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

Partial shape matching using CCP map and weighted graph transformation matching

La détection de la similarité ou de la différence entre les images et leur mise en correspondance sont des problèmes fondamentaux dans le traitement de l'image. Pour résoudre ces problèmes, on utilise, dans la littérature, différents algorithmes d'appariement. Malgré leur nouveauté, ces algorithmes sont pour la plupart inefficaces et ne peuvent pas fonctionner correctement dans les situations d’images bruitées. Dans ce mémoire, nous résolvons la plupart des problèmes de ces méthodes en utilisant un algorithme fiable pour segmenter la carte des contours image, appelée carte des CCPs, et une nouvelle méthode d'appariement. Dans notre algorithme, nous utilisons un descripteur local qui est rapide à calculer, est invariant aux transformations affines et est fiable pour des objets non rigides et des situations d’occultation. Après avoir trouvé le meilleur appariement pour chaque contour, nous devons vérifier si ces derniers sont correctement appariés. Pour ce faire, nous utilisons l'approche « Weighted Graph Transformation Matching » (WGTM), qui est capable d'éliminer les appariements aberrants en fonction de leur proximité et de leurs relations géométriques. WGTM fonctionne correctement pour les objets à la fois rigides et non rigides et est robuste aux distorsions importantes. Pour évaluer notre méthode, le jeu de données ETHZ comportant cinq classes différentes d'objets (bouteilles, cygnes, tasses, girafes, logos Apple) est utilisé. Enfin, notre méthode est comparée à plusieurs méthodes célèbres proposées par d'autres chercheurs dans la littérature. Bien que notre méthode donne un résultat comparable à celui des méthodes de référence en termes du rappel et de la précision de localisation des frontières, elle améliore significativement la précision moyenne pour toutes les catégories du jeu de données ETHZ.Matching and detecting similarity or dissimilarity between images is a fundamental problem in image processing. Different matching algorithms are used in literature to solve this fundamental problem. Despite their novelty, these algorithms are mostly inefficient and cannot perform properly in noisy situations. In this thesis, we solve most of the problems of previous methods by using a reliable algorithm for segmenting image contour map, called CCP Map, and a new matching method. In our algorithm, we use a local shape descriptor that is very fast, invariant to affine transform, and robust for dealing with non-rigid objects and occlusion. After finding the best match for the contours, we need to verify if they are correctly matched. For this matter, we use the Weighted Graph Transformation Matching (WGTM) approach, which is capable of removing outliers based on their adjacency and geometrical relationships. WGTM works properly for both rigid and non-rigid objects and is robust to high order distortions. For evaluating our method, the ETHZ dataset including five diverse classes of objects (bottles, swans, mugs, giraffes, apple-logos) is used. Finally, our method is compared to several famous methods proposed by other researchers in the literature. While our method shows a comparable result to other benchmarks in terms of recall and the precision of boundary localization, it significantly improves the average precision for all of the categories in the ETHZ dataset

Shape-based invariant features extraction for object recognition

International audienceThe emergence of new technologies enables generating large quantity of digital information including images; this leads to an increasing number of generated digital images. Therefore it appears a necessity for automatic systems for image retrieval. These systems consist of techniques used for query specification and re-trieval of images from an image collection. The most frequent and the most com-mon means for image retrieval is the indexing using textual keywords. But for some special application domains and face to the huge quantity of images, key-words are no more sufficient or unpractical. Moreover, images are rich in content; so in order to overcome these mentioned difficulties, some approaches are pro-posed based on visual features derived directly from the content of the image: these are the content-based image retrieval (CBIR) approaches. They allow users to search the desired image by specifying image queries: a query can be an exam-ple, a sketch or visual features (e.g., colour, texture and shape). Once the features have been defined and extracted, the retrieval becomes a task of measuring simi-larity between image features. An important property of these features is to be in-variant under various deformations that the observed image could undergo. In this chapter, we will present a number of existing methods for CBIR applica-tions. We will also describe some measures that are usually used for similarity measurement. At the end, and as an application example, we present a specific ap-proach, that we are developing, to illustrate the topic by providing experimental results

Shape matching by curve modelling and alignment

Automatic information retrieval in the eld of shape recognition has been widely covered by many research elds. Various techniques have been developed using different approaches such as intensity-based, modelbased and shape-based methods. Whichever is the way to represent the objects in images, a recognition method should be robust in the presence of scale change, translation and rotation. In this paper we present a new recognition method based on a curve alignment technique, for planar image contours. The method consists of various phases including extracting outlines of images, detecting signicant points and aligning curves. The dominant points can be manually or automatically detected. The matching phase uses the idea of calculating the overlapping indices between shapes as similarity measures. To evaluate the effectiveness of the algorithm, two databases of 216 and 99 images have been used. A performance analysis and comparison is provided by precision-recall curves

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

Bayesian data assimilation in shape registration

In this paper we apply a Bayesian framework to the problem of geodesic curve matching. Given a template curve, the geodesic equations provide a mapping from initial conditions\ud for the conjugate momentum onto topologically equivalent shapes. Here, we aim to recover the well defined posterior distribution on the initial momentum which gives rise to observed points on the target curve; this is achieved by explicitly including a reparameterisation in the formulation. Appropriate priors are chosen for the functions which together determine this field and the positions of the observation points, the initial momentum p0 and the reparameterisation vector field v, informed by regularity results about the forward model. Having done this, we illustrate how Maximum Likelihood Estimators (MLEs) can be used to find regions of high posterior density, but also how we can apply recently developed MCMC methods on function spaces to characterise the whole of the posterior density. These illustrative examples also include scenarios where the posterior distribution is multimodal and irregular, leading us to the conclusion that knowledge of a state of global maximal posterior density does not always give us the whole picture, and full posterior sampling can give better quantification of likely states and the overall uncertainty inherent in the problem

Shape localization, quantification and correspondence using Region Matching Algorithm

We propose a method for local, region-based matching of planar shapes, especially as those shapes that change over time. This is a problem fundamental to medical imaging, specifically the comparison over time of mammograms. The method is based on the non-emergence and non-enhancement of maxima, as well as the causality principle of integral invariant scale space. The core idea of our Region Matching Algorithm (RMA) is to divide a shape into a number of “salient” regions and then to compare all such regions for local similarity in order to quantitatively identify new growths or partial/complete occlusions. The algorithm has several advantages over commonly used methods for shape comparison of segmented regions. First, it provides improved key-point alignment for optimal shape correspondence. Second, it identifies localized changes such as new growths as well as complete/partial occlusion in corresponding regions by dividing the segmented region into sub-regions based upon the extrema that persist over a sufficient range of scales. Third, the algorithm does not depend upon the spatial locations of mammographic features and eliminates the need for registration to identify salient changes over time. Finally, the algorithm is fast to compute and requires no human intervention. We apply the method to temporal pairs of mammograms in order to detect potentially important differences between them