SimSearch: A new variant of dynamic programming based on distance series for optimal and near-optimal similarity discovery in biological sequences

http://www.informatik.uni-trier.de/%7Eley/db/conf/iwpacbb/iwpacbb2008.htmlIn this paper, we propose SimSearch, an algorithm implementing a new variant of dynamic programming based on distance series for optimal and near-optimal similarity discovery in biological sequences. The initial phase of SimSearch is devoted to fulfil the binary similarity matrices by signalling the distances between occurrences of the same symbol. The scoring scheme is further applied, when analysed the maximal extension of the pattern. Employing bit parallelism to analyse the global similarity matrix’s upper triangle, the new methodology searches the sequence(s) for all the exact and approximate patterns in regular or reverse order. The algorithm accepts parameterization to work with greater seeds for near-optimal results. Performance tests show significant efficiency improvement over traditional optimal methods based on dynamic programming. Comparing the new algorithm’s efficiency against heuristic based methods, equalizing the required sensitivity, the proposed algorithm remains acceptable.This work has been partially supported by PRODEP

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

Image Processing Applications in Real Life: 2D Fragmented Image and Document Reassembly and Frequency Division Multiplexed Imaging

In this era of modern technology, image processing is one the most studied disciplines of signal processing and its applications can be found in every aspect of our daily life. In this work three main applications for image processing has been studied. In chapter 1, frequency division multiplexed imaging (FDMI), a novel idea in the field of computational photography, has been introduced. Using FDMI, multiple images are captured simultaneously in a single shot and can later be extracted from the multiplexed image. This is achieved by spatially modulating the images so that they are placed at different locations in the Fourier domain. Finally, a Texas Instruments digital micromirror device (DMD) based implementation of FDMI is presented and results are shown. Chapter 2 discusses the problem of image reassembly which is to restore an image back to its original form from its pieces after it has been fragmented due to different destructive reasons. We propose an efficient algorithm for 2D image fragment reassembly problem based on solving a variation of Longest Common Subsequence (LCS) problem. Our processing pipeline has three steps. First, the boundary of each fragment is extracted automatically; second, a novel boundary matching is performed by solving LCS to identify the best possible adjacency relationship among image fragment pairs; finally, a multi-piece global alignment is used to filter out incorrect pairwise matches and compose the final image. We perform experiments on complicated image fragment datasets and compare our results with existing methods to show the improved efficiency and robustness of our method. The problem of reassembling a hand-torn or machine-shredded document back to its original form is another useful version of the image reassembly problem. Reassembling a shredded document is different from reassembling an ordinary image because the geometric shape of fragments do not carry a lot of valuable information if the document has been machine-shredded rather than hand-torn. On the other hand, matching words and context can be used as an additional tool to help improve the task of reassembly. In the final chapter, document reassembly problem has been addressed through solving a graph optimization problem

Shape classification through structured learning of matching measures

Many traditional methods for shape classification involve establishing point correspondences between shapes to produce matching scores, which are in turn used as similarity measures for classification. Learning techniques have been applied only in the second stage of this process, after the matching scores have been obtained. In this paper, instead of simply taking for granted the scores obtained by matching and then learning a classifier, we learn the matching scores themselves so as to produce shape similarity scores that minimize the classification loss. The solution is based on a max-margin formulation in the structured prediction setting. Experiments in shape databases reveal that such an integrated learning algorithm substantially improves on existing methods

Exploratory search through large video corpora

Activity retrieval is a growing field in electrical engineering that specializes in the search and retrieval of relevant activities and events in video corpora. With the affordability and popularity of cameras for government, personal and retail use, the quantity of available video data is rapidly outscaling our ability to reason over it. Towards the end of empowering users to navigate and interact with the contents of these video corpora, we propose a framework for exploratory search that emphasizes activity structure and search space reduction over complex feature representations. Exploratory search is a user driven process wherein a person provides a system with a query describing the activity, event, or object he is interested in finding. Typically, this description takes the implicit form of one or more exemplar videos, but it can also involve an explicit description. The system returns candidate matches, followed by query refinement and iteration. System performance is judged by the run-time of the system and the precision/recall curve of of the query matches returned. Scaling is one of the primary challenges in video search. From vast web-video archives like youtube (1 billion videos and counting) to the 30 million active surveillance cameras shooting an estimated 4 billion hours of footage every week in the United States, trying to find a set of matches can be like looking for a needle in a haystack. Our goal is to create an efficient archival representation of video corpora that can be calculated in real-time as video streams in, and then enables a user to quickly get a set of results that match. First, we design a system for rapidly identifying simple queries in large-scale video corpora. Instead of focusing on feature design, our system focuses on the spatiotemporal relationships between those features as a means of disambiguating an activity of interest from background. We define a semantic feature vocabulary of concepts that are both readily extracted from video and easily understood by an operator. As data streams in, features are hashed to an inverted index and retrieved in constant time after the system is presented with a user's query. We take a zero-shot approach to exploratory search: the user manually assembles vocabulary elements like color, speed, size and type into a graph. Given that information, we perform an initial downsampling of the archived data, and design a novel dynamic programming approach based on genome-sequencing to search for similar patterns. Experimental results indicate that this approach outperforms other methods for detecting activities in surveillance video datasets. Second, we address the problem of representing complex activities that take place over long spans of space and time. Subgraph and graph matching methods have seen limited use in exploratory search because both problems are provably NP-hard. In this work, we render these problems computationally tractable by identifying the maximally discriminative spanning tree (MDST), and using dynamic programming to optimally reduce the archive data based on a custom algorithm for tree-matching in attributed relational graphs. We demonstrate the efficacy of this approach on popular surveillance video datasets in several modalities. Finally, we design an approach for successive search space reduction in subgraph matching problems. Given a query graph and archival data, our algorithm iteratively selects spanning trees from the query graph that optimize the expected search space reduction at each step until the archive converges. We use this approach to efficiently reason over video surveillance datasets, simulated data, as well as large graphs of protein data

A Framework for the Design and Analysis of High-Performance Applications on FPGAs using Partial Reconfiguration

The field-programmable gate array (FPGA) is a dynamically reconfigurable digital logic chip used to implement custom hardware. The large densities of modern FPGAs and the capability of the on-thely reconfiguration has made the FPGA a viable alternative to fixed logic hardware chips such as the ASIC. In high-performance computing, FPGAs are used as co-processors to speed up computationally intensive processes or as autonomous systems that realize a complete hardware application. However, due to the limited capacity of FPGA logic resources, denser FPGAs must be purchased if more logic resources are required to realize all the functions of a complex application. Alternatively, partial reconfiguration (PR) can be used to swap, on demand, idle components of the application with active components. This research uses PR to swap components to improve the performance of the application given the limited logic resources available with smaller but economical FPGAs. The swap is called ”resource sharing PR”. In a pipelined design of multiple hardware modules (pipeline stages), resource sharing PR is a technique that uses PR to improve the performance of pipeline bottlenecks. This is done by reconfiguring other pipeline stages, typically those that are idle waiting for data from a bottleneck, into an additional parallel bottleneck module. The target pipeline of this research is a two-stage “slow-toast” pipeline where the flow of data traversing the pipeline transitions from a relatively slow, bottleneck stage to a fast stage. A two stage pipeline that combines FPGA-based hardware implementations of well-known Bioinformatics search algorithms, the X! Tandem algorithm and the Smith-Waterman algorithm, is implemented for this research; the implemented pipeline demonstrates that characteristics of these algorithm. The experimental results show that, in a database of unknown peptide spectra, when matching spectra with 388 peaks or greater, performing resource sharing PR to instantiate a parallel X! Tandem module is worth the cost for PR. In addition, from timings gathered during experiments, a general formula was derived for determining the value of performing PR upon a fast module