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Gene Expression Clustering: a Novel Graph Partitioning Approach

Gene Expression Clustering: a Novel Graph Partitioning Appro...

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International Joint Conference on Neural Networks (IJCNN)

作者： Yanhua Chen Ming Dong Manjeet Rege Machine Vision and Pattern Recognition Laboratory Department of Computer Science Wayne State University Detroit MI USA

In order to help understand how the genes are affected by different disease conditions in a biological system, clustering is typically performed to analyze gene expression data. In this paper, we propose to solve the clustering problem using a graph theoretical approach, and apply a novel graph partitioning model -isoperimetric graph partitioning (IGP), to group biological samples from gene expression data. The IGP algorithm has several advantages compared to the well-established spectral graph partitioning (SGP) model. First, IGP requires a simple solution to a sparse system of linear equations instead of the eigen-problem in the SGP model. Second, IGP avoids degenerate cases produced by spectral approach to achieve a partition with higher accuracy. Moreover, we integrate unsupervised gene selection into the proposed approach through two-way ordering of gene expression data, such that we can eliminate irrelevant or redundant genes in the data and obtain an improved clustering result. We evaluate our approach on several well-known problems involving gene expression profiles of colon cancer and leukemia subtypes. Our experiment results demonstrate that IGP constantly outperforms SGP and produces a better result that is closer to the original labeling of sample sets provided by domain experts. Furthermore, the clustering accuracy is improved significantly when IGP is integrated with the unsupervised gene (feature) selection.

关键词： Gene expression Biological system modeling Diseases Biological systems Data analysis Performance analysis Clustering algorithms Partitioning algorithms Equations Colon

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Sparse MRF appearance models for fast anatomical structure localisation

Sparse MRF appearance models for fast anatomical structure l...

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2007 18th British Machine vision Conference, BMVC 2007

作者： Donner, René Mičušsík, Branislav Langs, Georg Bischof, Horst Institute for Computer Graphics and Vision Graz University of Technology Austria Pattern Recognition and Image Processing Group Vienna University of Technology Austria GALEN Group Laboratoire de Mathématiques Appliquées Aux Systèmes Ecole Centrale de Paris France

ISBN: (纸本)1901725340

Image segmentation methods like active shape models, active appearance models or snakes require an initialisation that guarantees a considerable overlap with the object to be segmented. In this paper we present an approach that localises anatomical structures in a global manner by means of Markov Random Fields (MRF). It does not need initialisation, but finds the most plausible match of the query structure in the image. It provides for precise, reliable and fast detection of the structure and can serve as initialisation for more detailed segmentation steps. Sparse MRF Appearance Models (SAMs) encode a priori information about the geometric configurations of interest points, local features at these points and local features along the edges of adjacent points. This information is used to formulate a Markov Random Field and the mapping of the modeled object (e.g. a sequence of vertebrae) to the query image interest points is performed by the MAX-SUM algorithm. The local image information is captured by novel symmetry-based interest points and local descriptors derived from Gradient Vector Flow. Experimental results are reported for two data-sets showing the applicability to complex medical data.

关键词： Image segmentation

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Incorporating User Provided Constraints into Document Clustering

Incorporating User Provided Constraints into Document Cluste...

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IEEE International Conference on Data Mining (ICDM)

作者： Yanhua Chen Manjeet Rege Ming Dong Jing Hua Department of Computer Science Machine Vision and Pattern Recognition Laboratory Detroit MI USA Department of Computer Science Graphics and Imaging Laboratory Detroit MI USA

Document clustering without any prior knowledge or background information is a challenging problem. In this paper, we propose SS-NMF: a semi-supervised non- negative matrix factorization framework for document clustering. In SS-NMF, users are able to provide supervision for document clustering in terms of pairwise constraints on a few documents specifying whether they "must" or "cannot" be clustered together. Through an iterative algorithm, we perform symmetric tri-factorization of the document- document similarity matrix to infer the document clusters. Theoretically, we show that SS-NMF provides a general framework for semi-supervised clustering and that existing approaches can be considered as special cases of SS-NMF. Through extensive experiments conducted on publicly available data sets, we demonstrate the superior performance of SS-NMF for clustering documents.

关键词： Iterative algorithms Clustering algorithms Symmetric matrices Data mining Databases Clustering methods Couplings Machine vision pattern recognition computer graphics

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Off-Line Handwritten Character Recognition of Devnagari Script

Off-Line Handwritten Character Recognition of Devnagari Scri...

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International Conference on Document Analysis and Recognition

作者： U. Pal N. Sharma T. Wakabayashi F. Kimura Computer Vision and Pattern Recognition Unit Indian Statistical Institute Kolkata India Graduate School of Engineering Mie University Tsu Japan

In this paper we present a system towards the recognition of off-line handwritten characters of Devnagari, the most popular script in India. The features used for recognition purpose are mainly based on directional information obtained from the arc tangent of the gradient. To get the feature, at first, a 2times2 mean filtering is applied 4 times on the gray level image and a non-linear size normalization is done on the image. The normalized image is then segmented to 49times49 blocks and a Roberts filter is applied to obtain gradient image. Next, the arc tangent of the gradient (direction of gradient) is initially quantized into 32 directions and the strength of the gradient is accumulated with each of the quantized direction. Finally, the blocks and the directions are down sampled using Gaussian filter to get 392 dimensional feature vector. A modified quadratic classifier is applied on these features for recognition. We used 36172 handwritten data for testing our system and obtained 94.24% accuracy using 5-fold cross-validation scheme.

关键词： Character recognition Handwriting recognition Filters Filtering pattern recognition Image segmentation Automation computer vision System testing Natural languages

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Handwritten Numeral Recognition of Six Popular Indian Scripts

Handwritten Numeral Recognition of Six Popular Indian Script...

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International Conference on Document Analysis and Recognition

作者： U. Pal N. Sharma T. Wakabayashi F. Kimura Computer Vision and Pattern Recognition Unit Indian Statistical Institute Kolkata India Graduate School of Engineering Mie University Tsu Japan

ISBN: (纸本)9780769528229;0769528228

India is a multi-lingual multi-script country but there is not much work towards handwritten character recognition of Indian languages. In this paper we propose a modified quadratic classifier based scheme towards the recognition of off-line handwritten numerals of six popular Indian scripts. Here we consider Devnagari, Bangla, Telugu, Oriya, Kannada and Tamil scripts for our experiment. The features used in the classifier are obtained from the directional information of the numerals. For feature computation, the bounding box of a numeral is segmented into blocks and the directional features are computed in each of the blocks. These blocks are then down sampled by a Gaussian filter and the features obtained from the down sampled blocks are fed to a modified quadratic classifier for recognition. Here we have used two sets of feature. We have used 64 dimensional features for high-speed recognition and 400 dimensional features for high-accuracy recognition in our proposed system. A five-fold cross validation technique has been used for result computation and we obtained 99.56%, 98.99%, 99.37%, 98.40%, 98.71% and 98.51% accuracy from Devnagari, Bangla, Telugu, Oriya, Kannada, and Tamil scripts, respectively.

关键词： Handwriting recognition Natural languages Character recognition Automation pattern recognition Filters Sorting computer vision Feature extraction Writing

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A comparision of Model-based methods for knee cartilage segmentation

A comparision of Model-based methods for knee cartilage segm...

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2nd International Conference on computer vision Theory and Applications, VISAPP 2007

作者： Cheong, J. Faggian, N. Langs, G. Suter, D. Cicuttini, F. Dept. of Electrical Dept. of Computer Systems Engineering Monash University Australia Clayton School of Information Technology Monash University Australia Institute for Computer Graphics and Vision Graz University of Technology Austria Pattern Recognition and Image Processing Group Vienna University of Technology Austria Dept. of Epidemiology Dept. of Preventive Medicine Monash University Australia

Osteoarthritis is a chronic and crippling disease affecting an increasing number of people each year. With no known cure, it is expected to reach epidemic proportions in the near future. Accurate segmentation of knee cartilage from magnetic resonance imaging (MRI) scans facilitates the measurement of cartilage volume present in a patient's knee, thus enabling medical clinicians to detect the onset of osteoarthritis and also crucially, to study its effects. This paper compares four model-based segmentation methods popular for medical data segmentation, namely Active Shape Models (ASM) (Cootes et al., 1995), Active Appearance Models (AAM) (Cootes et al., 2001), Patch-based Active Appearance Models (PAAM) (Faggian et al., 2006), and Active Feature Models (AFM) (Langs et al., 2006). A comprehensive analysis of how accurately these methods segment human tibial cartilage is presented. The results obtained were benchmarked against the current "gold standard" (cartilage segmented manually by trained clinicians) and indicate that modeling local texture features around each landmark provides the best results for segmenting human tibial cartilage.

关键词： Medical imaging

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Text/Graphics Separation in Color Maps

Text/Graphics Separation in Color Maps

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International Conference on Computing: Theory and Applications, ICCTA

作者： Partha Pratim Roy Josep Llados Umapada Pal Computer Science Department Universitat Autònoma de Barcelona Barcelona Bellaterra Spain Computer Vision and Pattern Recognition Unit Indian Statistical Institute Kolkata Kolkata India

Text/graphics separation in document image analysis is one of the main concerns in present research work. The complexity enhances when both text and graphics overlap in the context of maps in color images. This paper discusses a number of improvements to text/graphics separation methods to make it suitable for maps. Emphasize is given to the overlapping regions of text and graphics. It also discusses a method of color separation using clustering method for the purpose of text/graphics separation

关键词： computer graphics Image color analysis Image segmentation Histograms Bit error rate computer vision Text analysis Clustering methods Engineering drawings Testing

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Handwritten Bangla Compound Character Recognition Using Gradient Feature

Handwritten Bangla Compound Character Recognition Using Grad...

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International Conference on Information Technology (ICIT)

作者： U. Pal T. Wakabayashi F. Kimura Computer Vision and Pattern Recognition Unit Indian Statistical Institute Kolkata India Graduate School of Engineering Mie University Tsu Mie Japan

Recognition of handwritten characters of Indian script is difficult because of the presence of many complex shaped compound characters (cluster characters) as well as variability involved in the writing style of different individuals. This paper deals with recognition of off-line Bangla handwritten compound characters using modified quadratic discriminant function (MQDF). The features used for recognition purpose are mainly based on directional information obtained from the arc tangent of the gradient. To get the feature, at first, a 2 times 2 mean filtering is applied 4 times on the gray level image and a non-linear size normalization is done on the image. A Roberts filter is then applied on the normalized image to obtain gradient image. Next, the arc tangent of the gradient (direction of gradient) is initially quantized into 32 directions and the strength of the gradient is accumulated with each of the quantized direction. Finally, the frequencies of these directions are down sampled using Gaussian filter to get 392 dimensional feature vectors. Using 5-fold cross validation technique we obtained 85.90% accuracy from a dataset of Bangla compound characters containing 20,543 samples.

关键词： Character recognition Handwriting recognition Filters pattern recognition Filtering Automation Information technology computer vision Writing Frequency

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A System for Off-Line Oriya Handwritten Character Recognition Using Curvature Feature

A System for Off-Line Oriya Handwritten Character Recognitio...

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International Conference on Information Technology (ICIT)

作者： U. Pal T. Wakabayashi F. Kimura Computer Vision and Pattern Recognition Unit Indian Statistical Institute Kolkata India Graduate School of Engineering Mie University Tsu Mie Japan

In this paper we present a system towards the recognition of off-line Oriya handwritten characters. Since most of the Oriya characters have curve-like stroke, we use curvature feature for the recognition purpose. To get the feature, at first, the input image is size normalized and segmented into 49times49 blocks. Curvature is then computed using bi-quadratic interpolation method and quantized into 3 levels according to concave, linear and convex regions. Next direction of gradient is quantized into 32 levels with pi/16 intervals, and strength of the gradient is accumulated in each of the 32 directions and in each of the 3 curvature levels of every block. A spatial resolution is made to get 7times7 blocks from 49times49 blocks and a directional resolution is made to get 8 directions from 32 directions. Using curvature features for 3 levels we get 1176 (7times7 blocks times 8 directions times 3 levels) dimensional features. Finally using principal component analysis we reduce the dimension 1176 to 392 and this 392 dimensional feature vector is fed to a quadratic classifier for recognition. We tested 18190 samples of Oriya handwritten samples and obtained 94.60% accuracy from our proposed system.

关键词： Character recognition Shape Handwriting recognition computer vision Spatial resolution Speech recognition Information technology pattern recognition Image segmentation Interpolation

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Benchmarking 3D reconstructions from Next Best View planning

Benchmarking 3D reconstructions from Next Best View planning

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10th IAPR Conference on Machine vision Applications, MVA 2007

作者： Munkelt, Christoph Trummer, Michael Denzler, Joachim Wenhardt, Stefan Fraunhofer IOF Albert-Einstein-Straße 7 07745 Jena Germany Department of Computer Vision Friedrich Schiller University of Jena Ernst-Abbe-Platz 2 07743 Jena Germany Department of Pattern Recognition Friedrich Alexander University of Erlangen Martensstr. 3 91058 Erlangen Germany

ISBN: (纸本)9784901122078

The problem of planning the Next Best View (NBV) still poses many questions. However, the achieved methods and algorithms are hard to compare, since researchers use their own test objects for planning and reconstruction and compute specific quality measures. Consequently, these numbers make different statements about different objects. Thus, the quality of the results and the performance of the methods are not easily comparable. In order to mend this lack of measure and comparability, this paper suggests a test object together with a reference benchmark. These allow comparison of reconstruction results from different NBV algorithms achieved with different techniques and various kinds of sensors.

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