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

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Aggregated Indexing of Biomedical Time Series Data 生物医学时间序列数据的聚合索引
Jonathan Woodbridge, B. Mortazavi, M. Sarrafzadeh, A. Bui
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.
远程和可穿戴医疗传感具有创建非常庞大和高维数据集的潜力。医疗时间序列数据库必须能够有效地存储、索引和挖掘这些数据集,以使医疗专业人员能够有效地分析从患者那里收集的数据。传统的高维标引方法分为两个阶段。首先,从数据库中高效提取真实匹配的超集。其次,通过将超集的每个对象与查询对象进行比较并拒绝落在预定半径之外的任何对象来修剪超集。这个修剪阶段在很大程度上支配了大多数传统搜索算法的计算复杂度。因此,通过减少剪枝的数量可以显著改进索引算法。本文提出了一种在线聚合生物医学时间序列数据的算法,在不影响搜索结果质量的前提下,显著减少了搜索空间(索引大小)。该算法是建立在观察生物医学时间序列信号是由周期性和经常相似的模式。该算法接受一个片段流,并将它们分组为高度集中的集合。局部敏感散列(LSH)用于降低算法的整体复杂性,使其能够在线运行。此聚合的输出用于填充索引。所提出的算法使指数(相对于对象总数)呈对数增长,同时保持灵敏度和特异性在98%以上。当使用聚合索引时,时间序列搜索的内存和运行时复杂性都得到了改善。此外,数据挖掘任务(如集群)在聚合索引上运行时的运行时间要快几个数量级。
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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
M. Grando, A. Boxwala, R. Schwab, N. Alipanah
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.
我们开发了一个基于本体的主体权限和组织义务模型,该模型由知情同意过程产生。为了对本体论进行初步评估,我们模拟了一份知情同意文件的研究计划,该文件目前被UCSD摩尔癌症中心(MCC)用于收集和储存用于癌症研究的生物标本。我们还用同意参与研究的患者的去识别临床数据和样本数据填充了本体。此外,我们提供了推理机制,以支持来自真实用例的请求,包括研究人员向MCC请求使用收集的临床数据和生物标本。我们通过识别可重用的资源来支持这些请求,同时检查是否符合先前存在的主题的权限。根据本研究的经验教训,我们提出了一个可扩展的框架,用于指定受试者的权限,并根据给定的权限检查研究人员的资源请求。建议的框架是对现有的基于XACML(可扩展访问控制标记语言)的通用策略引擎的扩展,并结合了基于本体的推理。鉴于缺乏共享、整合和检查受试者同意遵守情况的标准,我们的研究可能会对未来产生重要的实际影响。
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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
Aaron Mandel, Michael Kamerick, Douglas Berman, Lisa Dahm
The University of California has committed to the development of a system to encourage collaboration among its 5 Medical Center campuses. The name of this system is UCReX, for the UC Research eXchange. The goals of UCReX are to: (1) Enhance access to clinical data for research, (2) Build a technical infrastructure to allow crossinstitutional sharing of harmonized clinical data, (3) Inform data collection processes.
加州大学致力于开发一个系统,以鼓励其5个医疗中心校区之间的合作。这个系统的名字是UCReX, UC研究交流。UCReX的目标是:(1)加强对临床研究数据的访问,(2)建立技术基础设施,允许跨机构共享统一的临床数据,(3)为数据收集过程提供信息。
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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
S. Sohn, Sean P. Murphy, Siddhartha R. Jonnalagadda, K. Wagholikar, Stephen T Wu, C. Chute, Hongfang Liu, Scott R. Halgrim
In clinical notes, medication information follows certain semantic patterns and some medication descriptions contain additional word(s) between medication attributes. Therefore, it is essential to understand the semantic patterns as well as the patterns of the context interspersed among them for natural language processing tools to effectively extract comprehensive medication information. We examined both semantic and context patterns and compared those found in Mayo Clinic and i2b2 challenge data. We found that some variations exist between the institutions but the dominant patterns are common.
在临床记录中,药物信息遵循一定的语义模式,一些药物描述在药物属性之间包含额外的单词。因此,自然语言处理工具要有效地提取综合用药信息,就必须了解语义模式以及穿插其间的上下文模式。我们检查了语义和上下文模式,并比较了梅奥诊所和i2b2挑战数据中发现的模式。我们发现制度之间存在一些差异,但主导模式是共同的。
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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
B. Chapman, Wei Wei, W. Chapman
We assess the relative frequency that lexical items defined in the pyConTextNLP package occur within radiology, history and physical, and emergency department texts. While we found significant disparity in term frequency between the text types nearly half of the lexical items were not found in any of the texts indicating that significant pruning of the lexical knowledge base could be attempted. However, the study is limited by the small number of texts studied.
我们评估pyConTextNLP包中定义的词汇项在放射学、历史和物理以及急诊科文本中出现的相对频率。虽然我们发现文本类型之间的词汇频率存在显著差异,但近一半的词汇项目在任何文本中都没有发现,这表明可以尝试对词汇知识库进行重大修剪。然而,由于研究的文本数量较少,研究受到了限制。
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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
E. M. Hinz, L. Bastarache, J. Denny
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.
深静脉血栓形成和肺栓塞是具有显著发病率和死亡率的疾病。众所周知,静脉血栓栓塞性疾病(VTE)的危险因素包括不活动、创伤和遗传性高凝状态,但许多病例没有已知的相关先前风险。潜在地确定缺失的危险因素的研究最好能确定所有静脉血栓栓塞病例。由于静脉血栓栓塞治疗的时间长短不一、治疗方式与其他慢性疾病的交叉以及与住院相关的预防治疗,在电子健康记录中定义静脉血栓栓塞更具挑战性。我们设计了一种通用的自然语言(NLP)算法,以在去识别的电子健康记录中回顾性地捕获急性和历史的血栓栓塞性疾病病例。将NLP算法应用于单独的评估集,f值为0.897,阳性预测值为84.7%,灵敏度为95.3%,与训练集0.925相似。在没有VTE的icd -9患者的问题列表中使用相同的算法导致PPV为83%。VTE ICD-9阳性病例和非ICD-9阳性问题清单的NLP为捕获急性和历史静脉血栓栓塞性疾病病例提供了有效手段。
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引用次数: 1
Cloud Computing Considerations for Biomedical Applications 生物医学应用的云计算考虑
R. Rauscher
This poster considers the practical barriers to public cloud use for biomedical applications and the advantages of private cloud use for such applications. In addition, it discusses operating environment statistics that are relevant to correctly allocating resources in a private cloud.
这张海报考虑了将公共云用于生物医学应用的实际障碍以及将私有云用于此类应用的优势。此外,本文还讨论了与在私有云中正确分配资源相关的操作环境统计信息。
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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
Yang Chen, Xiaofeng Ren, Guo-Qiang Zhang, Rong Xu
Building a comprehensive medical image database, in the spirit of the UMLS, can be beneficial for assisting diagnosis, patient education and self-care. However, a highly curated, comprehensive image database is difficult to collect as well as to annotate. We present an approach to combine visual object detection technologies with medical ontology to automatically mine web photos and retrieve a large number of disease manifestation images with minimal manual labeling. Comparing to a supervised approach, our ontology-guided approach reduces manual labeling effort to 1/10 on a variety of eye/ear/mouth diseases and improves the precision of retrieval by over 10% in many cases.
本着UMLS的精神,建立一个全面的医学图像数据库,有助于协助诊断、患者教育和自我保健。然而,一个高度策划的、全面的图像数据库很难收集和注释。提出了一种将视觉对象检测技术与医学本体相结合的方法,以最少的人工标注,自动挖掘网络照片,检索大量疾病表现图像。与监督方法相比,我们的本体引导方法将各种眼/耳/口疾病的人工标记工作量减少到1/10,并且在许多情况下将检索精度提高了10%以上。
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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
Mayank Agarwal, Javed Mostafa
In this paper, we propose ViewFinder Medicine (vfM) for automatically identifying cohort classes for MRI scans. It involves predicting a cohort class for the heretofore unseen patient (and related images) and offering linkages to historical diagnosis data associated with the members of the predicted cohort class. The basic idea is to offer a relatively accurate cohort class for a new patient so that the cohort can be used as a baseline to understand current patient's status and develop a treatment plan.
在本文中,我们提出了ViewFinder Medicine (vfM)来自动识别MRI扫描的队列类别。它包括预测迄今为止未见过的患者(和相关图像)的队列类别,并提供与预测队列类别成员相关的历史诊断数据的链接。其基本思路是为新患者提供一个相对准确的队列分类,以便该队列可以作为了解当前患者状态和制定治疗计划的基线。
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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
Salvatore Loguercio, Erik L. Clarke, Benjamin M. Good, A. Su
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.
基因本体(Gene Ontology, GO)提供了一个对基因功能进行系统分类和注释的框架。与氧化石墨烯相关的注释在现代生物学中起着至关重要的作用,涵盖了许多生物体。对于人类基因组,超过10,000个GO术语用于在超过200,000个注释的扩展数据库中注释基因功能。由于GO注释在现代生物学中的重要性,已经投入了大量的努力来评估注释的质量。如果研究人员要在实际应用程序中放心地使用注释,那么提供注释完整性、准确性和精度的度量是至关重要的。在这里,我们描述了一种基于任务的方法,通过基因富集分析的镜头来检查GO注释的完整性和实用性。我们的方法可以用来对GO注释随时间的发展进行建模,无论是针对特定的兴趣区域还是整个注释体。利用这一框架,我们对来自NCBI基因表达综合数据库(GEO)的基因表达数据集进行了大规模分析。特别是,我们通过对生物医学数据的语义注释来确定每个数据集的感兴趣术语,然后跟踪这些术语作为时间函数的行为。初步结果提供了关于GO注释随时间推移的进展和特征的重要信息。该框架具有足够的灵活性,可以跨多个物种和各种富集方法检查全部或部分GO注释。我们还讨论了如何使用这个框架来评估不同的注释方法。例如,通过将特定方法生成的注释的性能与规范注释的性能进行比较,可以确定它们的相对质量。
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引用次数: 2
期刊
2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology
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