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2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)

2-4 Nov. 2007

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Displaying Results 1 - 25 of 71
  • 2007 IEEE International Conference on Bioinformatics and Biomedicine - Cover

    Publication Year: 2007, Page(s): c1
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  • 2007 IEEE International Conference on Bioinformatics and Biomedicine - Title

    Publication Year: 2007, Page(s):i - iii
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  • 2007 IEEE International Conference on Bioinformatics and Biomedicine - Copyright

    Publication Year: 2007, Page(s): iv
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  • 2007 IEEE International Conference on Bioinformatics and Biomedicine - Table of contents

    Publication Year: 2007, Page(s):v - x
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  • Preface

    Publication Year: 2007, Page(s): xi
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  • Organizing Committee

    Publication Year: 2007, Page(s): xii
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  • Program Committee

    Publication Year: 2007, Page(s): xiii
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  • Sponsors

    Publication Year: 2007, Page(s): xvii
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  • Combining Simulation and Machine Learning to Recognize Function in 4D

    Publication Year: 2007, Page(s): 3
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (137 KB) | HTML iconHTML

    This paper is a talk by Russ Biagio Altman. It discusses structure-based protein function annotation using machine learning, physics-based simulation of structure, and how they can be profitably combined to improve our understanding of molecular structure and function. View full abstract»

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  • Statistical Machine Learning and Computational Biology

    Publication Year: 2007, Page(s): 4
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (88 KB) | HTML iconHTML

    This talk will trace the growing influence of fundamental ideas from computer science on the nature of research in a number of scientific fields. There is a growing awareness that information processing lies at the heart of the processes studied in fields as diverse as quantum mechanics, statistical physics, nanotechnology, neuroscience, linguistics, economics and sociology. Increasingly, mathemat... View full abstract»

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  • Computer Science as a Lens on the Sciences: The Example of Computational Molecular Biology

    Publication Year: 2007, Page(s): 5
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (86 KB) | HTML iconHTML

    This talk will trace the growing influence of fundamental ideas from computer science on the nature of research in a number of scientific fields. There is a growing awareness that information processing lies at the heart of the processes studied in fields as diverse as quantum mechanics, statistical physics, nanotechnology, neuroscience, linguistics, economics and sociology. Increasingly, mathemat... View full abstract»

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  • Feature Cluster Selection for High-Throughput Data Analysis

    Publication Year: 2007, Page(s):9 - 14
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (171 KB) | HTML iconHTML

    Although feature selection has proven effective in sample class prediction, it is not adequate for identifying leads for potentially useful biomarkers by high-throughput biological data analysis. The large number of equally good predictive sets and the disparity among them reveals the gap between feature selection and biomarker identification. We propose to bridge this gap by a new data mining tas... View full abstract»

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  • GenMiner: Mining Informative Association Rules from Genomic Data

    Publication Year: 2007, Page(s):15 - 22
    Cited by:  Papers (6)
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (189 KB) | HTML iconHTML

    GENMINER is a smart adaptation of closed itemsets based association rules extraction to genomic data. It takes advantage of the novel NORDI discretization method and of the CLOSE [27] algorithm to efficiently generate min- imal non-redundant association rules. GENMINER facili- tates the integration of numerous sources of biological in- formation such as gene expressions and annotations, and can ta... View full abstract»

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  • EGGS: Extraction of Gene Clusters Using Genome Context Based Sequence Matching Techniques

    Publication Year: 2007, Page(s):23 - 28
    Cited by:  Papers (5)
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (642 KB) | HTML iconHTML

    Functionally related genes co-evolve, probably due to selection pressures during evolution, This phenomenon leads to conservation of gene clusters across genomes, especially in microbial genomes. In this paper, we propose novel iterative constraint relaxation algorithms which make use of genome contexts to effectively remove noise and extract gene clusters: PairEGGS that generates gene clusters in... View full abstract»

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  • A Machine Learning Approach for Identification of Head and Neck Squamous Cell Carcinoma

    Publication Year: 2007, Page(s):29 - 34
    Cited by:  Papers (1)
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (420 KB) | HTML iconHTML

    Squamous cell carcinoma is the most common type of head and neck cancer affecting about 30,000 Americans each year [1]. Diagnosis of tumor is backed by histopathologic examination of excised tissue in which lesion is speckled. Computer vision systems have yet to contribute significantly to the investigation of tumor areas in terms of histological slide analysis. Recently the improvements in imagin... View full abstract»

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  • Analysis of Protein Protein Dimeric Interfaces

    Publication Year: 2007, Page(s): 35
    Cited by:  Papers (1)
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (256 KB) | HTML iconHTML

    We analyzed the structural properties and the local surface environment of surface amino acid residues of proteins using a large, non-redundant dataset of 2383 protein chains in dimeric complexes from PDB. We compared the interface residues and non-interface residues based on six properties: side chain orientation, surface roughness, solid angle, ex value, hydrophobicity and interface cluster size... View full abstract»

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  • A Hybrid Abbreviation Extraction Technique for Biomedical Literature

    Publication Year: 2007, Page(s):42 - 47
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (294 KB) | HTML iconHTML

    In this paper, we propose a novel technique to extract abbreviation combining natural language processing techniques and the Support Vector Machine (SVM) in biomedical literature. The proposed technique gives us the comparative advantages over others in the following aspects: 1) It incorporates lexical analysis techniques to supervised learning for extracting abbreviations. 2) It makes use of text... View full abstract»

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  • Hypothesis-Driven Specialization of Gene Expression Association Rules

    Publication Year: 2007, Page(s):48 - 55
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (437 KB) | HTML iconHTML

    This paper focuses on analyzing patterns mined from gene expression data. Whether a particular gene is "turned on" (expressed) or not is controlled by particular DNA se- quences (motifs). Multiple motifs are commonly involved in the expression of each gene, and the position and spacing of these motifs may be important. However, most available computational tools consider the importance only of ind... View full abstract»

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  • A New Fuzzy ARTMAP Approach for Predicting Biological Activity of Potential HIV-1 Protease Inhibitors

    Publication Year: 2007, Page(s):56 - 61
    Cited by:  Papers (4)
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (207 KB) | HTML iconHTML

    The Fuzzy ARTMAP with Relevance factor (FAMR) is a Fuzzy ARTMAP (FAM) neural architecture with the following property: Each training pair has a relevance factor assigned to it, proportional to the importance of that pair during the learning phase. Using a relevance factor adds more flexibility to the training phase, allowing ranking of sample pairs according to the confidence we have in the inform... View full abstract»

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  • Multi-topic Aspects in Clinical Text Classification

    Publication Year: 2007, Page(s):62 - 70
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (172 KB) | HTML iconHTML

    This paper investigates multi-topic aspects in automatic classification of clinical free text. In many practical situ- ations, we need to deal with documents overlapping with multiple topics. Automatic assignment of multiple ICD-9- CM codes to clinical free text in medical records is a typi- cal multi-topic text classification problem. In this paper, we facilitate two different views on multi-topi... View full abstract»

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  • A Comparison of Unsupervised Dimension Reduction Algorithms for Classification

    Publication Year: 2007, Page(s):71 - 77
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (157 KB) | HTML iconHTML

    Distance preserving dimension reduction (DPDR) using the singular value decomposition has recently been introduced. In this paper, for disease diagnosis using gene or protein expression data, we present empirical comparison results between DPDR and other various dimension reduction (DR) methods (i.e. PC A, MDS, Isomap, and LLE) when using support vector machines with radial basis function kernel. ... View full abstract»

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  • Pathological Image Analysis Using the GPU: Stroma Classification for Neuroblastoma

    Publication Year: 2007, Page(s):78 - 88
    Cited by:  Papers (10)
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (552 KB) | HTML iconHTML

    Neuroblastoma is one of the most malignant childhood cancers affecting infants mostly. The current prognosis is based on microscopic examination of slides by expert pathologists, a process that is error-prone, time consuming and may lead to inter- and intra-reader variations. Therefore, we are developing a Computer Aided Prognosis (CAP) system which provides computerized image analysis to assist p... View full abstract»

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  • MAGMA: An Algorithm for Mining Multi-level Patterns in Genomic Data

    Publication Year: 2007, Page(s):89 - 94
    Cited by:  Papers (1)
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (292 KB) | HTML iconHTML

    Genome comparison is very useful for deriving evolutionary and functional relationships between genomes. Previous works on genome comparison focus mainly on comparing the entire genome at the nucleotide level. As interesting patterns exist also at the gene and segment level, we propose an algorithm called Multi- Level Genome Comparison Algorithm (MGC) that can allow genome comparison to be perform... View full abstract»

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  • Computational Identification of Protein-Coding Sequences by Comparative Analysis

    Publication Year: 2007, Page(s):95 - 102
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (187 KB) | HTML iconHTML

    Gene prediction is an essential step in understanding the genome of a species once it has been sequenced. For that, a promising direction in current research on gene finding is a comparative genomics approach. In this paper, we present a novel approach to identifying evolutionarily conserved protein-coding sequences in genomes. The method takes advantage of the specific substitution pattern of cod... View full abstract»

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  • Multi-agent System for Translation Initiation Site Prediction

    Publication Year: 2007, Page(s):103 - 110
    Cited by:  Papers (3)
    Request permission for reuse | Click to expandAbstract | PDF file iconPDF (158 KB) | HTML iconHTML

    Accurate translation initiation site (TIS) prediction is very important for genomic analysis. It is a com- mon understanding that analyzing the large amount of genomic data by pure biological methods is impracti- cal if not impossible. Therefore many approaches have been proposed which apply some machine learning tech- nique to analyze a particular aspect of the data. We believe, however, that tak... View full abstract»

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