Analysis of Three-Dimensional Protein Images

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains labor intensive and relies on an expert's ability to derive and evaluate a protein scene model. In this paper, the problem of protein structure determination is formulated as an exercise in scene analysis. A computational methodology is presented in which a 3D image of a protein is segmented into a graph of critical points. Bayesian and certainty factor approaches are described and used to analyze critical point graphs and identify meaningful substructures, such as alpha-helices and beta-sheets. Results of applying the methodologies to protein images at low and medium resolution are reported. The research is related to approaches to representation, segmentation and classification in vision, as well as to top-down approaches to protein structure prediction.Comment: See http://www.jair.org/ for any accompanying file

3D Reconstruction of Indoor Corridor Models Using Single Imagery and Video Sequences

In recent years, 3D indoor modeling has gained more attention due to its role in decision-making process of maintaining the status and managing the security of building indoor spaces. In this thesis, the problem of continuous indoor corridor space modeling has been tackled through two approaches. The first approach develops a modeling method based on middle-level perceptual organization. The second approach develops a visual Simultaneous Localisation and Mapping (SLAM) system with model-based loop closure. In the first approach, the image space was searched for a corridor layout that can be converted into a geometrically accurate 3D model. Manhattan rule assumption was adopted, and indoor corridor layout hypotheses were generated through a random rule-based intersection of image physical line segments and virtual rays of orthogonal vanishing points. Volumetric reasoning, correspondences to physical edges, orientation map and geometric context of an image are all considered for scoring layout hypotheses. This approach provides physically plausible solutions while facing objects or occlusions in a corridor scene. In the second approach, Layout SLAM is introduced. Layout SLAM performs camera localization while maps layout corners and normal point features in 3D space. Here, a new feature matching cost function was proposed considering both local and global context information. In addition, a rotation compensation variable makes Layout SLAM robust against cameras orientation errors accumulations. Moreover, layout model matching of keyframes insures accurate loop closures that prevent miss-association of newly visited landmarks to previously visited scene parts. The comparison of generated single image-based 3D models to ground truth models showed that average ratio differences in widths, heights and lengths were 1.8%, 3.7% and 19.2% respectively. Moreover, Layout SLAM performed with the maximum absolute trajectory error of 2.4m in position and 8.2 degree in orientation for approximately 318m path on RAWSEEDS data set. Loop closing was strongly performed for Layout SLAM and provided 3D indoor corridor layouts with less than 1.05m displacement errors in length and less than 20cm in width and height for approximately 315m path on York University data set. The proposed methods can successfully generate 3D indoor corridor models compared to their major counterpart

Computation of protein geometry and its applications: Packing and function prediction

This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulation, and the alpha shapes. These geometric constructs enable fast and analytical computaton of shapes of biomoleculres (including features such as voids and pockets) and metric properties (such as area and volume). The algorithms of Delaunay triangulation, computation of voids and pockets, as well volume/area computation are also described. In addition, applications in packing analysis of protein structures and protein function prediction are also discussed.Comment: 32 pages, 9 figure

Search and Result Presentation in Scientific Workflow Repositories

We study the problem of searching a repository of complex hierarchical workflows whose component modules, both composite and atomic, have been annotated with keywords. Since keyword search does not use the graph structure of a workflow, we develop a model of workflows using context-free bag grammars. We then give efficient polynomial-time algorithms that, given a workflow and a keyword query, determine whether some execution of the workflow matches the query. Based on these algorithms we develop a search and ranking solution that efficiently retrieves the top-k grammars from a repository. Finally, we propose a novel result presentation method for grammars matching a keyword query, based on representative parse-trees. The effectiveness of our approach is validated through an extensive experimental evaluation