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2012 ASE/IEEE International Conference on BioMedical Computing (BioMedCom)最新文献

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Early Results from Metamorphic Testing of Epidemiological Models 流行病学模型变形试验的早期结果
Pub Date : 2012-12-14 DOI: 10.1109/BIOMEDCOM.2012.17
L. Pullum, O. Ozmen
The research reported in this paper is motivated by the need to validate models of disease spread. To date, reasoned confidence in the results of these models is complicated by the increasing complexity of the models and by their desired predictive use. As part of an overall approach to verification and validation of disease spread models, we investigate metamorphic testing. In this paper, we present early results of initial metamorphic testing on agent-based epidemiological models.
本文中报道的研究是由验证疾病传播模型的需要所推动的。到目前为止,对这些模型结果的合理信心由于模型的日益复杂和它们期望的预测用途而变得复杂。作为验证和确认疾病传播模型的整体方法的一部分,我们研究了变质试验。在本文中,我们提出了基于主体的流行病学模型的初始变质测试的早期结果。
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引用次数: 34
3-D Tomosynthesis Image Reconstruction Using Total Variation 基于全变分的三维断层合成图像重建
Pub Date : 2012-12-14 DOI: 10.1109/BIOMEDCOM.2012.7
M. Ertas, A. Akan, K. Cengiz, M. Kamasak, S. Seyyedi, I. Yildirim
In tomosynthesis imaging, out-of-focus slice blur problem arises due to incomplete sampling problem. Several approaches have been proposed to deal with this problem. Algebraic reconstruction technique (ART) is one of the most commonly used methods. Total variation (TV) minimization has recently been applied to improve performance of the classical approaches. Though it is able to provide improved results, its sensitivity to the regularization parameter is still an important issue. Former studies addressed largely 2-D tomosynthesis image reconstruction problem. In this study, a 3-D phantom model was used to understand the effect of total variation minimization on a 3-D image reconstruction problem. The significance of selecting an appropriate regularization parameter of TV not addressed in the prior studies was also investigated by means of comparing root mean square error (RMSE) and contrast to noise ratio (CNR) values.
在断层合成成像中,由于采样不完全的问题,产生了散焦切片模糊问题。已经提出了几种方法来处理这个问题。代数重建技术(ART)是最常用的方法之一。总变差(TV)最小化最近被应用于改进经典方法的性能。虽然它能够提供改进的结果,但它对正则化参数的敏感性仍然是一个重要的问题。以往的研究主要针对二维断层合成图像重建问题。在本研究中,利用三维幻像模型来理解总变差最小化对三维图像重建问题的影响。通过比较均方根误差(RMSE)和噪声比(CNR)值,探讨了选择合适的TV正则化参数的重要性。
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引用次数: 2
Security Engineering Based on Structured Formal Reasoning 基于结构化形式推理的安全工程
Pub Date : 2012-12-14 DOI: 10.1109/BIOMEDCOM.2012.30
A. Fuchs, C. Rudolph
Security by Design and Secure Engineering are among the most pressing challenges in IT Security research and practice. Increased attacker potential and dependence on IT-Systems in economy and in critical infrastructures cause a higher demand in securely engineered systems and thus in new approaches and methodologies. This paper introduces a consistent methodology for designing secure systems during the specification phase. The Security Modeling Framework SeMF serves as basis for its security vocabulary. We extend SeMF by the concept of SeMF Building Blocks SeBBs as reasoning tool and provide a security design process utilizing them as refinement artifacts. This process guides the decision making during the system specification phase focused on the security aspects and integrates with refinement driven functional engineering processes. Our approach further results in a security design documentation and residual assumptions that can serve as a basis for risk assessment, code review, and organizational security means during deployment.
安全设计和安全工程是IT安全研究和实践中最紧迫的挑战之一。在经济和关键基础设施中,攻击者潜在的增加和对it系统的依赖导致对安全工程系统的更高需求,因此对新方法和方法的需求也更高。本文介绍了在规范阶段设计安全系统的一致方法。安全建模框架SeMF作为其安全词汇表的基础。我们通过将SeMF构建块sebb作为推理工具的概念扩展SeMF,并提供利用它们作为细化工件的安全设计过程。此过程在系统规范阶段指导决策制定,重点关注安全方面,并与精细化驱动的功能工程过程集成。我们的方法进一步产生了安全设计文档和剩余假设,这些假设可以作为部署期间风险评估、代码审查和组织安全手段的基础。
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引用次数: 0
A Process for Visualizing Disordered Molecular Data with a Case Study in Bulk Water 无序分子数据的可视化过程——以散装水为例
Pub Date : 2012-12-14 DOI: 10.1109/BIOMEDCOM.2012.12
Nick Leaf, K. Ma, Cui Zhang, G. Galli
Existing molecular visualizations do a good job of illuminating well-defined structures, but are ill-suited to visualizing subtle organization when the data is almost entirely disordered. We introduce a process to explore these subtle structures by visualizing an abstraction of the data. The process includes a quantitative verification step to mitigate the ambiguity induced by abstraction. We perform a case study using molecular dynamics simulation data of bulk water to demonstrate the efficacy of our process. The visualized abstractions show molecular behaviors which only happen amongst aggregates, and which would be occluded or indiscernible in a direct visualization. The effect is shown across multiple data sets with different temporal and thermal parameters. In conjunction with domain experts from the Chemistry department who performed the simulation, we confirm our observations using the quantitative verification step of our process.
现有的分子可视化可以很好地说明定义良好的结构,但是当数据几乎完全无序时,就不适合可视化细微的组织。我们介绍了一个过程,通过可视化数据的抽象来探索这些微妙的结构。该过程包括一个定量验证步骤,以减轻抽象引起的歧义。我们使用散装水的分子动力学模拟数据进行了一个案例研究,以证明我们的方法的有效性。可视化的抽象显示了分子行为,这些行为只发生在聚集体之间,而这些行为在直接的可视化中是被遮挡或无法分辨的。该效应在具有不同时间和热参数的多个数据集上得到了体现。与执行模拟的化学部门领域专家一起,我们使用流程的定量验证步骤来确认我们的观察结果。
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引用次数: 1
Study of HRV Dynamics and Comparison Using Wavelet Analysis and Pan Tompkins Algorithm 基于小波分析和Pan Tompkins算法的HRV动力学研究与比较
Pub Date : 2012-12-14 DOI: 10.1109/BIOMEDCOM.2012.13
Y. Goyal, A. Jain
Heart rate variability (HRV) provides a non-invasive means of quantifying cardiac autonomic activity. It has been shown to be a powerful predictor of arrhythmia related complications in patients surviving the acute phase of myocardial infarction. It has also increasingly been used to measure autonomic nervous system activities. This work aims to study heart rate variability during normal or abnormal functioning of the heart and whether it can be used to predict the occurrence of any abnormality. Additionally, it aims to compare results based on wavelet analysis and Pan Tompkins algorithm. Both time domain analysis and frequency domain analysis of HRV are presented. The HRV dynamics is evaluated using non-parametric (Fast Fourier Transform) method. Results of stimulations in MATLAB are presented.
心率变异性(HRV)提供了一种量化心脏自主活动的非侵入性手段。它已被证明是心梗急性期存活患者心律失常相关并发症的有力预测指标。它也越来越多地被用于测量自主神经系统的活动。这项工作旨在研究心脏正常或异常功能期间的心率变异性,以及是否可以用来预测任何异常的发生。并对基于小波分析和Pan Tompkins算法的结果进行比较。给出了HRV的时域分析和频域分析。采用非参数(快速傅立叶变换)方法对HRV动力学进行了评估。给出了在MATLAB环境下的仿真结果。
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引用次数: 4
Quantifying Uncertainty in Epidemiological Models 量化流行病学模型中的不确定性
Pub Date : 2012-12-14 DOI: 10.1109/BIOMEDCOM.2012.20
S. K. Jha, A. Ramanathan
Modern epidemiology has made use of a number of mathematical models, including ordinary differential equation (ODE) based models and agent based models (ABMs) to describe the dynamics of how a disease may spread within a population and enable the rational design of strategies for intervention that effectively contain the spread of the disease. Although such predictions are of fundamental importance in preventing the next global pandemic, there is a significant gap in trusting the outcomes/predictions solely based on such models. Hence, there is a need to develop approaches such that mathematical models can be calibrated against historical data. In addition, there is a need to develop rigorous uncertainty quantification approaches that can provide insights into when a model will fail and characterize the confidence in the (possibly multiple) model outcomes/predictions, when such retrospective analysis cannot be performed. In this paper, we outline an approach to develop uncertainty quantification approaches for epidemiological models using formal methods and model checking. By specifying the outcomes expected from a model in a suitable spatio-temporal logic, we use probabilistic model checking methods to quantify the probability with which the epidemiological model satisfies a given behavioral specification. We argue that statistical model checking methods can solve the uncertainty quantification problem for complex epidemiological models.
现代流行病学利用了许多数学模型,包括基于常微分方程(ODE)的模型和基于agent的模型来描述疾病如何在人群中传播的动态,并能够合理设计有效控制疾病传播的干预策略。虽然这种预测对预防下一次全球大流行病具有根本重要性,但完全相信基于这种模型的结果/预测存在重大差距。因此,有必要开发一种方法,使数学模型能够根据历史数据进行校准。此外,有必要开发严格的不确定性量化方法,以便在无法进行回顾性分析时,能够洞察模型何时会失效,并表征(可能是多个)模型结果/预测的置信度。在本文中,我们概述了使用形式化方法和模型检查为流行病学模型开发不确定性量化方法的方法。通过在适当的时空逻辑中指定模型的预期结果,我们使用概率模型检查方法来量化流行病学模型满足给定行为规范的概率。我们认为统计模型检验方法可以解决复杂流行病学模型的不确定性量化问题。
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引用次数: 9
Agent-Based vs. Equation-Based Epidemiological Models: A Model Selection Case Study 基于主体与基于方程的流行病学模型:模型选择案例研究
Pub Date : 2012-12-14 DOI: 10.1109/BIOMEDCOM.2012.19
S. Sukumar, J. Nutaro
This paper is motivated by the need to design model validation strategies for epidemiological disease-spread models. We consider both agent-based and equation-based models of pandemic disease spread and study the nuances and complexities one has to consider from the perspective of model validation. For this purpose, we instantiate an equation-based model and an agent-based model of the 1918 Spanish flu and we leverage data published in the literature for our case study. We present our observations from the perspective of each implementation and discuss the application of model-selection criteria to compare the risk in choosing one modeling paradigm to another. We conclude with a discussion of our experience and document future ideas for a model validation framework.
本文的动机是需要为流行病学疾病传播模型设计模型验证策略。我们考虑基于主体和基于方程的大流行疾病传播模型,并从模型验证的角度研究必须考虑的细微差别和复杂性。为此,我们实例化了一个基于方程的模型和一个基于主体的1918年西班牙流感模型,并利用文献中发表的数据进行案例研究。我们从每个实现的角度展示了我们的观察结果,并讨论了模型选择标准的应用,以比较选择一种建模范式与另一种建模范式的风险。最后,我们讨论了我们的经验,并记录了模型验证框架的未来想法。
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引用次数: 14
Scalable and Reusable Attack Aware Software 可扩展和可重用的攻击感知软件
Pub Date : 2012-12-14 DOI: 10.1109/BIOMEDCOM.2012.23
W. Kim, C. S. Moon, S. Chung, T. Escrig, B. Endicott-Popovsky
Developing and maintaining security software systems can be cost-prohibitive for all but the largest organizations. New requirements of hardware and software quickly outdate current security systems. Modern software architecture technology, such as Spring Framework, and the new deployment paradigm of cloud computing infrastructure services can help with the challenge of maintaining software security systems. Spring Framework allows for better reusability of our code to adapt to different input vulnerabilities and cloud computing helps to deploy quickly and easily. The application of software architectural patterns and cloud computing to the development of attack aware software improves reusability and scalability.
开发和维护安全软件系统的成本可能会让所有组织望而却步,但大型组织除外。硬件和软件的新要求很快使当前的安全系统过时。现代软件架构技术(如Spring Framework)和云计算基础设施服务的新部署范例可以帮助应对维护软件安全系统的挑战。Spring框架允许我们的代码更好地重用,以适应不同的输入漏洞,云计算有助于快速轻松地部署。软件架构模式和云计算在攻击感知软件开发中的应用提高了可重用性和可扩展性。
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引用次数: 1
Verification of Compartmental Epidemiological Models Using Metamorphic Testing, Model Checking and Visual Analytics 用变形检验、模型检验和可视化分析验证区隔流行病学模型
Pub Date : 2012-12-14 DOI: 10.1109/BIOMEDCOM.2012.18
A. Ramanathan, C. Steed, L. Pullum
Compartmental models in epidemiology are widely used as a means to model disease spread mechanisms and understand how one can best control the disease in case an outbreak of a widespread epidemic occurs. However, a significant challenge within the community is in the development of approaches that can be used to rigorously verify and validate these models. In this paper, we present an approach to quantify and verify the behavioral properties of compartmental epidemiological models under several common modeling scenarios including: birth/death rates and multi-host/pathogen species. We build a workflow that uses metamorphic testing, novel visualization tools and model checking to gain insights into the functionality of compartmental epidemiological models. Our initial results indicate that metamorphic testing can be used to verify the implementation of these models and provide insights into special conditions where these mathematical models may fail. The visualization front-end allows the end-user to scan through a variety of parameters commonly used in these models to elucidate the conditions under which an epidemic can occur. Furthermore, specifying these models using a process algebra allows one to automatically construct behavioral properties that can be rigorously verified using model checking. Together, our approach allows for detecting implementation errors as well as handling conditions under which compartmental epidemiological models may fail to provide insights into disease spread dynamics.
流行病学中的区隔模型被广泛用于模拟疾病传播机制,并了解在发生大范围流行病爆发时如何最好地控制疾病。然而,社区内的一个重大挑战是开发可用于严格验证和验证这些模型的方法。在本文中,我们提出了一种量化和验证区隔流行病学模型在几种常见建模情景下的行为特性的方法,包括:出生率/死亡率和多宿主/病原体物种。我们建立了一个工作流程,使用变形测试,新颖的可视化工具和模型检查来深入了解分区流行病学模型的功能。我们的初步结果表明,变质试验可以用来验证这些模型的实现,并提供对这些数学模型可能失败的特殊条件的见解。可视化前端允许最终用户扫描这些模型中常用的各种参数,以阐明可能发生流行病的条件。此外,使用流程代数指定这些模型允许自动构建可以使用模型检查严格验证的行为属性。总之,我们的方法允许检测实施错误以及处理在这种情况下,分区流行病学模型可能无法提供对疾病传播动态的见解。
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引用次数: 25
Identification of Surface and Deep Layer Muscle Activity by EMG Propagation Direction 肌电图传播方向识别浅层和深层肌肉活动
Pub Date : 2012-12-14 DOI: 10.1109/BIOMEDCOM.2012.14
T. Koshio, S. Sakurazawa, M. Toda, J. Akita, K. Kondo, Y. Nakamura
It is generally difficult to identify surface and deep layer muscle activity. If we could identify surface and deep layer muscle activity, we can provide effective tools for rehabilitation. Therefore, in this study, we aim to identify surface and deep layer muscle activity using surface electrodes. We focused on the intersection of muscle fibers of surface layer muscle and deep layer muscle. On such a place, we found that we could measure independent muscle activity along each muscle fiber. In this result, we could confirm that we could measure surface layer muscle activity independently by comparing with the signal which is measured on extended line of surface muscle fiber and on outside of the deep layer muscle. Additionally, we identified propagation direction of EMG signal using electrode array. It was determined from delay time of EMG signal measured on each electrode. When we activated surface and deep layer muscle independently, each propagation direction of EMG signal corresponded to each muscle fiber direction. Thus, we indicated that identification of surface and deep layer muscle activity is possible.
通常很难识别表层和深层肌肉活动。如果我们能够识别表层和深层肌肉活动,我们可以提供有效的康复工具。因此,在本研究中,我们的目标是使用表面电极识别表层和深层肌肉活动。我们重点研究了表层肌肉和深层肌肉纤维的交点。在这样一个地方,我们发现我们可以测量每条肌肉纤维的独立肌肉活动。通过与表面肌纤维延长线和深层肌外测得的信号进行比较,可以证实我们可以独立测量表层肌肉活动。此外,我们还利用电极阵列确定了肌电信号的传播方向。由各电极上测得的肌电信号延迟时间确定。当我们分别激活表层和深层肌肉时,肌电信号的每个传播方向对应于每个肌纤维方向。因此,我们表明识别表层和深层肌肉活动是可能的。
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引用次数: 1
期刊
2012 ASE/IEEE International Conference on BioMedical Computing (BioMedCom)
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