2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology最新文献_第2页

Aggregated Indexing of Biomedical Time Series Data 生物医学时间序列数据的聚合索引

2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology Pub Date : 2012-09-27 DOI: 10.1109/HISB.2012.13

Jonathan Woodbridge, B. Mortazavi, M. Sarrafzadeh, A. Bui

{"title":"Aggregated Indexing of Biomedical Time Series Data","authors":"Jonathan Woodbridge, B. Mortazavi, M. Sarrafzadeh, A. Bui","doi":"10.1109/HISB.2012.13","DOIUrl":"https://doi.org/10.1109/HISB.2012.13","url":null,"abstract":"Remote and wearable medical sensing has the potential to create very large and high dimensional datasets. Medical time series databases must be able to efficiently store, index, and mine these datasets to enable medical professionals to effectively analyze data collected from their patients. Conventional high dimensional indexing methods are a two stage process. First, a superset of the true matches is efficiently extracted from the database. Second, supersets are pruned by comparing each of their objects to the query object and rejecting any objects falling outside a predetermined radius. This pruning stage heavily dominates the computational complexity of most conventional search algorithms. Therefore, indexing algorithms can be significantly improved by reducing the amount of pruning. This paper presents an online algorithm to aggregate biomedical times series data to significantly reduce the search space (index size) without compromising the quality of search results. This algorithm is built on the observation that biomedical time series signals are composed of cyclical and often similar patterns. This algorithm takes in a stream of segments and groups them to highly concentrated collections. Locality Sensitive Hashing (LSH) is used to reduce the overall complexity of the algorithm, allowing it to run online. The output of this aggregation is used to populate an index. The proposed algorithm yields logarithmic growth of the index (with respect to the total number of objects) while keeping sensitivity and specificity simultaneously above 98%. Both memory and runtime complexities of time series search are improved when using aggregated indexes. In addition, data mining tasks, such as clustering, exhibit runtimes that are orders of magnitudes faster when run on aggregated indexes.","PeriodicalId":375089,"journal":{"name":"2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology","volume":"97 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115138041","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

Ontological Approach for the Management of Informed Consent Permissions 知情同意许可管理的本体方法

2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology Pub Date : 2012-09-27 DOI: 10.1109/HISB.2012.19

M. Grando, A. Boxwala, R. Schwab, N. Alipanah

{"title":"Ontological Approach for the Management of Informed Consent Permissions","authors":"M. Grando, A. Boxwala, R. Schwab, N. Alipanah","doi":"10.1109/HISB.2012.19","DOIUrl":"https://doi.org/10.1109/HISB.2012.19","url":null,"abstract":"We have developed an ontology-based model of subject's permissions and organization's obligations resulting from the informed consent process. For the initial evaluation of the ontology we modeled the research plan of an informed consent document currently used by the UCSD Moores Cancer Center (MCC) for collecting and banking biospecimens for use in cancer research. We have also populated the ontology with de-identified clinical data and sample data from patients who consented to participate in the study. Furthermore, we provided reasoning mechanisms to support requests from real uses cases involving researchers approaching MCC requesting access to use collected clinical data and biospecimens. We supported those requests by identifying resources available for reuse, while checking conformance with preexisting subject's permissions. Based on the lessons learned from this study we propose a scalable framework for specifying subject's permission and checking researcher's resource requests in compliance with given permissions. The proposed framework is an extension of an existing general-purpose policy engine based on XACML (eXtensible Access Control Markup Language), incorporating ontology-based reasoning. Given the lack of standards for sharing, integrating and checking compliance with subject's consents our research could have an important future practical impact.","PeriodicalId":375089,"journal":{"name":"2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology","volume":"41 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133075773","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

University of California Research eXchange (UCReX): A Federated Cohort Discovery System 加州大学研究交流(UCReX):联邦队列发现系统

2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology Pub Date : 2012-09-27 DOI: 10.1109/HISB.2012.71

Aaron Mandel, Michael Kamerick, Douglas Berman, Lisa Dahm

引用次数: 4

Systematic Analysis of Cross-Institutional Medication Description Patterns in Clinical Notes 临床记录中跨机构药物描述模式的系统分析

2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology Pub Date : 2012-09-27 DOI: 10.1109/HISB.2012.43

S. Sohn, Sean P. Murphy, Siddhartha R. Jonnalagadda, K. Wagholikar, Stephen T Wu, C. Chute, Hongfang Liu, Scott R. Halgrim

引用次数: 0

The Frequency of ConText Lexical Items in Diverse Medical Texts 不同医学文本中语境词项的频率

2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology Pub Date : 2012-09-27 DOI: 10.1109/HISB.2012.60

B. Chapman, Wei Wei, W. Chapman

引用次数: 2

A General Purpose Phenotype Algorithm for Venous Thromboembolism Using Billing Codes and Natural Language Processing 使用计费代码和自然语言处理的静脉血栓栓塞的通用表型算法

2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology Pub Date : 2012-09-27 DOI: 10.1109/HISB.2012.74

E. M. Hinz, L. Bastarache, J. Denny

{"title":"A General Purpose Phenotype Algorithm for Venous Thromboembolism Using Billing Codes and Natural Language Processing","authors":"E. M. Hinz, L. Bastarache, J. Denny","doi":"10.1109/HISB.2012.74","DOIUrl":"https://doi.org/10.1109/HISB.2012.74","url":null,"abstract":"Deep venous thrombosis and pulmonary embolism are diseases associated with significant morbidity and mortality. Well described risk factors for venous thromboembolic disease (VTE) include immobility, trauma and genetic hypercoagulabilty states, still many cases have no known associated antecedent risks. Studies to potentially define the missing risk factors preferably identify all cases of VTE. Defining VTE in the electronic health record is more challenging due to the variable duration of VTE treatment, crossover of therapeutic modalities to other chronic diseases and prevention treatment related to hospitalizations. We designed a general purpose Natural Language (NLP) algorithm to capture acute and historical cases of thromboembolic disease retrospectively in a de-identified electronic health record. Applying the NLP algorithm to a separate evaluation set found a positive predictive value of 84.7% and sensitivity of 95.3% for an F-measure of 0.897, which was similar to the training set of 0.925. Use of the same algorithm on problem lists in patients without VTE ICD-9s resulted in a PPV of 83%. NLP of VTE ICD-9 positive cases and non-ICD-9 positive problem lists provides an effective means for capture of both acute and historical cases of venous thromboembolic disease.","PeriodicalId":375089,"journal":{"name":"2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology","volume":"2015 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127790908","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

Cloud Computing Considerations for Biomedical Applications 生物医学应用的云计算考虑

2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology Pub Date : 2012-09-27 DOI: 10.1109/HISB.2012.67

R. Rauscher

引用次数: 4

Ontology-Guided Approach to Retrieving Disease Manifestation Images for Health Image Base Construction 面向健康图像库构建的疾病表现图像检索方法

2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology Pub Date : 2012-09-27 DOI: 10.1109/HISB.2012.32

Yang Chen, Xiaofeng Ren, Guo-Qiang Zhang, Rong Xu

引用次数: 1

Cohort Selection through Content-Based Image Retrieval: vfM A Case Study 基于内容的图像检索中的队列选择:vfM案例研究

2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology Pub Date : 2012-09-27 DOI: 10.1109/HISB.2012.42

Mayank Agarwal, Javed Mostafa

引用次数: 0

A Task-Based Approach for Large-Scale Evaluation of the Gene Ontology 基于任务的基因本体大规模评价方法

2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology Pub Date : 2012-09-27 DOI: 10.1109/HISB.2012.69

Salvatore Loguercio, Erik L. Clarke, Benjamin M. Good, A. Su

{"title":"A Task-Based Approach for Large-Scale Evaluation of the Gene Ontology","authors":"Salvatore Loguercio, Erik L. Clarke, Benjamin M. Good, A. Su","doi":"10.1109/HISB.2012.69","DOIUrl":"https://doi.org/10.1109/HISB.2012.69","url":null,"abstract":"The Gene Ontology (GO) provides a framework to systematically classify and annotate gene function. The annotations associated with GO play a critical role in modern biology and cover many organisms. For the human genome, over 10,000 GO terms are used to annotate gene function in an expansive database of over 200,000 annotations. Due to the importance of the GO annotations in modern biology, significant effort has been put into assessing the quality of the annotations. Providing measures of annotation completeness, accuracy, and precision is critical if researchers are to use the annotations in real-world applications with confidence. Here, we describe a task-based approach that examines the completeness and utility of GO annotations through the lens of gene enrichment analysis. Our approach can be used to model the progression of the GO annotations over time, either for a particular area of interest or for the body of annotations as a whole. Using this framework, we conducted a large-scale analysis of gene expression datasets from the NCBI Gene Expression Omnibus (GEO). In particular, we identified terms of interest for each dataset through semantic annotation of biomedical data, then tracked the behavior of these terms as a function of time. The preliminary results provide significant information about the progress and character of GO annotations over time. This framework is flexible enough to examine all or part of the GO annotations, across multiple species, and with various enrichment methods. We also discuss how this framework can be used to evaluate different annotation methods. For example, by comparing the performance of annotations generated with a particular method to the performance of canonical annotations, it is possible to determine their relative quality.","PeriodicalId":375089,"journal":{"name":"2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127808756","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