-spread tools and hardware resources.","PeriodicalId":119367,"journal":{"name":"18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05)","volume":"142 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124889388","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: 22
Preprocessing of mass spectrometry proteomics data on the grid 网格上质谱蛋白质组学数据的预处理
18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05) Pub Date : 2005-06-23 DOI: 10.1109/CBMS.2005.87
M. Cannataro, P. Guzzi, T. Mazza, G. Tradigo, P. Veltri
{"title":"Preprocessing of mass spectrometry proteomics data on the grid","authors":"M. Cannataro, P. Guzzi, T. Mazza, G. Tradigo, P. Veltri","doi":"10.1109/CBMS.2005.87","DOIUrl":"https://doi.org/10.1109/CBMS.2005.87","url":null,"abstract":"The combined use of mass spectrometry and data mining is a novel approach in proteomic pattern analysis for discovering novel biomarkers or identifying patterns and associations in proteomic profiles. Data produced by mass spectrometers are affected by errors and noise due to sample preparation and instrument approximation, so different preprocessing techniques need to be applied before analysis is conducted. We survey different techniques for spectra preprocessing, and we present a first design of a software tool that allows the preprocessing, management and analysis of mass spectrometry data on the Grid.","PeriodicalId":119367,"journal":{"name":"18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05)","volume":"60 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122628555","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: 33
Classifying craniosynostosis deformations by skull shape imaging 颅骨形状成像对颅缝闭合变形的分类
18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05) Pub Date : 2005-06-23 DOI: 10.1109/CBMS.2005.42
S. Ruiz-Correa, R. Sze, H. J. Lin, L. Shapiro, M. Speltz, M. Cunningham
{"title":"Classifying craniosynostosis deformations by skull shape imaging","authors":"S. Ruiz-Correa, R. Sze, H. J. Lin, L. Shapiro, M. Speltz, M. Cunningham","doi":"10.1109/CBMS.2005.42","DOIUrl":"https://doi.org/10.1109/CBMS.2005.42","url":null,"abstract":"Craniosynostosis is a serious and common disease of children, caused by premature fusion of the sutures of the skull. The resulting abnormal skull growth can lead to severe deformity, increased intra-cranial pressure, vision, hearing and breathing problems. In this work we develop an algorithmic framework to accurately classify deformations caused by sagittal craniosynostosis. The basic idea is to combine our novel cranial image shape descriptors and off-the-shelf classification technologies to encode morphological variations that characterize the synostotic skull. We demonstrate the efficacy of our approach in a series of large-scale classification experiments that compare the performance of our proposed image descriptors to those of traditional clinical indices and Fourier-based measurements.","PeriodicalId":119367,"journal":{"name":"18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05)","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125257005","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: 18
An ontology-driven clustering method for supporting gene expression analysis 支持基因表达分析的本体驱动聚类方法
18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05) Pub Date : 2005-06-23 DOI: 10.1109/CBMS.2005.29
Haiying Wang, F. Azuaje, O. Bodenreider
{"title":"An ontology-driven clustering method for supporting gene expression analysis","authors":"Haiying Wang, F. Azuaje, O. Bodenreider","doi":"10.1109/CBMS.2005.29","DOIUrl":"https://doi.org/10.1109/CBMS.2005.29","url":null,"abstract":"The gene ontology (GO) is an important knowledge resource for biologists and bioinformaticians. This paper explores the integration of similarity information derived from GO into clustering-based gene expression analysis. A system that integrates GO annotations, similarity patterns and expression data in yeast is assessed. In comparison with a clustering model based only on expression data correlation, the proposed framework not only produces consistent results, but also it offers alternative, potentially meaningful views of the biological problem under study. Moreover, it provides the basis for developing other automated, knowledge-driven data mining systems in this and related application areas.","PeriodicalId":119367,"journal":{"name":"18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05)","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127252875","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: 31
Application of a digital deconvolution technique to brain temperature measurement and its correlation with other physiological parameters 数字反褶积技术在脑温度测量中的应用及其与其他生理参数的相关性
18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05) Pub Date : 2005-06-23 DOI: 10.1109/CBMS.2005.32
C. Merino, M. Luis-Garcia, S. Hernández, F. Martin, O. Casanova, D. Gomez, M. Castellano, J. González-Mora
{"title":"Application of a digital deconvolution technique to brain temperature measurement and its correlation with other physiological parameters","authors":"C. Merino, M. Luis-Garcia, S. Hernández, F. Martin, O. Casanova, D. Gomez, M. Castellano, J. González-Mora","doi":"10.1109/CBMS.2005.32","DOIUrl":"https://doi.org/10.1109/CBMS.2005.32","url":null,"abstract":"The underlying reason for the local hyperthermia changes produced after a stimulus is not very well known and the relationship between local temperature changes and other physiological parameters has never been established. Current local temperature measurements are not completely accurate over time due to the physical constraints of the sensor, such as heat accumulation and dissipation. To clarify this issue, simultaneous in vivo measurements of local temperature, local blood-flow by laser Doppler flowmetry and neurotransmitter extracellular release using in vivo amperometry were performed with the aim of establishing their interrelationship. Local brain temperature measurements are usually obtained using thermocouples and thermistors, generally because of their small size and high level of accuracy. However, due to heat accumulation and dissipation effects on the sensor, the transient temperature measurement is not as accurate. In this paper, a simple method to obtain actual temperature fluctuations from measured values is proposed using classical digital signal processing techniques; the sensor was modeled via its transfer function. Deconvolution provides a method for obtaining actual temperature changes, enabling further comparative kinetic studies of all those physiological parameters, and helps to clarify the probable mechanism that underlies neurovascular coupling.","PeriodicalId":119367,"journal":{"name":"18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05)","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124160642","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
Precedence temporal networks from gene expression data 基因表达数据的优先时间网络
18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05) Pub Date : 2005-06-23 DOI: 10.1109/CBMS.2005.83
L. Sacchi, R. Bellazzi, Riccardo Porreca, C. Larizza, P. Magni
{"title":"Precedence temporal networks from gene expression data","authors":"L. Sacchi, R. Bellazzi, Riccardo Porreca, C. Larizza, P. Magni","doi":"10.1109/CBMS.2005.83","DOIUrl":"https://doi.org/10.1109/CBMS.2005.83","url":null,"abstract":"In this paper we introduce a novel method to extract from data and graphically represent the temporal relationships between events, called precedence temporal network. The new approach first derives events from time series by exploiting the temporal abstraction technique, then derives temporal precedence between abstractions in terms of association rules and finally expresses the relationships as a labeled graph. The method is applied to the problem of representing the temporal behavior of gene expressions, as they are collected by DNA microarrays. In particular, in this paper we present the results obtained from the analysis of the expression of a subset of the genes involved in cell-cycle regulation.","PeriodicalId":119367,"journal":{"name":"18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130381174","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
Generating a synthetic diffusion tensor dataset 生成一个合成扩散张量数据集
18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05) Pub Date : 2005-06-23 DOI: 10.1109/CBMS.2005.58
Ørjan Bergmann, A. Lundervold, T. Steihaug
{"title":"Generating a synthetic diffusion tensor dataset","authors":"Ørjan Bergmann, A. Lundervold, T. Steihaug","doi":"10.1109/CBMS.2005.58","DOIUrl":"https://doi.org/10.1109/CBMS.2005.58","url":null,"abstract":"During the last years, many techniques for de-noising, segmentation and fiber-tracking have been applied to diffusion tensor MR image data (DTI) from human and animal brains. However, evaluating such methods may be difficult on these data since there is no gold standard regarding the true geometry of the brain anatomy or fiber bundles reconstructed in each particular case. In order to study, validate and compare various de-noising and fiber-tracking methods, there is a need for a (mathematical) phantom consisting of semi-realistic images with well-known properties. In this work we generate such a phantom and provide a description of the calculation process all the way up to voxel-wise diffusion tensor visualization.","PeriodicalId":119367,"journal":{"name":"18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05)","volume":"62 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132984543","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: 9
An online analysis and information fusion platform for heterogeneous biomedical informatics data 异构生物医学信息学数据在线分析与信息融合平台
18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05) Pub Date : 2005-06-23 DOI: 10.1109/CBMS.2005.28
S. R. Ganta, Jyotsna Kasturi, J. Gilbertson, R. Acharya
{"title":"An online analysis and information fusion platform for heterogeneous biomedical informatics data","authors":"S. R. Ganta, Jyotsna Kasturi, J. Gilbertson, R. Acharya","doi":"10.1109/CBMS.2005.28","DOIUrl":"https://doi.org/10.1109/CBMS.2005.28","url":null,"abstract":"Current research in biomedical informatics involves analysis of multiple heterogeneous data sets. This includes patient demographics, clinical and pathology data, treatment history, patient outcomes as well as gene expression, DNA sequences and other information sources such as gene ontologies. Analysis of these data sets could lead to better disease diagnosis, prognosis, treatment and drug discovery. However, the extent of knowledge that can be extracted from individual data sets is limited Recently, there has been a lot of focus on techniques that analyze genomic data sources in an integrated manner through information fusion. This places a need for an online platform to analyze biomedical informatics data sets using these techniques. We present here an online data warehouse to perform data exploration and analysis across heterogeneous biomedical informatics data sets with the aid of information fusion. The prototype platform is available at http://biogeowarehouse.cse.psu.edu.","PeriodicalId":119367,"journal":{"name":"18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05)","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128345072","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
Decision support system using multimedia case history quantitative comparison and multivariate statistical analysis 决策支持系统采用多媒体案例历史定量比较和多元统计分析
18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05) Pub Date : 2005-06-23 DOI: 10.1109/CBMS.2005.47
N. Shklovskiy-Kordi, V. V. Shakin, Grigory O. Ptashko, M. Surin, B. Zingerman, S. Goldberg, M. Krol
{"title":"Decision support system using multimedia case history quantitative comparison and multivariate statistical analysis","authors":"N. Shklovskiy-Kordi, V. V. Shakin, Grigory O. Ptashko, M. Surin, B. Zingerman, S. Goldberg, M. Krol","doi":"10.1109/CBMS.2005.47","DOIUrl":"https://doi.org/10.1109/CBMS.2005.47","url":null,"abstract":"A decision support system (DSS) for modeling and generalization of verified clinical information on individual patients is being developed. The data set for each patient is collected inform of multimedia case history (MMCH). The paper presents an approach to the data processing. The approach is based on case-to-case and case-to-cluster comparative and multivariate statistical analysis of the patients' data. Namely, the DSS use the normalization procedures in individual time-and-subspace domain and the interpolation techniques for multimedia data. It makes the individual MMCH data to be pair-wise comparable. Some evaluation results of the approach in area of hematology are presented. Sample set of relevant MMCH data has been obtained for a dozen of Chernobyl patients. The approach developed is to provide backgrounds for a unified language to meet needs of WHO in quantitative description, comparison and generalization of individual patients' patterns.","PeriodicalId":119367,"journal":{"name":"18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05)","volume":"174 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123837126","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
Case-based tissue classification for monitoring leg ulcer healing 基于病例的组织分类监测腿部溃疡愈合
18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05) Pub Date : 2005-06-23 DOI: 10.1109/CBMS.2005.39
M. Galushka, Huiru Zheng, D. Patterson, L. Bradley
{"title":"Case-based tissue classification for monitoring leg ulcer healing","authors":"M. Galushka, Huiru Zheng, D. Patterson, L. Bradley","doi":"10.1109/CBMS.2005.39","DOIUrl":"https://doi.org/10.1109/CBMS.2005.39","url":null,"abstract":"The ability to automatically monitor the wound healing process would reduce the workload of professionals, provide standardization, reduce costs, and improve the quality of care for patients. Here we propose an automatic monitoring system for leg ulcers based on case-based reasoning. We focus on the first stage of the monitoring process in this work, that of tissue classification and examine a number of different feature extraction techniques based on texture and Red, Green, and Blue histograms. Results clearly show a case-based approach to be ideal for this type of task.","PeriodicalId":119367,"journal":{"name":"18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05)","volume":"44 3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114231101","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: 37
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