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Separation of nonlinear image mixtures by denoising source separation

6th International Conference on Independent Component Analysis and Blind Signal Separation, ICA 2006

作者： Almeida, Mariana S. C. Valpola, Harri Särelä, Jaakko Institute de Telecomunicações Av. Rovisco Pais - 1 1049-001 Lisboa Portugal Laboratory of Computational Engineering Helsinki University of Technology P.O. Box 9203 FI-02015 HUT Espoo Finland Adaptive Informatics Research Centre Laboratory of Computer and Information Science Helsinki University of Technology P.O. Box 5400 FI-02015 HUT Espoo Finland

ISBN: (纸本)3540326308

The denoising source separation framework is extended to nonlinear separation of image mixtures. MLP networks are used to model the nonlinear unmixing mapping. Learning is guided by a denoising function which uses prior knowledge about the sparsity of the edges in images. The main benefit of the method is that it is simple and computationally efficient. Separation results on a real-world image mixture proved to be comparable to those achieved with MISEP. © Springer-Verlag Berlin Heidelberg 2006.

关键词： Imaging techniques

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High performance statistical computing with parallel R: applications to biology and climate modelling

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Journal of Physics: Conference Series 2006年第1期46卷

作者： Nagiza F Samatova Marcia Branstetter Auroop R Ganguly Robert Hettich Shiraj Khan Guruprasad Kora Jiangtian Li Xiaosong Ma Chongle Pan Arie Shoshani Srikanth Yoginath Computer Science and Mathematics Division USA Computational Sciences and Engineering Division USA Chemical Sciences Division Oak Ridge National Laboratory USA Department of Computer Science North Carolina State University USA Genome Science and Technology Graduate School ORNL-UTK USA Computational Research Division Lawrence Berkeley National Laboratory USA

Ultrascale computing and high-throughput experimental technologies have enabled the production of scientific data about complex natural phenomena. With this opportunity, comes a new problem – the massive quantities of data so produced. Answers to fundamental questions about the nature of those phenomena remain largely hidden in the produced data. The goal of this work is to provide a scalable high performance statistical data analysis framework to help scientists perform interactive analyses of these raw data to extract knowledge. Towards this goal we have been developing an open source parallel statistical analysis package, called Parallel R, that lets scientists employ a wide range of statistical analysis routines on high performance shared and distributed memory architectures without having to deal with the intricacies of parallelizing these routines.

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Identification of functional modules in protein complexes via hyperclique pattern discovery

Identification of functional modules in protein complexes vi...

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10th Pacific Symposium on Biocomputing, PSB 2005

作者： Xiong, Hui He, Xiaofeng Ding, Chris Zhang, Ya Kumar, Vipin Holbrook, Stephen R. Computer Science and Engineering University of Minnesota MN United States Lawrence Berkeley National Laboratory Computational Research Division Berkeley CA United States Information Sciences and Technology Penn State University PA United States

ISBN: (纸本)9812560467

Proteins usually do not act isolated in a cell but function within complicated cellular pathways, interacting with other proteins either in pairs or as components of larger complexes. While many protein complexes have been identified by large- scale experimental studies 7,8, due to a large number of false-positive interactions existing in current protein complexes 10, it is still difficult to obtain an accurate understanding of functional modules, which encompass groups of proteins involved in common elementary biological function. In this paper, we present a hyper- clique pattern discovery approach for extracting functional modules (hyperclique patterns) from protein complexes. A hyperclique pattern is a type of association pattern containing proteins that are highly affiliated with each other. The analysis of hyperclique patterns shows that proteins within the same pattern tend to present in the protein complex together. Also, statistically significant annotations of proteins in a pattern using the Gene Ontology suggest that proteins within the same hyperclique pattern more likely perform the same function and participate in the same biological process. More interestingly, the 3-D structural view of proteins within a hyperclique pattern reveals that these proteins physically interact with each other. In addition, we show that several hyperclique patterns corresponding to different functions can participate in the same protein complex as independent modules. Finally, we demonstrate that a hyperclique pattern can be involved in different complexes performing different higher-order biological functions, although the pattern corresponds to a specific elementary biological function.

关键词： Proteins

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Robustness in gene circuits: clustering of functional responses

Robustness in gene circuits: clustering of functional respon...

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American Control Conference (ACC)

作者： M.J. Dunlop M.E. Wall Division of Engineering and Applied Science California Institute of Technology CA USA Computer and Computational Sciences Division and Bioscience Division Los Alamos National Laboratory Los Alamos NM USA

In contrast to engineering applications, in which the structure of control laws are designed to satisfy prescribed function requirements, in biology it is often necessary to infer gene-circuit function from incomplete data on gene-circuit structure. By using the feed-forward loop as a model system, this paper introduces a technique for classifying gene-circuit function given gene-circuit structure. In simulations performed on a comprehensive set of models that span a broad range of parameter space, some designs are robust, producing one unique type of functional response regardless of parameter selection. Other designs may exhibit a variety of functional responses, depending upon parameter values. We conclude that, although some feed-forward loop models have designs that lend themselves to unique function inference, others have designs for which the function type may be uncertain.

关键词： Robustness Feedforward systems Genetics Biological system modeling Design engineering Circuit synthesis Gene expression Data engineering Biological control systems Biology

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Kondo Resonances and Anomalous Gate Dependence in the Electrical Conductivity of Single-Molecule Transistors

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Physical Review Letters 2005年第25期95卷 256803-256803页

作者： L. H. Yu Z. K. Keane J. W. Ciszek L. Cheng J. M. Tour T. Baruah M. R. Pederson D. Natelson Department of Physics and Astronomy Rice University 6100 Main Street Houston Texas 77005 USA Department of Chemistry and Center for Nanoscale Science and Technology Rice University 6100 Main Street Houston Texas 77005 USA Center for Computational Materials Science Code 6390-Naval Research Laboratory Washington DC 20375-5435 USA Department of Physics SUNY Stony Brook New York 11794 USA Department of Electrical and Computer Engineering Rice University 6100 Main Street Houston Texas 77005 USA

We report Kondo resonances in the conduction of single-molecule transistors based on transition metal coordination complexes. We find Kondo temperatures in excess of 50 K, comparable to those in purely metallic systems. The observed gate dependence of the Kondo temperature is inconsistent with observations in semiconductor quantum dots and a simple single-dot-level model. We discuss possible explanations of this effect, in light of electronic structure calculations.

关键词： Transistors

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Dynamic right-sizing in FTP (drsFTP): Enhancing Grid performance in user-space

Dynamic right-sizing in FTP (drsFTP): Enhancing Grid perform...

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International Symposium on High Performance Distributed Computing

作者： M.K. Gardner Wu-chun Feng M. Fisk Research & Development in Advanced Network Technology (RADIANT) Computer & Computational Sciences Division Los Alamos National Laboratory Los Alamos NM USA Network Security Team Network Engineering Group Computing Communications & Networking Division Los Alamos National Laboratory Los Alamos NM USA

With the advent of computational grids, networking performance over the wide-area network (WAN) has become a critical component in the grid infrastructure. Unfortunately, many high-performance grid applications only use a small fraction of the available bandwidth because operating systems and their associated protocol stacks are still tuned for yesterdays WAN speeds. As a result, network gurus undertake the tedious process of manually, tuning system buffers to allow TCP flow control to scale to today's WAN grid environments. Although recent research has shown how to set the size of these system buffers automatically at connection set-up, the buffer sizes are only appropriate at the beginning of the connection's lifetime. To address these problems, we describe an automated and scalable technique called dynamic right-sizing. We implement this technique in user space (in particular for bulk-data transfer) so that end users do not have to modify the kernel to achieve a significant increase in throughput.

关键词： Wide area networks computer networks Grid computing Bandwidth Operating systems Protocols Automatic control Control systems Kernel Throughput

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Towards a complete North American Anabaptist genealogy: A systematic approach to merging partially overlapping genealogy resources†

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American Journal of Medical Genetics Part A 1999年第2期86卷

作者： Richa Agarwala Leslie G. Biesecker James F. Tomlin Alejandro A. Schäffer Inherited Diseases Research Branch National Human Genome Research Institute National Institutes of Health Bethesda Maryland Genetic Diseases Research Branch National Human Genome Research Institute National Institutes of Health Bethesda Maryland Center for Information Technology Computational Bioscience and Engineering Laboratory National Institutes of Health Bethesda Maryland

Genetic studies on closed populations benefit from comprehensive, searchable genealogy resources. To support studies of Anabaptists, a computerized database has been developed that merges two large genealogy books, the “Fisher Family History” and the “Amish and Amish Mennonite Genealogies.” The former is more current but the latter is more comprehensive for the 18th and 19th centuries. Therefore, the merger of the two books is significantly more useful than either book alone. We demonstrate the utility of the merged database with two results: an increase in inbreeding coefficients and the identification of parent–child relationships that do not exist in either book. Am. J. Med. Genet. 86:156–161, 1999. Published 1999 Wiley-Liss, Inc.

关键词： autosomal recessive inheritance Amish Mennonite consanguinity inbreeding

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A bioinformatics tool to mine sequences for microarray studies of mouse models of oncogenesis

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Nature Genetics 1999年第3期23卷 43-43页

作者： Mary E. Edgerton Ronald Taylor John I. Powell Richard Simon Edison T. Liu Department of Pathology and Laboratory Medicine Hospital of the University of Pennsylvania Philadelphia USA Division of Cancer Treatment and Diagnosis Biometric Research Branch Cancer Therapy Evaluation Program National Cancer Institute Bethesda USA Bioinformatics and Molecular Analysis Section Computational Bioscience and Engineering Laboratory Center for Information Technology National Institutes of Health Bethesda USA Division of Clinical Sciences National Cancer Institute Bethesda USA

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LINE-I element insertion at the t(11;22) translocation breakpoint of a desmoplastic small round cell tumor

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Genes, Chromosomes and Cancer 1998年第3期18卷

作者： Jun Liu Marion M. Nau Jessica Zucman-Rossi John I. Powell Carmen J. Allegra John J. Wright NCI-Navy Medical Oncology Branch National Cancer Institute Bethesda Maryland Laboratoire de Genetique des Tumeurs Institut Curie Paris France Computational Bioscience and Engineering Laboratory Division of Computer Research and Technology National Institutes of Health Bethesda Maryland

A t(11;22)(p13;p12) chromosomal translocation, juxtaposing the Wilms' tumor ( WTI ) and Ewing's sarcoma ( EWS ) genes, is the cytogenetic hallmark of desmoptastic small round cell tumor (DSRCT), a primitive multiphenotypic sarcoma arising in serosal tissues. Chimeric transcripts generated by this rearrangement encode an aberrant transcription factor that fuses the 5′ region of EWS with a 3′ WTI segment. We describe the insertion of a LINE-I DNA mobile genetic element at the genomic breakpoint of a DSRCT chromosomal translocation. A 480 bp heterologous DNA segment with homology to the LINE-I DNA consensus sequence was located between EWS intron 8 and WTI exon 8 in the productively rearranged allele. Sequence homology corresponded to the LINE-I ORF-2, which encodes a protein with reverse-transcriptase activity. The heterologous inserted fragment was not evident in the germline of normal tissue from the patient, suggesting that transposition occurred in somatic cells, possibly during the process of chromosomal rearrangement. This case represents the first example of LINE-I DNA transposition at the fusion site of a tumor-associated chromosomal rearrangement. Genes Chromosom. Cancer 18:232–239, 1997 . © 1997 Wiley-Liss, Inc.

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Parallel algorithms in molecular biology

Parallel algorithms in molecular biology

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International Conference and Exhibition on High-Performance Computing and Networking, HPCN Europe 1997

作者： Martino, Robert L. Yap, Tieng K. Suh, Edward B. Computational Bioscience and Engineering Laboratory Division of Computer Research and Technology National Institutes of Health Building 12A Room 2033 12 South Drive MSC 5624 BethesdaMD20892 United States

ISBN: (纸本)3540628983

Scalable parallel computer architectures provide the computational performance needed for advanced computing problems in molecular biology. Many scientific challenges in molecular biology have associated with them a computational requirement that must be solved before scientific progress can be made. We have developed a number of parallel algorithms and techniques useful in determining biological structure and function. Two example applications are the alignment of multiple DNA and protein sequences using speculative computation and the calculation of the solvent accessible surface area of proteins used to predict the three-dimensional conformation of these molecules from their primary structure. Timing results demonstrate substantial performance improvements with parallel implementations compared with conventional sequential systems. As the developed methods allow molecular biologists to perform computational tasks that would not otherwise be possible, we continue to develop parallel algorithms useful to this important scientific field. © 1997 Springer-Verlag Berlin Heidelberg.

关键词： Parallel algorithms

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