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检索条件"任意字段=IEEE Computational Systems Bioinformatics Conference"

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Solving the mobile robot localization problem using string matching algorithms

Solving the mobile robot localization problem using string m...

引用

ieee International Workshop on Intelligent Robots and systems (IROS)

作者： C. Gonzalez-Buesa J. Campos Departamento de Informática e Ingenieía de Sistemas Universidad de Zaragoza Zaragoza Spain

In this paper we address the mobile robot localization using some techniques borrowed from the computational biology community. The specific problem studied here is also known as the kidnapped robot problem. Our proposal is to solve this problem by string matching algorithms, which have experienced a large advance in the last years due to (for example) the Genoma Project. The paper uses three different algorithms to solve the mentioned problem and shows their advantages, such as the robustness of the results and the memory and time efficiency. These results are validated by real experimentation using panoramic images of indoor buildings, and compared and discussed with existing techniques that have been used over the same test-bed.

关键词： Mobile robots Testing Vehicles Sequences Proposals Genomics bioinformatics Robustness Robot sensing systems Feature extraction

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Asynchronous HMM with applications to speech recognition

Asynchronous HMM with applications to speech recognition

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International conference on Acoustics, Speech, and Signal Processing (ICASSP)

作者： A. Garg S. Balakrishnan S. Vaithyanathan IBM Almaden Research Center San Jose CA USA

We develop a novel formalism for modeling speech signals which are irregularly or incompletely sampled. This situation can arise in real world applications where the speech signal is being transmitted over an error prone channel where parts of the signal can be dropped. Typical speech systems based on hidden Markov models, cannot handle such data since HMMs rely on the assumption that observations are complete and made at regular intervals. We introduce the asynchronous HMM, a variant of the inhomogeneous HMM commonly used in bioinformatics, and show how it can be used to model irregularly or incompletely sampled data. A nested EM algorithm is presented in brief which can be used to learn the parameters of this asynchronous HMM. Evaluation on real world speech data, which has been modified to simulate channel errors, shows that this model and its variants significantly outperform the standard HMM and methods based on data interpolation.

关键词： Hidden Markov models Speech recognition Interpolation bioinformatics Random variables Speech analysis computational modeling Computer errors Computer vision Text analysis

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Surface approximation based image simplification and applications

Surface approximation based image simplification and applica...

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ieee International conference on systems, Man and Cybernetics

作者： Mingen Lin Jinhui Xu S. Bhattacharya R. Berezney Department of Computer Science and Engineering State University of New York University at Buffalo Buffalo NY USA Department of Computer Science and Engineering University of Buffallo Buffalo NY USA Department of Biological Sciences State University of New York University at Buffalo Buffalo NY USA

In this paper, we consider the problems of simplifying microscopic images of cell nucleus and segmenting genomic structures (such as DNA replication/transcription sites or foci and chromatin domains) from such images. DNA foci often have small sizes, and could be hidden by diffuse signals or quasi-foci (fanned by the overlapping of some neighboring foci), making the simplification and segmentation tasks extremely challenging. Existing simplification algorithms often yield large-sized images and take unreasonably long execution time. Available segmentation algorithms either fail reporting all DNA foci or generate incorrect boundaries. Based on an interesting observation on the intensity of microscopic images of cell nucleus, we present in this paper a novel approach for simplifying microscopic images by approximating the intensity surface of images by a set of normal distribution functions. Our technique yields much smaller-sized simplified images and runs in near linear time. With this technique, we further develop an efficient algorithm for segmenting DNA foci. Comparing with existing segmentation algorithms (such as watershed method), our algorithm detects all possible foci and generates much more accurate boundary of the detected foci. Our techniques are readily extendable to other types of images.

关键词： DNA Image segmentation Pixel Genomics bioinformatics Computer vision Application software computational geometry Optical microscopy Partitioning algorithms

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The role and efficacy of non-linear models in decision making and prognostication

The role and efficacy of non-linear models in decision makin...

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Annual International conference of the ieee Engineering in Medicine and Biology Society (EMBC)

作者： A.F.G. Taktak A.C. Fisher A.S. Jones B.E. Damato Department of Clinical Engineering Royal Liverpool University Hospital Liverpool UK Head and Neck Oncology Group University Hospital Aintree Liverpool UK Department of Ophthalmology Royal Liverpool University Hospital Liverpool UK

In few types of cancer, genomic abnormalities have been linked to the phenotype and carcinogenesis with a degree of precision. For most cancers, however, this is not the case and the literature provides no clear indication of any logical process. The main difficulties are the great redundancy within the genome and proteome, the vast number of interconnections and the vast number of feedback loops. Such complicated systems can be modelled, but will require highly sophisticated analysis using computational mathematics techniques. Neural networks have been in common use in medical research for the past 20 years. They have been used for classification and for prediction of hazard or failure but are still not widely used for explanation. The binary output can be modified by, for example, adding a Bayesian function to the output stage so that survival probabilities can be given. We looked at the application of probabilistic neural networks in providing prognosis in two types of cancer; laryngeal carcinoma which has a relatively short hazard time and a medium survival rate and ocular melanoma with longer hazard time and higher survival rate. We compared their performance with the more traditional methods and studied their limitations and boundaries.

关键词： Decision making Cancer Hazards Genomics bioinformatics Neural networks Feedback loop Mathematical model Mathematics Bayesian methods

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Proceedings of the 2003 ieee bioinformatics conference, CSB 2003

Proceedings of the 2003 IEEE Bioinformatics Conference, CSB ...

引用

2nd International ieee Computer Society computational systems bioinformatics conference, CSB 2003

ISBN: (纸本)0769520006

The proceedings contain 134 papers. The topics discussed include: stepping up the pace of discovery: the genomes to life program;the role of algorithmic research in computational genomics;high performance computational biology - past progress and future promise;bridging paradigm gaps between biology and engineering;microbial functional genomics: pulling together a variety of approaches and concepts;the sea urchin endomesoderm gene regulatory network, an encoded logic map for early development;epitope prediction algorithms for peptide-based vaccine design;eulerian path methods for multiple sequence alignment;integrating bioinformatics advances into disease management systems to improve quality of care;motifs and modules in cellular signal processing: applications to microbial stress response pathways;and analysis of the genetic potential and gene expression of microbial communities involved in the in situ bioremediation of uranium and harvesting electrical energy from organic matter.

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Pathway bioinformatics 2

Pathway bioinformatics

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2nd International computational systems bioinformatics conference

作者： Karp, P SRI Int Bioinformat Res Grp Menlo Pk CA 94025 USA

ISBN: (纸本)0769520006

Pathway bioinformatics is a subfield of bioinformatics that is concerned with pathway algorithms, ontologies, visualizations, and databases [4]. This talk will provide an overview of the pathway databases and software under development in the bioinformatics research group at SRI International, and will then discuss three pathway algorithms in detail. © 2003 ieee.

关键词： bioinformatics

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Development and assessment of bioinformatics tools for species conservation and habitat management 2

Development and assessment of bioinformatics tools for speci...

引用

2nd International computational systems bioinformatics conference

作者： Sutton, MA Deneke, L Eme, J Bennett, W Wray, F Univ W Florida Dept Biol Pensacola FL 32514 USA

ISBN: (纸本)0769520006

This project represents an interdisciplinary approach to integrating computational methods into the knowledge-discovery process associated with understanding biological systems impacted by the loss or destruction of sensitive habitats. We specifically developed bioinformatics tools for the study of (1) beach mouse communities and (2) marginal fish habitats. Data mining was used in these projects to intelligently query databases and to elucidate broad patterns that facilitate overall data interpretation. Visualization techniques that were developed present mined data in ways where context, perceptual cues, and spatial reasoning skills can be applied to uncover significant trends in behavioral patterns, habitat use, species diversity, and community composition.

关键词： Data visualization

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PTC: An interactive tool for phylogenetic tree construction 2

PTC: An interactive tool for phylogenetic tree construction

引用

2nd International computational systems bioinformatics conference

作者： Yang, C Khuri, S San Jose State Univ Dept Comp Sci San Jose CA 95192 USA

ISBN: (纸本)0769520006

A phylogenetic tree represents the evolutionary history of a group of organisms. In this work, we introduce a novel interactive tool for constructing phylogenetic trees, Phylogenetic Tree Construction package. The package supports four well-known algorithms, Unweighted Pair Group Method using Arithmetic average, Neighbor Joining, Fitch Margoliash, and Maximum Parsimony.

关键词： bioinformatics

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Using easel for modeling and simulating the interactions of cells in order to better understand the basics of biological processes and to predict their likely behaviors 2

Using easel for modeling and simulating the interactions of ...

引用

2nd International computational systems bioinformatics conference

作者： Stojkovic, V Steele, G Lupton, W MSU Baltimore MD USA

ISBN: (纸本)0769520006

Modeling, simulation, visualization, and animation play a significant role in the study of bioinformatics. Research in this area is generally multidisciplinary in nature and collaboratively conducted by researchers with expertise in biology, bioinformatics, computer science, artificial intelligence, mathematics, and statistics. Easel programming language is used for modeling, simulation, visualization, and animation of interactions of cells in order to better understand the basics of biological processes and to predict their likely behaviors. This paper presents a computer science - modeling, simulation, visualization, and animation approach to such research. The paper provides a brief overview of the basic ideas in the "Message Passing" Easel program to demonstrate the transmission of signals between cells based on their physical proximity.

关键词： bioinformatics

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A run-time reconfigurable system for gene-sequence searching 16

A run-time reconfigurable system for gene-sequence searching

引用

16th International conference on VLSI Design/2nd International conference on Embedded systems Design

作者： Puttegowda, K Worek, W Pappas, N Dandapani, A Athanas, P Dickerman, A Virginia Polytech Inst & State Univ Blacksburg VA 24061 USA

ISBN: (纸本)0769518680

Advances in the field of bio-technology has led to an ever increasing demand for computational resources to rapidly search large databases of genetic information. Databases with billions of data elements are routinely compared: and searched for matching and near-matching patterns. In this paper we present a system developed to search DNA sequence data using run-time reconfiguration of Field Programmable Gate Arrays (FPGAs). The system provides an order of magnitude increase in performance while reducing hardware complexity when compared to existing commercial systems.

关键词： bioinformatics Costs Databases DNA Field programmable gate arraysvGenetics Hardware Proteins Runtime Sequences

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