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Knowledge discovery of gene functions and metabolic pathways 基因功能和代谢途径的知识发现
Su-shing Chen
In the biosphere, biological phenomena manifest as gene functions and metabolic pathways. A challenging problem is the representation, learning and reasoning about these biochemical reactions, relationships between genotypes and phenotypes, and their interplay. Building knowledge bases of gene functions and metabolic pathways often requires integrating various different kinds of knowledge into a single hierarchical framework. On one hand, the knowledge of metabolic pathways consists of kinetic simulation, graphical representation and databases. On the other hand, the complexity of gene functions includes QTL (quantitative trait locus) mappings and higher-level data mining analysis. This paper describes a hierarchical model of cognitive maps for representing signaling and metabolism knowledge as well as genotype-to-phenotype mappings. Cognitive maps are bi-directional graphs that can learn and reason quantitatively and qualitatively. This knowledge representation scheme, coupled with numerical and statistical packages, becomes a useful tool for understanding genomics and metabolism.
在生物圈中,生物现象表现为基因功能和代谢途径。一个具有挑战性的问题是表征,学习和推理这些生化反应,基因型和表型之间的关系,以及它们之间的相互作用。建立基因功能和代谢途径的知识库通常需要将各种不同类型的知识整合到一个单一的层次框架中。一方面,代谢途径的知识由动力学模拟、图形表示和数据库组成。另一方面,基因功能的复杂性包括QTL(数量性状位点)映射和更高层次的数据挖掘分析。本文描述了表征信号和代谢知识以及基因型到表型映射的认知地图的层次模型。认知地图是双向图形,可以定量和定性地学习和推理。这种知识表示方案,加上数值和统计包,成为理解基因组学和代谢的有用工具。
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引用次数: 2
New generation intelligent hearing prosthetics 新一代智能助听器
A. Radhakrishnan, V. Viswanathan, R. Gao, L. Tsoukalas, S. Basseas
This article describes an endeavor to help the hearing impaired through the use of neuro-fuzzy methodologies to tune prosthetic hearing devices in an efficient and tractable manner. The integration of a graphical user interface, a hearing aid emulator module and a fuzzy inference engine into the framework of an intelligent tool that can be used to tune prosthetic hearing devices is described. The graphical user interface permits the extraction of perceptual information pertaining to the patient's aural response to test stimuli in the form of speech patterns. This interface could significantly reduce the role of the acoustician in fine-tuning the hearing aid thereby reducing possible human error and facilitating a more direct involvement of the patient in the tuning procedure. A hearing aid emulator permits one to test the working of the entire tool in a device independent fashion. The test speech patterns are passed through a filter bank that mimics the frequency response of the hearing aid. Testing, simulation results and possible future work form the remainder of the paper.
本文描述了通过使用神经模糊方法以有效和可处理的方式调整义肢听力装置来帮助听力受损者的努力。描述了将图形用户界面、助听器仿真器模块和模糊推理引擎集成到一个可用于调整义肢助听器的智能工具框架中。图形用户界面允许以语音模式的形式提取与患者对测试刺激的听觉反应有关的感知信息。这种界面可以显著减少声学师在微调助听器中的作用,从而减少可能的人为错误,并促进患者更直接地参与调整过程。助听器仿真器允许人们以独立于设备的方式测试整个工具的工作情况。测试语音模式通过一个滤波器组,模仿助听器的频率响应。测试、模拟结果和可能的未来工作构成了论文的其余部分。
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引用次数: 1
Classification and estimation of ultrasound speckle noise with neural networks 超声散斑噪声的神经网络分类与估计
M. Wachowiak, Adel Said Elmaghraby, Renata Wachowiak-Smolíkova, J. Zurada
Presents a neural-based approach to classifying and estimating the statistical parameters of speckle noise found in biomedical ultrasound images. Speckle noise, a very complex phenomenon, has been modeled in a variety of different ways: and there is currently no clear consensus as to its precise statistical characteristics. In this study, different neural network architectures are used to classify ultrasound images contaminated with three types of noise, based upon three one-parameter statistical distributions. At the same time: the parameter is estimated. It is expected that accurate characterization of ultrasound speckle noise will benefit existing post-processing methods, and may lead to new refinements in these techniques.
提出了一种基于神经网络的生物医学超声图像中散斑噪声统计参数的分类和估计方法。散斑噪声是一种非常复杂的现象,人们已经用各种不同的方法对其进行了建模,目前对其精确的统计特征还没有明确的共识。在本研究中,基于三种单参数统计分布,使用不同的神经网络架构对三种噪声污染的超声图像进行分类。同时:对参数进行估计。预计超声散斑噪声的准确表征将有利于现有的后处理方法,并可能导致这些技术的新改进。
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引用次数: 26
Reconstructing specimens using DIC microscope images 使用DIC显微镜图像重建标本
F. Kagalwala, T. Kanade
Differential Interference Contrast (DIC) microscopy is a powerful visualization tool used to study live biological cells. Its use, however, has been limited to qualitative observations. The inherent nonlinear relationship between the object properties and the image intensity makes quantitative analysis difficult. Towards quantitatively measuring optical properties of objects from DIC images, the authors develop a method to reconstruct the specimen's optical properties over a three-dimensional volume. The method is a nonlinear optimization which uses hierarchical representations of the specimen and data. As a necessary tool, the authors have developed and validated a computational model for the DIC image formation process. They test their algorithm by reconstructing the optical properties of known specimens.
差分干涉对比显微镜(DIC)是一种强大的可视化工具,用于研究活的生物细胞。然而,它的使用仅限于定性观察。物体特性与图像强度之间固有的非线性关系给定量分析带来困难。为了从DIC图像中定量测量物体的光学特性,作者开发了一种重建三维体积上标本光学特性的方法。该方法是一种非线性优化方法,它使用样本和数据的分层表示。作为必要的工具,作者开发并验证了DIC图像形成过程的计算模型。他们通过重建已知标本的光学特性来测试他们的算法。
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引用次数: 35
Integrating life sciences data-with a little Garlic 整合生命科学数据,加上一点大蒜
L. Haas, P. Kodali, J. Rice, P. Schwarz, William Swope
Vast amounts of life sciences data today reside in specialized data sources, with specialized query processing capabilities. Data from one source must often be combined with data from other sources to give users the information they desire. Database middleware systems such as Garlic allow users to combine data from multiple sources in a single query. Garlic provides the user with a virtual database to which they can pose arbitrarily complex queries, though the actual data needed to answer the query may be stored in several different sources, and those sources may not even possess all the functionality needed to answer such a query themselves. The Garlic technology, as incorporated in IBM's DB2 product, forms the basis of the DiscoveryLink service offering for the life sciences industry. We describe the DiscoveryLink offering, focusing on two key contributions of Garlic, the wrapper architecture and the query optimizer, and illustrate how it can be used to integrate life sciences data from heterogeneous data sources.
如今,大量的生命科学数据驻留在专门的数据源中,具有专门的查询处理功能。来自一个来源的数据通常必须与来自其他来源的数据相结合,以向用户提供他们想要的信息。像Garlic这样的数据库中间件系统允许用户在一个查询中组合来自多个数据源的数据。Garlic为用户提供了一个虚拟数据库,用户可以向该数据库提出任意复杂的查询,尽管回答查询所需的实际数据可能存储在几个不同的源中,而这些源甚至可能不具备回答此类查询所需的所有功能。集成在IBM DB2产品中的Garlic技术构成了生命科学行业的DiscoveryLink服务产品的基础。我们描述了DiscoveryLink产品,重点介绍了Garlic的两个关键贡献:包装器架构和查询优化器,并说明了如何使用它来集成来自异构数据源的生命科学数据。
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引用次数: 36
Logical and semantic database integration 逻辑和语义数据库集成
Jacob Köhler, Matthias Lange, R. Hofestädt, S. Schulze-Kremer
Two fundamental approaches for database integration exist: the data warehouse approach attempts to physically merge data sets from several source databases, whereas database federations simultaneously query source databases online. In this paper, a database federation approach based on two components is introduced. MARGBench is a system which, among other features, enables the querying of several databases in SQL by translating SQL queries into a source database-specific interface. In this system, SQL queries use the database field labels of the original database, i.e. fields that contain the same kind of information are labelled differently in different databases. In order to solve this problem, a second system, based on ontologies, is currently being developed. This ontology system not only includes information about the semantics of database fields but also contains information about the databases themselves. Thus, it facilitates both database binding and intelligent database querying. The main concepts and ideas of these two systems are explained. By using an imaginary database query, it is demonstrated how the two systems (the ontology system and MARGBench) work together in order to enable the querying of several databases simultaneously.
数据库集成有两种基本方法:数据仓库方法试图物理地合并来自多个源数据库的数据集,而数据库联合同时在线查询源数据库。本文介绍了一种基于两个组件的数据库联合方法。MARGBench是一个系统,在其他功能中,通过将SQL查询转换为特定于源数据库的接口,可以用SQL查询多个数据库。在本系统中,SQL查询使用原始数据库的数据库字段标签,即包含相同类型信息的字段在不同的数据库中被不同的标签。为了解决这个问题,目前正在开发基于本体的第二个系统。该本体系统不仅包含数据库字段的语义信息,还包含数据库本身的信息。因此,它方便了数据库绑定和智能数据库查询。阐述了这两个系统的主要概念和思想。通过使用一个假想的数据库查询,演示了这两个系统(本体系统和MARGBench)如何协同工作,以便同时对多个数据库进行查询。
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引用次数: 24
General non-invasive shape reconstruction and recognition method applied to 3D external biologic morphologies 应用于三维外部生物形态学的一般无创形状重建与识别方法
A. C. Zimmermann, Armando A. Gonçalves, J. Barreto
Presents early results of a potentially fast, efficient and reliable method to extract and recognize the shape of a general 3D external biological morphology. A computer vision based measurement system is used to acquire the 3D shape data. The recognition algorithm proposed here is based on distance calculation and is used to compute the proximity of the biologic shape under test and a reference shape. As an application example, the authors present a human face recognition case. The effectiveness of the algorithm is demonstrated here in two tests in which the same person is compared with himself within different facial expressions and with others persons with different expressions too. The results are presented in a comparative chart.
提出了一种潜在的快速、高效和可靠的方法来提取和识别一般3D外部生物形态的形状。采用基于计算机视觉的测量系统获取三维形状数据。本文提出的识别算法基于距离计算,用于计算被测生物形状与参考形状的接近度。作为应用实例,作者给出了一个人脸识别案例。这里通过两个测试来证明算法的有效性,在两个测试中,同一个人在不同的面部表情中与自己进行比较,并与其他具有不同表情的人进行比较。结果以比较图表的形式呈现出来。
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引用次数: 5
An XML repository for molecular sequence data 用于分子序列数据的XML存储库
R. Wong, F. Lam, S. C. Graham, William M. Shui
The emergence of the Extensible Markup Language (XML) as a new standard for data representation and exchange on the World Wide Web has created a new information revolution. Several proposals have been made to formulate molecular sequences in XML, however none of them mentioned the efficient storage and management of the resultant XML sequence data. This paper addresses some implementation issues of an XML repository for molecular sequence data.
可扩展标记语言(XML)作为万维网上数据表示和交换的新标准的出现,引发了一场新的信息革命。已经提出了几种用XML表示分子序列的建议,但是它们都没有提到有效地存储和管理生成的XML序列数据。本文讨论了分子序列数据XML存储库的一些实现问题。
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引用次数: 4
FURY: fuzzy unification and resolution based on edit distance FURY:基于编辑距离的模糊统一和分辨率
D. Gilbert, M. Schroeder
The authors present a theoretically founded framework for fuzzy unification and resolution based on edit distance over trees. Their framework extends classical unification and resolution conservatively. They prove important properties of the framework and develop the FURY system, which implements the framework efficiently using dynamic programming. The authors evaluate the framework and system on a large problem in the bioinformatics domain, that of detecting typographical errors in an enzyme name database.
提出了一种基于树上编辑距离的模糊统一与分辨框架。他们的框架保守地扩展了经典的统一和决议。他们证明了框架的重要性质,并开发了FURY系统,该系统使用动态规划有效地实现了框架。作者在生物信息学领域的一个大问题上评估了框架和系统,即检测酶名称数据库中的印刷错误。
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引用次数: 12
Achieving interoperability of genome databases through intelligent Web mediators 通过智能Web中介实现基因组数据库的互操作性
H. Jamil
Resolving the tension between the flexibilities offered by a database query language and the so-called "user friendliness" supported by a form-based or menu-driven database query interface is undoubtedly a daunting task. However, researchers believe that the flexibilities offered by a declarative query language should be fully exploited to harvest genetic solutions within the wealth of information offered by genomics and proteomics. Additionally, the need to query databases at different abstraction levels, in a set-based fashion, and to process the queries efficiently by resolving the structural and semantic disparities among the genomic databases in a user-transparent way has never been more evident than in recent years. Inspired by such needs, we have developed an SQL3-compliant database query language called the Genomic Query Language (GQL) for manipulating globally distributed genomic databases that are publicly accessible. GQL, an SQL-like language, is given a source-independent syntax and exploits a high-level global view of the underlying databases. The uniqueness of this language relies heavily on the supporting interface through which all communications take place and the interoperability of databases behind firewalls is realized. In this paper, we describe how the Web-based interface we have built for GQL makes it possible to understand the scheme of any participating database, assimilates the syntactic and semantic information into the global view, and responds to user queries. The interface is autonomous for many genomic databases and is also fully self-maintainable.
解决数据库查询语言提供的灵活性与基于表单或菜单驱动的数据库查询接口所支持的所谓“用户友好性”之间的紧张关系无疑是一项艰巨的任务。然而,研究人员认为,应该充分利用声明性查询语言提供的灵活性,从基因组学和蛋白质组学提供的丰富信息中获取遗传解决方案。此外,近年来,以基于集合的方式在不同抽象层次上查询数据库,并通过以用户透明的方式解决基因组数据库之间的结构和语义差异来有效地处理查询的需求从未像现在这样明显。受这些需求的启发,我们开发了一种符合sql3的数据库查询语言,称为基因组查询语言(Genomic query language, GQL),用于操作可公开访问的全球分布式基因组数据库。GQL是一种类似sql的语言,具有独立于源的语法,并利用底层数据库的高级全局视图。这种语言的独特性在很大程度上依赖于支持接口,所有通信都通过该接口进行,防火墙后面的数据库的互操作性也通过该接口实现。在本文中,我们描述了我们为GQL构建的基于web的接口如何能够理解任何参与数据库的方案,将语法和语义信息吸收到全局视图中,并响应用户查询。该接口对于许多基因组数据库来说是自治的,并且完全可以自我维护。
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引用次数: 9
期刊
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering
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