Enabling effective tree exploration using visual cues

© 2018 Elsevier Ltd This article presents a new interactive visualization for exploring large hierarchical structures by providing visual cues on a node link tree visualization. Our technique provides topological previews of hidden substructures with three types of visual cues including simple cues, tree cues and treemap cues. We demonstrate the visual cues on Degree-of-Interest Tree (DOITree) due to its familiar mapping, its capability of providing multiple focused nodes, and its dynamic rescaling of substructures to fit the available space. We conducted a usability study with 28 participants that measured completion time and accuracy across five different topology search tasks. The simple cues had the fastest completion time across three of the node identification tasks. The treemap cues had the highest rate of correct answers on four of the five tasks, although only reaching statistical significance for two of these. As predicted, user ratings demonstrated a preference for the easy to understand tree cues followed by the simple cue, despite this not consistently reflected in performance results

Exploiting Graphics Processing Units for Massively Parallel Multi-Dimensional Indexing

Department of Computer EngineeringScientific applications process truly large amounts of multi-dimensional datasets. To efficiently navigate such datasets, various multi-dimensional indexing structures, such as the R-tree, have been extensively studied for the past couple of decades. Since the GPU has emerged as a new cost-effective performance accelerator, now it is common to leverage the massive parallelism of the GPU in various applications such as medical image processing, computational chemistry, and particle physics. However, hierarchical multi-dimensional indexing structures are inherently not well suited for parallel processing because their irregular memory access patterns make it difficult to exploit massive parallelism. Moreover, recursive tree traversal often fails due to the small run-time stack and cache memory in the GPU. First, we propose Massively Parallel Three-phase Scanning (MPTS) R-tree traversal algorithm to avoid the irregular memory access patterns and recursive tree traversal so that the GPU can access tree nodes in a sequential manner. The experimental study shows that MPTS R-tree traversal algorithm consistently outperforms traditional recursive R-Tree search algorithm for multi-dimensional range query processing. Next, we focus on reducing the query response time and extending n-ary multi-dimensional indexing structures - R-tree, so that a large number of GPU threads cooperate to process a single query in parallel. Because the number of submitted concurrent queries in scientific data analysis applications is relatively smaller than that of enterprise database systems and ray tracing in computer graphics. Hence, we propose a novel variant of R-trees Massively Parallel Hilbert R-Tree (MPHR-Tree), which is designed for a novel parallel tree traversal algorithm Massively Parallel Restart Scanning (MPRS). The MPRS algorithm traverses the MPHR-Tree in mostly contiguous memory access patterns without recursion, which offers more chances to optimize the parallel SIMD algorithm. Our extensive experimental results show that the MPRS algorithm outperforms the other stackless tree traversal algorithms, which are designed for efficient ray tracing in computer graphics community. Furthermore, we develop query co-processing scheme that makes use of both the CPU and GPU. In this approach, we store the internal and leaf nodes of upper tree in CPU host memory and GPU device memory, respectively. We let the CPU traverse internal nodes because the conditional branches in hierarchical tree structures often cause a serious warp divergence problem in the GPU. For leaf nodes, the GPU scans a large number of leaf nodes in parallel based on the selection ratio of a given range query. It is well known that the GPU is superior to the CPU for parallel scanning. The experimental results show that our proposed multi-dimensional range query co-processing scheme improves the query response time by up to 12x and query throughput by up to 4x compared to the state-of-the-art GPU tree traversal algorithm.ope

Space Partitioning Schemes and Algorithms for Generating Regular and Spiral Treemaps

Treemaps have been widely applied to the visualization of hierarchical data. A treemap takes a weighted tree and visualizes its leaves in a nested planar geometric shape, with sub-regions partitioned such that each sub-region has an area proportional to the weight of its associated leaf nodes. Efficiently generating visually appealing treemaps that also satisfy other quality criteria is an interesting problem that has been tackled from many directions. We present an optimization model and five new algorithms for this problem, including two divide and conquer approaches and three spiral treemap algorithms. Our optimization model is able to generate superior treemaps that could serve as a benchmark for comparing the quality of more computationally efficient algorithms. Our divide and conquer and spiral algorithms either improve the performance of their existing counterparts with respect to aspect ratio and stability or perform competitively. Our spiral algorithms also expand their applicability to a wider range of input scenarios. Four of these algorithms are computationally efficient as well with quasilinear running times and the last algorithm achieves a cubic running time. A full version of this paper with all appendices, data, and source codes is available at \anonymizeOSF{\OSFSupplementText}

A framework for the analysis and evaluation of enterprise models

Bibliography: leaves 264-288.The purpose of this study is the development and validation of a comprehensive framework for the analysis and evaluation of enterprise models. The study starts with an extensive literature review of modelling concepts and an overview of the various reference disciplines concerned with enterprise modelling. This overview is more extensive than usual in order to accommodate readers from different backgrounds. The proposed framework is based on the distinction between the syntactic, semantic and pragmatic model aspects and populated with evaluation criteria drawn from an extensive literature survey. In order to operationalize and empirically validate the framework, an exhaustive survey of enterprise models was conducted. From this survey, an XML database of more than twenty relatively large, publicly available enterprise models was constructed. A strong emphasis was placed on the interdisciplinary nature of this database and models were drawn from ontology research, linguistics, analysis patterns as well as the traditional fields of data modelling, data warehousing and enterprise systems. The resultant database forms the test bed for the detailed framework-based analysis and its public availability should constitute a useful contribution to the modelling research community. The bulk of the research is dedicated to implementing and validating specific analysis techniques to quantify the various model evaluation criteria of the framework. The aim for each of the analysis techniques is that it can, where possible, be automated and generalised to other modelling domains. The syntactic measures and analysis techniques originate largely from the disciplines of systems engineering, graph theory and computer science. Various metrics to measure model hierarchy, architecture and complexity are tested and discussed. It is found that many are not particularly useful or valid for enterprise models. Hence some new measures are proposed to assist with model visualization and an original "model signature" consisting of three key metrics is proposed.Perhaps the most significant contribution ofthe research lies in the development and validation of a significant number of semantic analysis techniques, drawing heavily on current developments in lexicography, linguistics and ontology research. Some novel and interesting techniques are proposed to measure, inter alia, domain coverage, model genericity, quality of documentation, perspicuity and model similarity. Especially model similarity is explored in depth by means of various similarity and clustering algorithms as well as ways to visualize the similarity between models. Finally, a number of pragmatic analyses techniques are applied to the models. These include face validity, degree of use, authority of model author, availability, cost, flexibility, adaptability, model currency, maturity and degree of support. This analysis relies mostly on the searching for and ranking of certain specific information details, often involving a degree of subjective interpretation, although more specific quantitative procedures are suggested for some of the criteria. To aid future researchers, a separate chapter lists some promising analysis techniques that were investigated but found to be problematic from methodological perspective. More interestingly, this chapter also presents a very strong conceptual case on how the proposed framework and the analysis techniques associated vrith its various criteria can be applied to many other information systems research areas. The case is presented on the grounds of the underlying isomorphism between the various research areas and illustrated by suggesting the application of the framework to evaluate web sites, algorithms, software applications, programming languages, system development methodologies and user interfaces

DISTRIBUTED MULTIDIMENSIONAL INDEXING FOR SCIENTIFIC DATA ANALYSIS APPLICATIONS

Scientific data analysis applications require large scale computing power to effectively service client queries and also require large storage repositories for datasets that are generated continually from sensors and simulations. These scientific datasets are growing in size every day, and are becoming truly enormous. The goal of this dissertation is to provide efficient multidimensional indexing techniques that aid in navigating distributed scientific datasets. In this dissertation, we show significant improvements in accessing distributed large scientific datasets. The first approach we took to improve access to subsets of large multidimensional scientific datasets, was data chunking. The contents of scientific data files typically are a collection of multidimensional arrays, along with the corresponding metadata. Data chunking groups data elements into small chunks of a fixed, but data-specific, size to take advantage of spatio-temporal locality since it is not efficient to index individual data elements of large scientific datasets. The second approach was the design of an efficient multidimensional index for scientific datasets. This work investigates how existing multidimensional indexing structures perform on chunked scientific datasets, and compares their performance with that of our own indexing structure, SH-trees. Since R-trees were proposed, various multidimensional indexing structures have been proposed. However, there are a relatively small number of studies focused on improving the performance of indexing geographically distributed datasets, especially across heterogeneous machines. As a third approach, in an attempt to accelerate indexing performance for distributed datasets, we proposed several distributed multidimensional indexing schemes: replicated centralized indexing, hierarchical two level indexing, and decentralized two level indexing. Our experimental results show that great performance improvements are gained from distribution of multidimensional index. However, the design choices for distributed indexing, such as replication, partitioning, and decentralization, must be carefully considered since they may decrease the overall performance in certain situations. Therefore, this work provides performance guidelines to aid in selecting the best distributed multidimensional indexing scheme for various systems and applications. Finally, we describe how a distributed multidimensional indexing scheme can be used by a distributed multiple query optimization middleware as a case-study application to generate better query plans by leveraging information about the contents of remote caches

Visualization for Biological Models, Simulation, and Ontologies

In this dissertation, I present three browsers that I have developed for the purpose of exploring, understanding, and analyzing models, simulations, and ontologies in biology and medicine. The first browser visualizes multidimensional simulation data as an animation. The second browser visualizes the equations of a complex model as a network and puts structure and organization on top of equations and variables. The third browser is an ontology viewer and editor, directly intended for the Foundational Model of Anatomy (FMA), but applicable to other ontologies as well. This browser has two contributions. First, it is a lightweight deliverable that lets someone easily dabble with the FMA. Second, it lets the user edit an ontology to create a view of it. For the ontology browser, I also conduct user studies to refine and evaluate the software

Vesper: Visualising Species Archives.

Vesper (Visual Exploration of SPEcies-referenced Repositories) is a tool that visualises Darwin Core Archive (DwC-A) datasets, and is aimed at reducing the amount of time and effort expended by biologists to ascertain the quality of data they are generating or using. Currently, DwC-A quality checking is limited to table outputs of data ‘existence’ and compliance with DwC-A format guidelines via the online DwC-A archive validator and reader. While these tools thoroughly examine the presence of data, and the correctness of data structure against the DwC-A schema, they do not give any insight into the underlying quality of the data itself.Built on top of the D3 JavaScript library, Vesper analyses and displays DwC-A datasets in three fundamental dimensions - taxonomic, geographic and temporal - with a visualisation dedicated to each of these aspects of the data. By viewing a dataset’s composition in these dimensions, a data consumer can judge whether it is suitable for the tasks or analyses they have in mind, while a data provider can identify where a dataset they’ve constructed may fall short in terms of data quality i.e. does it contains data that is obviously incorrect such as the classic longitude inversion that places North American specimens in China. A further visualisation of the taxonomic dimension can reveal the subtaxa distribution of reference taxonomies - while a simple table reveals the presence or not of certain data types for each record to give an overall data ‘existence’ profile for the dataset. Selections of parts of a dataset within one visualisation are linked to the other visualisation displays for that dataset, permitting the discovery of whether data quality issues are restricted to identifiable sub-portions of the dataset.Vesper can handle client-side data sets of a million entities within a browser by judicious use of data filtering, as many of the data types within individual records are not necessary to judge the geographic, temporal or taxonomic distribution and extent of a dataset. Thus, many of the more verbose fields in the file can simply be passed over during an initial data decompression stage. Furthermore it can provide limited name and structure matching of a dataset against DwC-A packaged reference taxonomies to indicate data quality relative to sources outside the archive. A selection of annotated example scenarios shows how Vesper can reveal data quality issues in DwC-A archives

Strategies for image visualisation and browsing

PhDThe exploration of large information spaces has remained a challenging task even though the proliferation of database management systems and the state-of-the art retrieval algorithms is becoming pervasive. Signi cant research attention in the multimedia domain is focused on nding automatic algorithms for organising digital image collections into meaningful structures and providing high-semantic image indices. On the other hand, utilisation of graphical and interactive methods from information visualisation domain, provide promising direction for creating e cient user-oriented systems for image management. Methods such as exploratory browsing and query, as well as intuitive visual overviews of image collection, can assist the users in nding patterns and developing the understanding of structures and content in complex image data-sets. The focus of the thesis is combining the features of automatic data processing algorithms with information visualisation. The rst part of this thesis focuses on the layout method for displaying the collection of images indexed by low-level visual descriptors. The proposed solution generates graphical overview of the data-set as a combination of similarity based visualisation and random layout approach. Second part of the thesis deals with problem of visualisation and exploration for hierarchical organisation of images. Due to the absence of the semantic information, images are considered the only source of high-level information. The content preview and display of hierarchical structure are combined in order to support image retrieval. In addition to this, novel exploration and navigation methods are proposed to enable the user to nd the way through database structure and retrieve the content. On the other hand, semantic information is available in cases where automatic or semi-automatic image classi ers are employed. The automatic annotation of image items provides what is referred to as higher-level information. This type of information is a cornerstone of multi-concept visualisation framework which is developed as a third part of this thesis. This solution enables dynamic generation of user-queries by combining semantic concepts, supported by content overview and information ltering. Comparative analysis and user tests, performed for the evaluation of the proposed solutions, focus on the ways information visualisation a ects the image content exploration and retrieval; how e cient and comfortable are the users when using di erent interaction methods and the ways users seek for information through di erent types of database organisation

Integrating Exception Handling in Machine Development

In modern batch plants, alarm floods overwhelming the operator is a common problem of ever increasing severity. As plant hardware increase in complexity and performance, measures such as downtime and meantime between failures, increase in importance and the need for a well-functioning exception handling routine therefore grows critical. In order to minimize downtime and hence boost production efficiency, it is important that faulty or unexpected behaviour is noted early and diagnosed accurately. If it is, the machine or its operator can deal with it fast and accurately, perhaps even while production continues. If it is not, however, it basically means two bad things, the first being unnecessary production stops and the second a flooded alarm list. The alarm list is the screen on which all exceptions are listed and which is meant to tell the process operator what is wrong and what he should do about it. If no care is taken about it, the list will be flooded since one key exception will cause several others, leaving the operator with the quite unpleasant task of identifying what went wrong and how he should fix it. This master's thesis, carried out at Tetra Pak in Lund, Sweden, presents a well-structured exception handling method and a way of linking it to a workflow. It uses advantages of reusability, modularisation and linking to almost any structural model such as a Function Means Tree (used in WCE) or a UML-model. The linking has several advantages minimizing the work and improving evolutionary possibilities. Examples are being made for illustrational purposes but no implementational efforts or issues are addressed. A well-defined structure for information flow is also suggested to provide modular thinking that, for example, prepares the possibility to collect data for statistical analysis and such