From Keyword Search to Exploration: How Result Visualization Aids Discovery on the Web

A key to the Web's success is the power of search. The elegant way in which search results are returned is usually remarkably effective. However, for exploratory search in which users need to learn, discover, and understand novel or complex topics, there is substantial room for improvement. Human computer interaction researchers and web browser designers have developed novel strategies to improve Web search by enabling users to conveniently visualize, manipulate, and organize their Web search results. This monograph offers fresh ways to think about search-related cognitive processes and describes innovative design approaches to browsers and related tools. For instance, while key word search presents users with results for specific information (e.g., what is the capitol of Peru), other methods may let users see and explore the contexts of their requests for information (related or previous work, conflicting information), or the properties that associate groups of information assets (group legal decisions by lead attorney). We also consider the both traditional and novel ways in which these strategies have been evaluated. From our review of cognitive processes, browser design, and evaluations, we reflect on the future opportunities and new paradigms for exploring and interacting with Web search results

Graph indexing and retrieval based on graph prototypes

[ANGLÈS] Taking a query from a high number of data stored into a database, as fast as possible, is a recurrent problem in the field of computer sciences practically since its origins. At the existence of this problem, it’s necessary to add, moreover, the fact that actually databases contains data types of more diverse and unexpected character possible. Now we are not talking about originating databases which only contained sets of numbers or characters strings. (...) All that I want to make into the present work and I think that was achieved as far as possible, has been to develop and to present a methodology to carry out this process. The Metric Trees of prototypes are based on a well-known strategy, which is based on grouping the data stored in database at the smartest possible way. But also we has added the concept of a graph prototype. A structure that contains information of a set of instances represented by graphs, used until now for classification and recognition. In this thesis we have used graphs as representatives of elements that have to be queried in databases. Note that graphs have the capacity to represent complex objects, for this reason the number of graph databases is increasing. Due to in the literature appears different ways to build a prototype, the work presented here shows a comparative study between the main methods. Combining these two concepts, the Metric Tree and the graph prototype, we propose the construction of metric trees where the graph prototypes are routing nodes to help to decide the way to explore when we make a search in the tree. We have used Metric Trees to make classification and to find all instances that are lower than a maximum distance. (...)[CATALÀ] El trobar-nos davant una gran quantitat de dades i tenir que fer cerques d’aquestes el més ràpid possible és un problema recurrent en el camp de les ciències de la computació pràcticament des dels seus orígens. A l'existència d'aquest problema, se li ha d’afegir, a més a més, el fet de que actualment les bases de dades emmagatzemen tipus de dades de la naturalesa més diversa i molts cops inesperada possible. Ja no parlem de les bases de dades originaries que únicament contenien números o cadenes caràcters. (...) El que he volgut en aquest treball i penso que en la mesura del que era possible s'ha aconseguit, és desenvolupar i presentar una metodologia per portar a terme aquest procés. Els Metric Trees de prototips, que es basen en la ja coneguda estratègia d'agrupar les dades que anem guardant a una base de dades de la forma més intel·ligent possible per no haver d’explorar totes les instàncies que tenim quan volem fer una cerca, però a més a més s'ha afegit el concepte de prototip. Una estructura, que agrupa la informació d'un conjunt d'instàncies, utilitzada fins ara per a fer classificació i reconeixement. Conjugant aquests dos conceptes, el de Metric Tree i el de prototip, plantejem la construcció d'arbres de cerca on els prototips siguin els nodes intermedis, que ens ajudin a decidir quin camí explorar quan volem fer una cerca sobre l'arbre. I utilitzant, aquests tant per a fer classificació com per a buscar totes les instàncies que estiguin una distància més petita d’una distància máxima. Tot això tenint present, que les dades amb que treballem són grafs, és a dir que la metodologia presentada, té la versatilitat de poder-se aplicar, a qualsevol tipus d'informació que es pugui representar d'aquesta manera. (...

A graph-based approach for the retrieval of multi-modality medical images

Medical imaging has revolutionised modern medicine and is now an integral aspect of diagnosis and patient monitoring. The development of new imaging devices for a wide variety of clinical cases has spurred an increase in the data volume acquired in hospitals. These large data collections offer opportunities for search-based applications in evidence-based diagnosis, education, and biomedical research. However, conventional search methods that operate upon manual annotations are not feasible for this data volume. Content-based image retrieval (CBIR) is an image search technique that uses automatically derived visual features as search criteria and has demonstrable clinical benefits. However, very few studies have investigated the CBIR of multi-modality medical images, which are making a monumental impact in healthcare, e.g., combined positron emission tomography and computed tomography (PET-CT) for cancer diagnosis. In this thesis, we propose a new graph-based method for the CBIR of multi-modality medical images. We derive a graph representation that emphasises the spatial relationships between modalities by structurally constraining the graph based on image features, e.g., spatial proximity of tumours and organs. We also introduce a graph similarity calculation algorithm that prioritises the relationships between tumours and related organs. To enable effective human interpretation of retrieved multi-modality images, we also present a user interface that displays graph abstractions alongside complex multi-modality images. Our results demonstrated that our method achieved a high precision when retrieving images on the basis of tumour location within organs. The evaluation of our proposed UI design by user surveys revealed that it improved the ability of users to interpret and understand the similarity between retrieved PET-CT images. The work in this thesis advances the state-of-the-art by enabling a novel approach for the retrieval of multi-modality medical images

Graph-Based Approaches to Protein StructureComparison - From Local to Global Similarity

The comparative analysis of protein structure data is a central aspect of structural bioinformatics. Drawing upon structural information allows the inference of function for unknown proteins even in cases where no apparent homology can be found on the sequence level. Regarding the function of an enzyme, the overall fold topology might less important than the specific structural conformation of the catalytic site or the surface region of a protein, where the interaction with other molecules, such as binding partners, substrates and ligands occurs. Thus, a comparison of these regions is especially interesting for functional inference, since structural constraints imposed by the demands of the catalyzed biochemical function make them more likely to exhibit structural similarity. Moreover, the comparative analysis of protein binding sites is of special interest in pharmaceutical chemistry, in order to predict cross-reactivities and gain a deeper understanding of the catalysis mechanism. From an algorithmic point of view, the comparison of structured data, or, more generally, complex objects, can be attempted based on different methodological principles. Global methods aim at comparing structures as a whole, while local methods transfer the problem to multiple comparisons of local substructures. In the context of protein structure analysis, it is not a priori clear, which strategy is more suitable. In this thesis, several conceptually different algorithmic approaches have been developed, based on local, global and semi-global strategies, for the task of comparing protein structure data, more specifically protein binding pockets. The use of graphs for the modeling of protein structure data has a long standing tradition in structural bioinformatics. Recently, graphs have been used to model the geometric constraints of protein binding sites. The algorithms developed in this thesis are based on this modeling concept, hence, from a computer scientist's point of view, they can also be regarded as global, local and semi-global approaches to graph comparison. The developed algorithms were mainly designed on the premise to allow for a more approximate comparison of protein binding sites, in order to account for the molecular flexibility of the protein structures. A main motivation was to allow for the detection of more remote similarities, which are not apparent by using more rigid methods. Subsequently, the developed approaches were applied to different problems typically encountered in the field of structural bioinformatics in order to assess and compare their performance and suitability for different problems. Each of the approaches developed during this work was capable of improving upon the performance of existing methods in the field. Another major aspect in the experiments was the question, which methodological concept, local, global or a combination of both, offers the most benefits for the specific task of protein binding site comparison, a question that is addressed throughout this thesis

A Survey on Array Storage, Query Languages, and Systems

Since scientific investigation is one of the most important providers of massive amounts of ordered data, there is a renewed interest in array data processing in the context of Big Data. To the best of our knowledge, a unified resource that summarizes and analyzes array processing research over its long existence is currently missing. In this survey, we provide a guide for past, present, and future research in array processing. The survey is organized along three main topics. Array storage discusses all the aspects related to array partitioning into chunks. The identification of a reduced set of array operators to form the foundation for an array query language is analyzed across multiple such proposals. Lastly, we survey real systems for array processing. The result is a thorough survey on array data storage and processing that should be consulted by anyone interested in this research topic, independent of experience level. The survey is not complete though. We greatly appreciate pointers towards any work we might have forgotten to mention.Comment: 44 page

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