View subspaces for indexing and retrieval of 3D models

View-based indexing schemes for 3D object retrieval are gaining popularity since they provide good retrieval results. These schemes are coherent with the theory that humans recognize objects based on their 2D appearances. The viewbased techniques also allow users to search with various queries such as binary images, range images and even 2D sketches. The previous view-based techniques use classical 2D shape descriptors such as Fourier invariants, Zernike moments, Scale Invariant Feature Transform-based local features and 2D Digital Fourier Transform coefficients. These methods describe each object independent of others. In this work, we explore data driven subspace models, such as Principal Component Analysis, Independent Component Analysis and Nonnegative Matrix Factorization to describe the shape information of the views. We treat the depth images obtained from various points of the view sphere as 2D intensity images and train a subspace to extract the inherent structure of the views within a database. We also show the benefit of categorizing shapes according to their eigenvalue spread. Both the shape categorization and data-driven feature set conjectures are tested on the PSB database and compared with the competitor view-based 3D shape retrieval algorithmsComment: Three-Dimensional Image Processing (3DIP) and Applications (Proceedings Volume) Proceedings of SPIE Volume: 7526 Editor(s): Atilla M. Baskurt ISBN: 9780819479198 Date: 2 February 201

Spherical harmonics coeffcients for ligand-based virtual screening of cyclooxygenase inhibitors

Background: Molecular descriptors are essential for many applications in computational chemistry, such as ligand-based similarity searching. Spherical harmonics have previously been suggested as comprehensive descriptors of molecular structure and properties. We investigate a spherical harmonics descriptor for shape-based virtual screening. Methodology/Principal Findings: We introduce and validate a partially rotation-invariant three-dimensional molecular shape descriptor based on the norm of spherical harmonics expansion coefficients. Using this molecular representation, we parameterize molecular surfaces, i.e., isosurfaces of spatial molecular property distributions. We validate the shape descriptor in a comprehensive retrospective virtual screening experiment. In a prospective study, we virtually screen a large compound library for cyclooxygenase inhibitors, using a self-organizing map as a pre-filter and the shape descriptor for candidate prioritization. Conclusions/Significance: 12 compounds were tested in vitro for direct enzyme inhibition and in a whole blood assay. Active compounds containing a triazole scaffold were identified as direct cyclooxygenase-1 inhibitors. This outcome corroborates the usefulness of spherical harmonics for representation of molecular shape in virtual screening of large compound collections. The combination of pharmacophore and shape-based filtering of screening candidates proved to be a straightforward approach to finding novel bioactive chemotypes with minimal experimental effort

New Method for 3D Shape Retrieval

The recent technological progress in acquisition, modeling and processing of 3D data leads to the proliferation of a large number of 3D objects databases. Consequently, the techniques used for content based 3D retrieval has become necessary. In this paper, we introduce a new method for 3D objects recognition and retrieval by using a set of binary images CLI (Characteristic level images). We propose a 3D indexing and search approach based on the similarity between characteristic level images using Hu moments for it indexing. To measure the similarity between 3D objects we compute the Hausdorff distance between a vectors descriptor. The performance of this new approach is evaluated at set of 3D object of well known database, is NTU (National Taiwan University) database.Comment: 10 pages, 5 figures, publication pape

Exploring the potential of 3D Zernike descriptors and SVM for protein\u2013protein interface prediction

Abstract Background The correct determination of protein–protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been developed, but the interface prediction problem is still not fully understood. Experimental evidence suggests that the location of binding sites is imprinted in the protein structure, but there are major differences among the interfaces of the various protein types: the characterising properties can vary a lot depending on the interaction type and function. The selection of an optimal set of features characterising the protein interface and the development of an effective method to represent and capture the complex protein recognition patterns are of paramount importance for this task. Results In this work we investigate the potential of a novel local surface descriptor based on 3D Zernike moments for the interface prediction task. Descriptors invariant to roto-translations are extracted from circular patches of the protein surface enriched with physico-chemical properties from the HQI8 amino acid index set, and are used as samples for a binary classification problem. Support Vector Machines are used as a classifier to distinguish interface local surface patches from non-interface ones. The proposed method was validated on 16 classes of proteins extracted from the Protein–Protein Docking Benchmark 5.0 and compared to other state-of-the-art protein interface predictors (SPPIDER, PrISE and NPS-HomPPI). Conclusions The 3D Zernike descriptors are able to capture the similarity among patterns of physico-chemical and biochemical properties mapped on the protein surface arising from the various spatial arrangements of the underlying residues, and their usage can be easily extended to other sets of amino acid properties. The results suggest that the choice of a proper set of features characterising the protein interface is crucial for the interface prediction task, and that optimality strongly depends on the class of proteins whose interface we want to characterise. We postulate that different protein classes should be treated separately and that it is necessary to identify an optimal set of features for each protein class

Towards an All-Purpose Content-Based Multimedia Information Retrieval System

The growth of multimedia collections - in terms of size, heterogeneity, and variety of media types - necessitates systems that are able to conjointly deal with several forms of media, especially when it comes to searching for particular objects. However, existing retrieval systems are organized in silos and treat different media types separately. As a consequence, retrieval across media types is either not supported at all or subject to major limitations. In this paper, we present vitrivr, a content-based multimedia information retrieval stack. As opposed to the keyword search approach implemented by most media management systems, vitrivr makes direct use of the object's content to facilitate different types of similarity search, such as Query-by-Example or Query-by-Sketch, for and, most importantly, across different media types - namely, images, audio, videos, and 3D models. Furthermore, we introduce a new web-based user interface that enables easy-to-use, multimodal retrieval from and browsing in mixed media collections. The effectiveness of vitrivr is shown on the basis of a user study that involves different query and media types. To the best of our knowledge, the full vitrivr stack is unique in that it is the first multimedia retrieval system that seamlessly integrates support for four different types of media. As such, it paves the way towards an all-purpose, content-based multimedia information retrieval system