This paper proposes a prepositional method for hierarchical model-based clustering of relational data. We define a new type of aggregate - frequency aggregate, which has a vector data type and can be used to record no...
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ISBN:
(纸本)9781581138122
This paper proposes a prepositional method for hierarchical model-based clustering of relational data. We define a new type of aggregate - frequency aggregate, which has a vector data type and can be used to record not only the observed values but also the distribution of the values of an attribute. A hierarchical agglomerative clustering algorithm with log-likelihood distance is then applied to cluster the aggregated data tentatively, and a mixture model-based method with the EM algorithm is developed to perform a further relocation clustering, in which Bayes Information Criterion is used to determine the optimal number of clusters.
The Standard for Digital Imaging and Communications in Medicine (DICOM) specifies a non-proprietary digital imaging format, file structure and data interchange protocols for the transfer of biomedical images and non-i...
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ISBN:
(纸本)9781581138122
The Standard for Digital Imaging and Communications in Medicine (DICOM) specifies a non-proprietary digital imaging format, file structure and data interchange protocols for the transfer of biomedical images and non-image data related to such images - it is a specification of the components that are required in order to achieve inter-operability between biomedical imaging computer systems. In this paper we describe how a Grid-enabled medical imaging database - eDiaMoND - employs an object-relational approach to the storage of DICOM files. Although the work described has been carried out within the context of a particular mammography related project, the underlying principles are applicable to other medical imaging systems dealing either with other modalities or with other diseases.
In this paper, we report on implementing an experimental distributed computing application for bioinformatics consisting of basic high-performance computing environments (Grid and PC Cluster systems), multiple interfa...
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ISBN:
(纸本)1595934804;9781595934802
In this paper, we report on implementing an experimental distributed computing application for bioinformatics consisting of basic high-performance computing environments (Grid and PC Cluster systems), multiple interfaces at user portals that provide useful graphical interfaces to enable biologists who are not IT specialists to benefit directly from the use of high-performance technology. Copyright 2007 acm.
In this paper we present a data mining system, which allows the application of different clustering and cluster validity algorithms for DNA microarray data. This tool may improve the quality of the data analysis resul...
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ISBN:
(纸本)9781581138122
In this paper we present a data mining system, which allows the application of different clustering and cluster validity algorithms for DNA microarray data. This tool may improve the quality of the data analysis results, and may support the prediction of the number of relevant clusters in the microarray datasets. This systematic evaluation approach may significantly aid genome expression analyses for knowledge discovery applications. The developed software system may be effectively used for clustering and validating not only DNA microarray expression analysis applications but also other biomedical and physical data with no limitations. The program is freely available for non-profit use on request at http://***/***/***.
With the dramatically increasing amounts of genomic sequence database, there is a need for faster and more sensitive searching for sequence similarity analysis. The Smith-Waterman algorithm, which utilizes dynamic pro...
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With the dramatically increasing amounts of genomic sequence database, there is a need for faster and more sensitive searching for sequence similarity analysis. The Smith-Waterman algorithm, which utilizes dynamic programming, is a common method for performing exact local alignments between two protein or DNA sequences. The Smith-Waterman algorithm is exhaustive and generally considered to be the most sensitive, but long computation times limit the use of this algorithm. This paper presents a preliminary implementation of Smith-Waterman algorithm using a new chip multiprocessor architecture with multiple Digital Signal Processors (DSP) on a single chip leading to high performance at low cost.
In this short paper, we present our solution to index, store and retrieve the domain knowledge. The main principle exploits Lucene to index the domain knowledge under guide of the domain schema. The method to map doma...
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ISBN:
(纸本)1595934804;9781595934802
In this short paper, we present our solution to index, store and retrieve the domain knowledge. The main principle exploits Lucene to index the domain knowledge under guide of the domain schema. The method to map domain knowledge structure into Lucene index structure, store and update the indices, and to transfer RDF-based query into Lucene's query are presented. Copyright 2007 acm.
We describe a very intricate case of interlocked bio-processes: the blood clotting cascade, by using a set of tools from object-oriented design (OOD). Originally, OOD has been designed for the abstract specification o...
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We describe a very intricate case of interlocked bio-processes: the blood clotting cascade, by using a set of tools from object-oriented design (OOD). Originally, OOD has been designed for the abstract specification of complex software prior to programming. OOD brings a handful of concepts such as modularity, classes, methods and their inheritance hierarchies for concurrent process synchronization and cooperation. It appears that the set of OOD methods can be a very fruitful tool for the abstract description of biological processes apparently quite far away from software engineering. We give a moderately detailed view of the blood clotting cascade using the standard tool of OOD: Unified Modeling Language (UML) and its extension: Real-Time UML.
Realistic network traffic can exhibit the Long-Range Dependent (LRD) feature which is characterised by a hyperbolically decaying correlation function and has strong effects on the performance of communication networks...
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ISBN:
(纸本)9781581138122
Realistic network traffic can exhibit the Long-Range Dependent (LRD) feature which is characterised by a hyperbolically decaying correlation function and has strong effects on the performance of communication networks. As the convergence of simulations to a steady state under LRD workloads is often very slow, analytical models become cost-effective and versatile tools that can help designers to investigate system performance. This paper designs an analytical performance model for computing communication delay in adaptively routed hypercubic networks in the presence of LRD traffic. The model is derived in the context of pipelined circuit switching. The tractability and reasonable accuracy of the analytical model make it a practical and cost-effective evaluation tool to study the performance behaviour of hypercubic networks under LRD traffic.
This paper presents a simulation framework for UML models based upon a mapping schema of UML metamodel elements into Abstract State Machines (ASMs). Structural model elements are translated into an ASM vocabulary as c...
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This paper presents a simulation framework for UML models based upon a mapping schema of UML metamodel elements into Abstract State Machines (ASMs). Structural model elements are translated into an ASM vocabulary as collections of domains and functions, whereas the dynamic view is captured by multi-agent ASMs reflecting the behavior modeled by UML state machines. In the toolkit presented, input UML models can be drawn using any UML CASE Tool able to produce the XMI format for diagrams. This textual representation is exploited to initialize the ASM model for UML state machines which can be symbolically executed by AsmGofer, an advanced Abstract State Machine programming system. Tool features are described through the simulation of a simple stack-printer UML model showing the interactions among state machines by signals exchange and operation calls.
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