Generating Preview Tables for Entity Graphs

Users are tapping into massive, heterogeneous entity graphs for many applications. It is challenging to select entity graphs for a particular need, given abundant datasets from many sources and the oftentimes scarce information for them. We propose methods to produce preview tables for compact presentation of important entity types and relationships in entity graphs. The preview tables assist users in attaining a quick and rough preview of the data. They can be shown in a limited display space for a user to browse and explore, before she decides to spend time and resources to fetch and investigate the complete dataset. We formulate several optimization problems that look for previews with the highest scores according to intuitive goodness measures, under various constraints on preview size and distance between preview tables. The optimization problem under distance constraint is NP-hard. We design a dynamic-programming algorithm and an Apriori-style algorithm for finding optimal previews. Results from experiments, comparison with related work and user studies demonstrated the scoring measures' accuracy and the discovery algorithms' efficiency.Comment: This is the camera-ready version of a SIGMOD16 paper. There might be tiny differences in layout, spacing and linebreaking, compared with the version in the SIGMOD16 proceedings, since we must submit TeX files and use arXiv to compile the file

Using structured analysis and design technique (SADT) for simulation conceptual modelling

Conceptual Modelling (CM) has received little attention in the area of Modelling and Simulation (M&S) and more specifically in Discrete Event Simulation (DES). It is widely agreed that CM is least understood despite its importance. This is however, not the case in other fields of science and engineering (especially, computer science, systems engineering and software engineering). In Computer Science (CS) alone, CM has been extensively used for requirements specification and some well-established methods are in practice. The aim of the thesis is to propose a CM framework based on the principles of software engineering and CS. The development of the framework is adapted from a well-known software engineering method called Structured Analysis and Design Technique (SADT), hence it is called SADT CM. It is argued that by adapting approaches from CS, similar benefits can be achieved in terms of formality, understanding, communication and quality. A comprehensive cross-disciplinary review of CM in CS and M&S is undertaken, which highlights the dearth of standards within M&S CM when compared to CS. Three important sub-fields of CS are considered for this purpose namely, information systems, databases and software engineering. The review identifies two potential methods that could be adopted for developing a M&S CM framework. The first method called PREView was found unsuitable for M&S CM in DES domain. Hence, the thesis concentrates on developing the framework based on SADT. The SADT CM framework is evaluated on three-in depth test cases that investigate the feasibility of the approach. The study also contributes to the literature by conducting a usability test of the CM framework in an experimental setting. A comprehensive user-guide has also been developed as part of the research for users to follow the framewor

The EnzymeTracker: an open-source laboratory information management system for sample tracking

<p>Abstract</p> <p>Background</p> <p>In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone, as data do not undergo any validation process. To overcome spreadsheets inherent limitations, a number of proprietary systems have been developed, which laboratories need to pay expensive license fees for. Those costs are usually prohibitive for most laboratories and prevent scientists from benefiting from more sophisticated data management systems.</p> <p>Results</p> <p>In this paper, we propose the EnzymeTracker, a web-based laboratory information management system for sample tracking, as an open-source and flexible alternative that aims at facilitating entry, mining and sharing of experimental biological data. The EnzymeTracker features online spreadsheets and tools for monitoring numerous experiments conducted by several collaborators to identify and characterize samples. It also provides libraries of shared data such as protocols, and administration tools for data access control using OpenID and user/team management. Our system relies on a database management system for efficient data indexing and management and a user-friendly AJAX interface that can be accessed over the Internet. The EnzymeTracker facilitates data entry by dynamically suggesting entries and providing smart data-mining tools to effectively retrieve data. Our system features a number of tools to visualize and annotate experimental data, and export highly customizable reports. It also supports QR matrix barcoding to facilitate sample tracking.</p> <p>Conclusions</p> <p>The EnzymeTracker was designed to be easy to use and offers many benefits over spreadsheets, thus presenting the characteristics required to facilitate acceptance by the scientific community. It has been successfully used for 20 months on a daily basis by over 50 scientists. The EnzymeTracker is freely available online at <url>http://cubique.fungalgenomics.ca/enzymedb/index.html</url> under the GNU GPLv3 license.</p

A Framework for File Format Fuzzing with Genetic Algorithms

Secure software, meaning software free from vulnerabilities, is desirable in today\u27s marketplace. Consumers are beginning to value a product\u27s security posture as well as its functionality. Software development companies are recognizing this trend, and they are factoring security into their entire software development lifecycle. Secure development practices like threat modeling, static analysis, safe programming libraries, run-time protections, and software verification are being mandated during product development. Mandating these practices improves a product\u27s security posture before customer delivery, and these practices increase the difficulty of discovering and exploiting vulnerabilities. Since the 1980\u27s, security researchers have uncovered software defects by fuzz testing an application. In fuzz testing\u27s infancy, randomly generated data could discover multiple defects quickly. However, as software matures and software development companies integrate secure development practices into their development life cycles, fuzzers must apply more sophisticated techniques in order to retain their ability to uncover defects. Fuzz testing must evolve, and fuzz testing practitioners must devise new algorithms to exercise an application in unexpected ways. This dissertation\u27s objective is to create a proof-of-concept genetic algorithm fuzz testing framework to exercise an application\u27s file format parsing routines. The framework includes multiple genetic algorithm variations, provides a configuration scheme, and correlates data gathered from static and dynamic analysis to guide negative test case evolution. Experiments conducted for this dissertation illustrate the effectiveness of a genetic algorithm fuzzer in comparison to standard fuzz testing tools. The experiments showcase a genetic algorithm fuzzer\u27s ability to discover multiple unique defects within a limited number of negative test cases. These experiments also highlight an application\u27s increased execution time when fuzzing with a genetic algorithm. To combat increased execution time, a distributed architecture is implemented and additional experiments demonstrate a decrease in execution time comparable to standard fuzz testing tools. A final set of experiments provide guidance on fitness function selection with a CHC genetic algorithm fuzzer with different population size configurations

Image database system for glaucoma diagnosis support

Tato práce popisuje přehled standardních a pokročilých metod používaných k diagnose glaukomu v ranném stádiu. Na základě teoretických poznatků je implementován internetově orientovaný informační systém pro oční lékaře, který má tři hlavní cíle. Prvním cílem je možnost sdílení osobních dat konkrétního pacienta bez nutnosti posílat tato data internetem. Druhým cílem je vytvořit účet pacienta založený na kompletním očním vyšetření. Posledním cílem je aplikovat algoritmus pro registraci intenzitního a barevného fundus obrazu a na jeho základě vytvořit internetově orientovanou tři-dimenzionální vizualizaci optického disku. Tato práce je součásti DAAD spolupráce mezi Ústavem Biomedicínského Inženýrství, Vysokého Učení Technického v Brně, Oční klinikou v Erlangenu a Ústavem Informačních Technologií, Friedrich-Alexander University, Erlangen-Nurnberg.This master thesis describes a conception of standard and advanced eye examination methods used for glaucoma diagnosis in its early stage. According to the theoretical knowledge, a web based information system for ophthalmologists with three main aims is implemented. The first aim is the possibility to share medical data of a concrete patient without sending his personal data through the Internet. The second aim is to create a patient account based on a complete eye examination procedure. The last aim is to improve the HRT diagnostic method with an image registration algorithm for the fundus and intensity images and create an optic nerve head web based 3D visualization. This master thesis is a part of project based on DAAD co-operation between Department of Biomedical Engineering, Brno University of Technology, Eye Clinic in Erlangen and Department of Computer Science, Friedrich-Alexander University, Erlangen-Nurnberg.