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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
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering Pub Date : 2000-11-08 DOI: 10.1109/BIBE.2000.889610
Su-shing Chen
{"title":"Knowledge discovery of gene functions and metabolic pathways","authors":"Su-shing Chen","doi":"10.1109/BIBE.2000.889610","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889610","url":null,"abstract":"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.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"5 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120900656","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
New generation intelligent hearing prosthetics 新一代智能助听器
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering Pub Date : 2000-11-08 DOI: 10.1109/BIBE.2000.889617
A. Radhakrishnan, V. Viswanathan, R. Gao, L. Tsoukalas, S. Basseas
{"title":"New generation intelligent hearing prosthetics","authors":"A. Radhakrishnan, V. Viswanathan, R. Gao, L. Tsoukalas, S. Basseas","doi":"10.1109/BIBE.2000.889617","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889617","url":null,"abstract":"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.","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":"126999737","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
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
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering Pub Date : 2000-11-08 DOI: 10.1109/BIBE.2000.889614
M. Wachowiak, Adel Said Elmaghraby, Renata Wachowiak-Smolíkova, J. Zurada
{"title":"Classification and estimation of ultrasound speckle noise with neural networks","authors":"M. Wachowiak, Adel Said Elmaghraby, Renata Wachowiak-Smolíkova, J. Zurada","doi":"10.1109/BIBE.2000.889614","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889614","url":null,"abstract":"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.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"47 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114044797","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: 26
Reconstructing specimens using DIC microscope images 使用DIC显微镜图像重建标本
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering Pub Date : 2000-11-08 DOI: 10.1109/bibe.2000.889622
F. Kagalwala, T. Kanade
{"title":"Reconstructing specimens using DIC microscope images","authors":"F. Kagalwala, T. Kanade","doi":"10.1109/bibe.2000.889622","DOIUrl":"https://doi.org/10.1109/bibe.2000.889622","url":null,"abstract":"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.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"15 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":"114825550","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: 35
Integrating life sciences data-with a little Garlic 整合生命科学数据，加上一点大蒜
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering Pub Date : 2000-11-08 DOI: 10.1109/BIBE.2000.889583
L. Haas, P. Kodali, J. Rice, P. Schwarz, William Swope
{"title":"Integrating life sciences data-with a little Garlic","authors":"L. Haas, P. Kodali, J. Rice, P. Schwarz, William Swope","doi":"10.1109/BIBE.2000.889583","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889583","url":null,"abstract":"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.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"23 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":"127818518","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: 36
Logical and semantic database integration 逻辑和语义数据库集成
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering Pub Date : 2000-11-08 DOI: 10.1109/BIBE.2000.889592
Jacob Köhler, Matthias Lange, R. Hofestädt, S. Schulze-Kremer
{"title":"Logical and semantic database integration","authors":"Jacob Köhler, Matthias Lange, R. Hofestädt, S. Schulze-Kremer","doi":"10.1109/BIBE.2000.889592","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889592","url":null,"abstract":"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.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"78 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":"133775647","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: 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
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering Pub Date : 2000-11-08 DOI: 10.1109/BIBE.2000.889623
A. C. Zimmermann, Armando A. Gonçalves, J. Barreto
{"title":"General non-invasive shape reconstruction and recognition method applied to 3D external biologic morphologies","authors":"A. C. Zimmermann, Armando A. Gonçalves, J. Barreto","doi":"10.1109/BIBE.2000.889623","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889623","url":null,"abstract":"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.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"95 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":"124081604","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: 5
An XML repository for molecular sequence data 用于分子序列数据的XML存储库
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering Pub Date : 2000-11-08 DOI: 10.1109/BIBE.2000.889587
R. Wong, F. Lam, S. C. Graham, William M. Shui
{"title":"An XML repository for molecular sequence data","authors":"R. Wong, F. Lam, S. C. Graham, William M. Shui","doi":"10.1109/BIBE.2000.889587","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889587","url":null,"abstract":"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.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"5 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":"131772664","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
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
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering Pub Date : 2000-11-08 DOI: 10.1109/BIBE.2000.889625
D. Gilbert, M. Schroeder
{"title":"FURY: fuzzy unification and resolution based on edit distance","authors":"D. Gilbert, M. Schroeder","doi":"10.1109/BIBE.2000.889625","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889625","url":null,"abstract":"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.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"25 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":"128141013","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
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
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering Pub Date : 2000-11-08 DOI: 10.1109/BIBE.2000.889598
H. Jamil
{"title":"Achieving interoperability of genome databases through intelligent Web mediators","authors":"H. Jamil","doi":"10.1109/BIBE.2000.889598","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889598","url":null,"abstract":"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.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"64 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":"114762775","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
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