Atul Sajjanhar

Region-based shape representation and similarity measure suitable for content-based image retrieval

Abstract. A region-based approach to shape representation and similarity measure is presented. The shape representation is invariant to translation, scale and rotation. The similarity measure conforms to human similarity perception, i.e., perceptually similar shapes have high similarity measure. An experimental shape retrieval system has been developed and its performance has been studied. The shape retrieval performance of the proposed approach is better than that of the more established Fourier descriptor method.

Algorithm for Web Services Matching

UDDI is a standard for publishing and discovery of web services. UDDI registries provide keyword searches for web services. The search functionality is very simple and fails to account for relationships between web services. In this paper, we propose an algorithm which retrieves closely related web services. The proposed algorithm is based on singular value decomposition (SVD) in linear algebra, which reveals semantic relationships among web services. The preliminary evaluation shows the effectiveness and feasibility of the algorithm.

miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data

BackgroundSmall RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using miRDeep’s probabilistic model of miRNA biogenesis, but it depends on several third party tools and lacks a user-friendly interface. The objective of our miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction.ResultWe have developed a user-friendly plant miRNA prediction tool called miRPlant. We show using 16 plant miRNA datasets from four different plant species that miRPlant has at least a 10% improvement in accuracy compared to miRDeep-P, which is the most popular plant miRNA prediction tool. Furthermore, miRPlant uses a Graphical User Interface for data input and output, and identified miRNA are shown with all RNAseq reads in a hairpin diagram.ConclusionsWe have developed miRPlant which extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. miRPlant is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs. This feature will enable biologists to visualize novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. Moreover, miRPlant can be easily used by biologists with limited bioinformatics skills.miRPlant and its manual are freely available at http://www.australianprostatecentre.org/research/software/mirplant or http://sourceforge.net/projects/mirplant/.

J-Circos: an interactive Circos plotter

SUMMARY Circos plots are graphical outputs that display three dimensional chromosomal interactions and fusion transcripts. However, the Circos plot tool is not an interactive visualization tool, but rather a figure generator. For example, it does not enable data to be added dynamically nor does it provide information for specific data points interactively. Recently, an R-based Circos tool (RCircos) has been developed to integrate Circos to R, but similarly, Rcircos can only be used to generate plots. Thus, we have developed a Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable, it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into J-Circos using flat data formats, as well as from the Graphical user interface (GUI). J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data. AVAILABILITY AND IMPLEMENTATION J-circos and its manual are freely available at http://www.australianprostatecentre.org/research/software/jcircos CONTACT j.an@qut.edu.au SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Delivering Categorized News Items Using RSS Feeds and Web Services

In the past decade the massive growth of the Internet brought huge changes in the way humans live their daily life; however, the biggest concern with rapid growth of digital information is how to efficiently manage and filter unwanted data. In this paper, we propose a method for managing RSS feeds from various news websites. A Web service was developed to provide filtered news items extracted from RSS feeds and these were categorized based on classical text categorization algorithms. A client application consuming this Web service retrieves and displays such filtered information. A prototype was implemented using Rapidminer 4.3 as a data mining tool and SVM as a classification algorithm. Experimental results suggest that the proposed method is effective and saves a significant amount of user processing time.

Spherical Harmonics Descriptor for 2D-Image Retrieval

In this paper, spherical harmonics are proposed as shape descriptors for 2D images. We introduce the concept of connectivity; 2D images are decomposed using connectivity, which is followed by 3D model construction. Spherical harmonics are obtained for 3D models and used as descriptors for the underlying 2D shapes. Difference between two images is computed as the Euclidean distance between their spherical harmonics descriptors. Experiments are performed to test the effectiveness of spherical harmonics for retrieval of 2D images. Item S8 within the MPEG-7 still images content set is used for performing experiments; this dataset consists of 3621 still images. Experimental results show that the proposed descriptors for 2D images are effective

Spherical harmonics and distance transform for image representation and retrieval

In this paper, we have proposed a method for 2D image retrieval based on object shapes. The method relies on transforming the 2D images into 3D space based on distance transform. Spherical harmonics are obtained for the 3D data and used as descriptors for the underlying 2D images. The proposed method is compared against two existing methods which use spherical harmonics for shape based retrieval of images. MPEG-7 Still Images Content Set is used for performing experiments; this dataset consists of 3621 still images. Experimental results show that the performance of the proposed descriptors is significantly better than other methods in the same category.

A Composite Descriptor for Shape Retrieval

In this paper, a composite descriptor for shape retrieval has been proposed. The proposed descriptor is obtained from generic fourier descriptors (GFD) for the shape region and the shape contour. A composite descriptor derived from GFD of the shape region and the shape contour is used for indexing and retrieval of shapes. Difference between two images is computed as the Euclidean distance between their composite descriptors. Experiments are performed to test the effectiveness of the proposed descriptor for retrieval of 2d images. Sets of composite descriptors, obtained by assigning different weights to the region component and the contour component, are also evaluated. Item S8 within the MPEG-7 still images content set is used for performing experiments; this dataset consists of 3621 still images. Experimental results show that the proposed descriptor is effective.

Spectral shape descriptor using spherical harmonics

In this paper, we propose a spectral descriptor for shapes of objects. The method relies on transforming the 2D objects into 3D space; distance transform and scale space theory is used to transform objects into 3D space. Spherical harmonics of the voxel grid are used to obtain shape descriptors. The proposed methods are compared against two existing methods which use spherical harmonics for shape based retrieval of images. Comparison is done based on ranking of images which is articulated in recall-precision curves. MPEG-7 Still Images Content Set is used for performing experiments. Experimental results show that the performance of the proposed descriptor is significantly better than other methods in the same category.

Indexing 2D nonoccluded shapes for similarity retrieval

Segmented object shape is an important visual feature and one of the content based image retrieval techniques is the shape based technique which allows users to ask or objects similar in shape to a query object. We describe a method for shape representation and similarity measure which we call the grid based method and evaluate its performance by comparing it with two popular methods, namely, the Fourier descriptors method and the moment invariants method. The comparative study is done by performing the same queries on the same database for all the methods. We also test the methods for robustness to noise by performing the queries on the database of noisy shapes. Experimental results show that the method proposed by us performs favorably compared with the other two methods.