首页 > 最新文献

Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering最新文献

英文 中文
A model based contour searching method 一种基于模型的轮廓搜索方法
Yingjie Tang, Lei He, Xun Wang, W. Wee
A two-step model based approach to a contour extraction problem is developed to provide a solution to more challenging contour extraction problems of biomedical images. A biomedical contour image is initially processed by a deformable contour method to obtain a first order approximation of the contour. The two-step model includes a linked contour model and a posteriori probability model. Initially, the output contour from the deformable contour method is matched against the linked contour model for both model detection and corresponding landmark contour points identification. Segments obtained from these landmarks are matched for errors. Larger error are then passed on to a regionalized a posteriori probability model for further fine tuning to obtain a final result. Experiments on both MR brain images are most encouraging.
为解决生物医学图像中具有挑战性的轮廓提取问题,提出了一种基于两步模型的轮廓提取方法。采用可变形轮廓法对生物医学轮廓图像进行初始处理,得到该轮廓的一阶近似。两步模型包括一个连接的轮廓模型和一个后验概率模型。首先,将可变形轮廓法的输出轮廓与链接轮廓模型进行匹配,进行模型检测和相应的地标轮廓点识别。从这些地标得到的片段进行误差匹配。然后将较大的误差传递给区域化的后验概率模型进行进一步微调以获得最终结果。两种核磁共振成像的实验结果都非常令人鼓舞。
{"title":"A model based contour searching method","authors":"Yingjie Tang, Lei He, Xun Wang, W. Wee","doi":"10.1109/BIBE.2000.889627","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889627","url":null,"abstract":"A two-step model based approach to a contour extraction problem is developed to provide a solution to more challenging contour extraction problems of biomedical images. A biomedical contour image is initially processed by a deformable contour method to obtain a first order approximation of the contour. The two-step model includes a linked contour model and a posteriori probability model. Initially, the output contour from the deformable contour method is matched against the linked contour model for both model detection and corresponding landmark contour points identification. Segments obtained from these landmarks are matched for errors. Larger error are then passed on to a regionalized a posteriori probability model for further fine tuning to obtain a final result. Experiments on both MR brain images are most encouraging.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"372 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122926341","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: 7
Mouse genome informatics in a new age of biological inquiry 小鼠基因组信息学在生物探究的新时代
C. Bult, J. Richardson, J. Blake, J. Kadin, M. Ringwald, J. Eppig
Data integration is key to knowledge discovery in the age of genomics and represents a major, long-standing challenge for the genome informatics community. Integration of data across heterogeneous genome databases requires the identification of common data entities and mechanisms to ensure referential integrity and persistence of these common entities even as our understanding of their biological properties changes. The Mouse Genome Informatics (MGI) database group employs multiple strategies for achieving data integration and maintaining inter-connectedness with other databases, including: (1) the use of permanent, unique accession IDs for identifying core data entities, (2) the application of nomenclature standards for naming genes and strains of mice, and (3) the development and implementation of controlled vocabularies and ontologies to ensure semantic consistency of biological concepts within and across model organism databases.
数据集成是基因组学时代知识发现的关键,也是基因组信息学社区长期面临的主要挑战。跨异构基因组数据库的数据集成需要识别共同的数据实体和机制,以确保这些共同实体的参考完整性和持久性,即使我们对其生物学特性的理解发生了变化。小鼠基因组信息学(MGI)数据库组采用多种策略来实现数据集成并保持与其他数据库的互联性,包括:(1)使用永久的、唯一的接入id来识别核心数据实体;(2)应用命名标准来命名小鼠基因和品系;(3)开发和实施受控词汇表和本体,以确保模型生物数据库内部和跨模型生物数据库的生物学概念语义一致性。
{"title":"Mouse genome informatics in a new age of biological inquiry","authors":"C. Bult, J. Richardson, J. Blake, J. Kadin, M. Ringwald, J. Eppig","doi":"10.1109/BIBE.2000.889586","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889586","url":null,"abstract":"Data integration is key to knowledge discovery in the age of genomics and represents a major, long-standing challenge for the genome informatics community. Integration of data across heterogeneous genome databases requires the identification of common data entities and mechanisms to ensure referential integrity and persistence of these common entities even as our understanding of their biological properties changes. The Mouse Genome Informatics (MGI) database group employs multiple strategies for achieving data integration and maintaining inter-connectedness with other databases, including: (1) the use of permanent, unique accession IDs for identifying core data entities, (2) the application of nomenclature standards for naming genes and strains of mice, and (3) the development and implementation of controlled vocabularies and ontologies to ensure semantic consistency of biological concepts within and across model organism databases.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121808302","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: 20
A graph-based meta-data framework for interoperation between genome databases 基因组数据库间互操作的基于图的元数据框架
K. Cheung, Dong-Guk Shin
The proliferation, diversity and complexity of genome databases pose a significant challenge to the multidatabase research community. We propose a meta-data framework based on a graph modeling technique and show how this framework can be applied to making two genome databases interoperable. Our technique maps individual database schemas expressed in heterogeneous data models into a common graph representation. This graph-based framework is designed to express both regular data and meta-data. Modeling both types of data is necessary for establishing database correspondences. We show how inter-database relationships can be expressed in terms of correspondences amongst basic graph units, including nodes, edges and the "value path". We apply these basic graph units to perform query interoperation between two databases, namely DB/12 (Database of Human Chromosome 12) and GDB (Genome Database).
基因组数据库的增殖、多样性和复杂性对多数据库研究界提出了重大挑战。我们提出了一个基于图建模技术的元数据框架,并展示了如何将该框架应用于使两个基因组数据库可互操作。我们的技术将异构数据模型中表达的单个数据库模式映射到公共图形表示中。这个基于图的框架旨在表达常规数据和元数据。对这两种类型的数据建模对于建立数据库通信是必要的。我们展示了如何用基本图单元(包括节点、边和“值路径”)之间的对应关系来表达数据库间的关系。我们利用这些基本图单元在DB/12 (Human Chromosome 12)和GDB (Genome Database)两个数据库之间进行查询互操作。
{"title":"A graph-based meta-data framework for interoperation between genome databases","authors":"K. Cheung, Dong-Guk Shin","doi":"10.1109/BIBE.2000.889597","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889597","url":null,"abstract":"The proliferation, diversity and complexity of genome databases pose a significant challenge to the multidatabase research community. We propose a meta-data framework based on a graph modeling technique and show how this framework can be applied to making two genome databases interoperable. Our technique maps individual database schemas expressed in heterogeneous data models into a common graph representation. This graph-based framework is designed to express both regular data and meta-data. Modeling both types of data is necessary for establishing database correspondences. We show how inter-database relationships can be expressed in terms of correspondences amongst basic graph units, including nodes, edges and the \"value path\". We apply these basic graph units to perform query interoperation between two databases, namely DB/12 (Database of Human Chromosome 12) and GDB (Genome Database).","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"81 3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124780327","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
Registration by maximization of mutual information-a cross validation study 互信息最大化注册——交叉验证研究
L. Freire, F. Godinho
Mutual Information (MI), or relative entropy has been used as a similarity criterion in medical image registration. MI is a measure of the dispersive behavior of the joint histogram of geometrically related voxels' intensities in both images. This dispersion is assumed to be smaller when the images are aligned. Besides, no assumptions are made, before bringing images together or during MI calculation, regarding the nature of the relation between corresponding voxels. In this work the authors assess how the elaboration of joint histogram influences overall accuracy of maximization of MI registration method in unimodality and multimodality registration. For this purpose, across validation study is performed considering two other widespread registration algorithms: the SPM's registration package and multimodality AIR method. The correct elaboration of the joint histogram depends not only in the interpolation function used to resample the test image, but also in the re-scaling procedure used to fit images' values in the joint histogram and its subsequent update. The authors also evaluate if histogram's dimensions are important for overall accuracy.
互信息(MI)或相对熵被用作医学图像配准的相似度准则。MI是对两个图像中几何相关体素强度的联合直方图的色散行为的度量。当图像对齐时,假设这种色散较小。此外,在将图像放在一起之前或在MI计算过程中,没有对相应体素之间关系的性质进行假设。在这项工作中,作者评估了联合直方图的阐述如何影响单模态和多模态配准中MI配准方法最大化的整体准确性。为此,考虑到另外两种广泛使用的配准算法:SPM的配准包和多模态AIR方法,进行了跨验证研究。联合直方图的正确细化不仅取决于用于重新采样测试图像的插值函数,还取决于用于拟合联合直方图中图像值的重新缩放过程及其随后的更新。作者还评估了直方图的维度是否对整体准确性很重要。
{"title":"Registration by maximization of mutual information-a cross validation study","authors":"L. Freire, F. Godinho","doi":"10.1109/BIBE.2000.889624","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889624","url":null,"abstract":"Mutual Information (MI), or relative entropy has been used as a similarity criterion in medical image registration. MI is a measure of the dispersive behavior of the joint histogram of geometrically related voxels' intensities in both images. This dispersion is assumed to be smaller when the images are aligned. Besides, no assumptions are made, before bringing images together or during MI calculation, regarding the nature of the relation between corresponding voxels. In this work the authors assess how the elaboration of joint histogram influences overall accuracy of maximization of MI registration method in unimodality and multimodality registration. For this purpose, across validation study is performed considering two other widespread registration algorithms: the SPM's registration package and multimodality AIR method. The correct elaboration of the joint histogram depends not only in the interpolation function used to resample the test image, but also in the re-scaling procedure used to fit images' values in the joint histogram and its subsequent update. The authors also evaluate if histogram's dimensions are important for overall accuracy.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125002191","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: 6
An object relational approach to biomedical database 生物医学数据库的对象关系方法
P. Sheu, Brian J Cummings, C. Cotman, C. Chubb, Linhua Hu, Taehyung Wang, Julene Johnson, Scott Mobley, Tom Sitch, Yoshi Inagaki
As neuroscience research advances, there is an increasing need to integrate data from a single patient who has undergone multiple levels of analysis. In a biomedical application (such as an Alzheimer's clinic), a patient might have medical data, MRI data, cognitive data and autopsy data all collected at various times. This paper introduces "BioCompose", an object-relational database system that integrates clinical, neuropathological and image data sets into a uniform framework with a simple user interface. It addresses the advantages of taking an object-relational approach for a large and complex application.
随着神经科学研究的进步,越来越需要整合来自单个患者的数据,这些患者已经经历了多个层次的分析。在生物医学应用程序(例如阿尔茨海默氏症诊所)中,患者可能拥有在不同时间收集的医疗数据、MRI数据、认知数据和尸检数据。本文介绍了“BioCompose”,这是一个对象关系数据库系统,它将临床、神经病理和图像数据集集成到一个统一的框架中,具有简单的用户界面。它阐述了对大型复杂应用程序采用对象关系方法的优点。
{"title":"An object relational approach to biomedical database","authors":"P. Sheu, Brian J Cummings, C. Cotman, C. Chubb, Linhua Hu, Taehyung Wang, Julene Johnson, Scott Mobley, Tom Sitch, Yoshi Inagaki","doi":"10.1109/BIBE.2000.889594","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889594","url":null,"abstract":"As neuroscience research advances, there is an increasing need to integrate data from a single patient who has undergone multiple levels of analysis. In a biomedical application (such as an Alzheimer's clinic), a patient might have medical data, MRI data, cognitive data and autopsy data all collected at various times. This paper introduces \"BioCompose\", an object-relational database system that integrates clinical, neuropathological and image data sets into a uniform framework with a simple user interface. It addresses the advantages of taking an object-relational approach for a large and complex application.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"60 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131668442","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: 4
Scientific data integration: wrapping textual documents with a database view mechanism and an XML engine 科学数据集成:用数据库视图机制和XML引擎包装文本文档
Z. Lacroix
Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or from documents retrieved from the World Wide Web. We present an approach to querying flat files as well as Web data sources through an object database view based on a database system and a wrapper. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, secondly builds the expected output with respect to the virtual structure. Scientific data servers, and in particular the ones publicly available on the Web, usually provide information retrieval techniques to access data. Our wrappers are composed of a retrieval component, based on an intermediate object view mechanism called 'search views' mapping the source capabilities to attributes, and a XML engine to perform these two tasks. If the retrieval component is specific to each data source, this approach shows that the extraction component (the XML engine) can be common. We describe our system and focus on the retrieval component of the Object-Web Wrapper (OWW) for Web sources. The originality of our approach consists of (1) a common wrapper architecture for flat files and Web data sources sharing a XML engine for data extraction, (2) a generic view mechanism to access data sources with limited capabilities, and (3) the representation of hyperlinks as abstract attributes in the object view as well as their use in the search view. Our approach has been developed and demonstrated as part of a multidatabase system supporting queries via uniform Object Protocol Model (OPM) interfaces.
为科学数据建立数字图书馆需要访问和操作从平面文件或从万维网检索的文档中提取的数据。我们提出了一种通过基于数据库系统和包装器的对象数据库视图查询平面文件和Web数据源的方法。通常,包装器有两个任务:首先向源发送查询以检索数据,其次根据虚拟结构构建预期的输出。科学数据服务器,特别是在Web上公开可用的服务器,通常提供信息检索技术来访问数据。我们的包装器由检索组件和执行这两项任务的XML引擎组成。检索组件基于一种称为“搜索视图”的中间对象视图机制,将源功能映射到属性。如果检索组件特定于每个数据源,那么这种方法表明提取组件(XML引擎)可以是通用的。我们描述了我们的系统,并将重点放在Web源的对象Web包装器(OWW)的检索组件上。我们方法的独创性包括:(1)平面文件和Web数据源的通用包装架构,共享用于数据提取的XML引擎,(2)访问功能有限的数据源的通用视图机制,以及(3)将超链接表示为对象视图中的抽象属性以及它们在搜索视图中的使用。我们的方法是作为支持通过统一对象协议模型(OPM)接口进行查询的多数据库系统的一部分开发和演示的。
{"title":"Scientific data integration: wrapping textual documents with a database view mechanism and an XML engine","authors":"Z. Lacroix","doi":"10.1109/BIBE.2000.889591","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889591","url":null,"abstract":"Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or from documents retrieved from the World Wide Web. We present an approach to querying flat files as well as Web data sources through an object database view based on a database system and a wrapper. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, secondly builds the expected output with respect to the virtual structure. Scientific data servers, and in particular the ones publicly available on the Web, usually provide information retrieval techniques to access data. Our wrappers are composed of a retrieval component, based on an intermediate object view mechanism called 'search views' mapping the source capabilities to attributes, and a XML engine to perform these two tasks. If the retrieval component is specific to each data source, this approach shows that the extraction component (the XML engine) can be common. We describe our system and focus on the retrieval component of the Object-Web Wrapper (OWW) for Web sources. The originality of our approach consists of (1) a common wrapper architecture for flat files and Web data sources sharing a XML engine for data extraction, (2) a generic view mechanism to access data sources with limited capabilities, and (3) the representation of hyperlinks as abstract attributes in the object view as well as their use in the search view. Our approach has been developed and demonstrated as part of a multidatabase system supporting queries via uniform Object Protocol Model (OPM) interfaces.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"68 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134438244","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: 7
BioSig: a bioinformatic system for studying the mechanism of inter-cell signaling BioSig:用于研究细胞间信号传导机制的生物信息学系统
B. Parvin, G. Cong, G. Fontenay, John R. Taylor, R. Henshal, M. Barcellos-Hoff
Mapping inter-cell signaling pathways requires an integrated view of experimental and informatic protocols. BioSig provides the foundation of cataloging inter-cell responses as a function of particular conditioning, treatment, staining, etc. for either in vivo or in vitro experiments. This paper outlines the system architecture, a functional data model for representing experimental protocols, algorithms for image analysis, and the required statistical analysis. The architecture provides remote shared operation of an inverted optical microscope, and couples instrument operation with images acquisition and annotation. The information is stored in an object-oriented database. The algorithms extract structural information such as morphology and organization, and map it to functional information such as inter-cellular responses. An example of usage of this system is included.
绘制细胞间信号通路需要实验和信息协议的综合视图。BioSig提供了编目细胞间反应的基础,作为体内或体外实验的特定条件,处理,染色等功能。本文概述了系统架构、表示实验协议的功能数据模型、图像分析算法以及所需的统计分析。该架构提供了倒置光学显微镜的远程共享操作,并将仪器操作与图像采集和注释相结合。信息存储在面向对象的数据库中。该算法提取结构信息,如形态和组织,并将其映射到功能信息,如细胞间响应。最后给出了该系统的一个使用实例。
{"title":"BioSig: a bioinformatic system for studying the mechanism of inter-cell signaling","authors":"B. Parvin, G. Cong, G. Fontenay, John R. Taylor, R. Henshal, M. Barcellos-Hoff","doi":"10.1109/BIBE.2000.889619","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889619","url":null,"abstract":"Mapping inter-cell signaling pathways requires an integrated view of experimental and informatic protocols. BioSig provides the foundation of cataloging inter-cell responses as a function of particular conditioning, treatment, staining, etc. for either in vivo or in vitro experiments. This paper outlines the system architecture, a functional data model for representing experimental protocols, algorithms for image analysis, and the required statistical analysis. The architecture provides remote shared operation of an inverted optical microscope, and couples instrument operation with images acquisition and annotation. The information is stored in an object-oriented database. The algorithms extract structural information such as morphology and organization, and map it to functional information such as inter-cellular responses. An example of usage of this system is included.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"167 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132527574","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: 12
Surface parameterization in volumetric images for feature classification 用于特征分类的体积图像表面参数化
Richard W. I. Yarger, Francis K. H. Quek
Curvature-based surface features are well suited for use in multimodal medical image registration. The accuracy of such feature-based registration techniques is dependent upon the reliability of the feature computation. The computation of curvature features requires second derivative information that is best obtained from a parametric surface representation. The authors present a method of explicitly parametrizing surfaces from volumetric data. Surfaces are extracted, without a global thresholding, using active contour models. A monge basis for each surface patch is estimated and used to transform the patch into local, or parametric, coordinates. Surface patches are fit to a bicubic polynomial in local coordinates using least squares solved by singular value decomposition. The authors tested their method by reconstructing surfaces from the surface model and analytically computing gaussian and mean curvatures. The model was tested on analytical and medical data.
基于曲率的表面特征非常适合用于多模态医学图像配准。这种基于特征的配准技术的准确性取决于特征计算的可靠性。曲率特征的计算需要二阶导数信息,这种信息最好从参数曲面表示中获得。作者提出了一种从体积数据中显式参数化曲面的方法。曲面的提取,没有全局阈值,使用活动轮廓模型。估计每个表面patch的monge基,并用于将patch转换为局部或参数坐标。利用奇异值分解法求解最小二乘,在局部坐标下拟合表面斑块的双三次多项式。作者通过从曲面模型重建曲面并解析计算高斯曲率和平均曲率来验证他们的方法。该模型在分析数据和医学数据上进行了测试。
{"title":"Surface parameterization in volumetric images for feature classification","authors":"Richard W. I. Yarger, Francis K. H. Quek","doi":"10.1109/BIBE.2000.889621","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889621","url":null,"abstract":"Curvature-based surface features are well suited for use in multimodal medical image registration. The accuracy of such feature-based registration techniques is dependent upon the reliability of the feature computation. The computation of curvature features requires second derivative information that is best obtained from a parametric surface representation. The authors present a method of explicitly parametrizing surfaces from volumetric data. Surfaces are extracted, without a global thresholding, using active contour models. A monge basis for each surface patch is estimated and used to transform the patch into local, or parametric, coordinates. Surface patches are fit to a bicubic polynomial in local coordinates using least squares solved by singular value decomposition. The authors tested their method by reconstructing surfaces from the surface model and analytically computing gaussian and mean curvatures. The model was tested on analytical and medical data.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"28 19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128548904","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: 14
Amplification of perspectives in the use of evolutionary computation 在使用进化计算中扩大视角
J. Falqueto, J. Barreto, Paulo Sergio da Silva Borges
Initially, different areas of research in computer science based on models inspired by nature are approached. The area entitled "evolutionary computation" is discussed in a general view. After this, emphasis is placed on the human tendency to copy and to find answers to new problems by adopting similar solutions from other equivalent issues that have already been resolved by nature. Finally, we demonstrate that, in the case of evolutionary computation, even if success is achieved in many cases, most of what nature has attained was either severely simplified or truncated in the simulation process. Also, in several cases, a more detailed and more faithful copy could have yielded better results for already-existing systems or for new ones.
最初,基于受自然启发的模型的计算机科学研究的不同领域进行了探讨。“进化计算”这一领域是在一般情况下讨论的。在此之后,重点放在人类倾向于复制和通过采用已经被自然解决的其他等效问题的类似解决方案来寻找新问题的答案。最后,我们证明,在进化计算的情况下,即使在许多情况下取得了成功,自然界所获得的大部分东西在模拟过程中要么被严重简化,要么被截断。此外,在一些情况下,对于已经存在的系统或新的系统,更详细和更忠实的副本可以产生更好的结果。
{"title":"Amplification of perspectives in the use of evolutionary computation","authors":"J. Falqueto, J. Barreto, Paulo Sergio da Silva Borges","doi":"10.1109/BIBE.2000.889602","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889602","url":null,"abstract":"Initially, different areas of research in computer science based on models inspired by nature are approached. The area entitled \"evolutionary computation\" is discussed in a general view. After this, emphasis is placed on the human tendency to copy and to find answers to new problems by adopting similar solutions from other equivalent issues that have already been resolved by nature. Finally, we demonstrate that, in the case of evolutionary computation, even if success is achieved in many cases, most of what nature has attained was either severely simplified or truncated in the simulation process. Also, in several cases, a more detailed and more faithful copy could have yielded better results for already-existing systems or for new ones.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"16 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117000132","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
On parameter estimation for neuron models 神经元模型的参数估计
Jeffrey L. Madden, Zina Ben-Miled, R. Chin, J. Schild
Membrane bound ion channels give rise to many of the electrical signal characteristics exhibited by neurons. Ion channel models of neural function such as that proposed by Hodgkin-Huxley can be represented as a set of differential equations. Solving these differential equations for a given neuron involves finding optimal values for the parameters that define the Hodgkin-Huxley equations. Most often, these parameters are evaluated using an optimization algorithm that takes as input ion channel current data recorded from a neuron using the voltage clamp technique. Real-valued optimization algorithms often fail to find a global optimum for the parameters of the Hodgkin-Huxley differential equations. Here, the authors show that interval analysis based optimization algorithm, a branch and bound algorithm, provides an accurate solution for the Hodgkin-Huxley model.
膜结合离子通道产生了神经元所表现出的许多电信号特征。神经功能的离子通道模型,如霍奇金-赫胥黎提出的,可以表示为一组微分方程。求解给定神经元的这些微分方程需要找到定义霍奇金-赫胥黎方程的参数的最优值。大多数情况下,这些参数是使用一种优化算法来评估的,该算法将使用电压钳技术从神经元记录的离子通道电流数据作为输入。实值优化算法往往不能找到霍奇金-赫胥黎微分方程参数的全局最优解。在这里,作者证明了基于区间分析的优化算法,即分支定界算法,为Hodgkin-Huxley模型提供了一个精确的解。
{"title":"On parameter estimation for neuron models","authors":"Jeffrey L. Madden, Zina Ben-Miled, R. Chin, J. Schild","doi":"10.1109/BIBE.2000.889615","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889615","url":null,"abstract":"Membrane bound ion channels give rise to many of the electrical signal characteristics exhibited by neurons. Ion channel models of neural function such as that proposed by Hodgkin-Huxley can be represented as a set of differential equations. Solving these differential equations for a given neuron involves finding optimal values for the parameters that define the Hodgkin-Huxley equations. Most often, these parameters are evaluated using an optimization algorithm that takes as input ion channel current data recorded from a neuron using the voltage clamp technique. Real-valued optimization algorithms often fail to find a global optimum for the parameters of the Hodgkin-Huxley differential equations. Here, the authors show that interval analysis based optimization algorithm, a branch and bound algorithm, provides an accurate solution for the Hodgkin-Huxley model.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121146146","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: 4
期刊
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1