Uncertainty representation in software models: a survey

This paper provides a comprehensive overview and analysis of research work on how uncertainty is currently represented in software models. The survey presents the definitions and current research status of different proposals for addressing uncertainty modeling and introduces a classification framework that allows to compare and classify existing proposals, analyze their current status and identify new trends. In addition, we discuss possible future research directions, opportunities and challenges.This work is partially supported by the European Commission (FEDER) and the Spanish Government under projects APOLO (US1264651), HORATIO (RTI2018-101204-B-C21), EKIPMENT-PLUS (P18-FR-2895) and COSCA (PGC2018-094905-B-I00)

Relational grounding facilitates development of scientifically useful multiscale models

We review grounding issues that influence the scientific usefulness of any biomedical multiscale model (MSM). Groundings are the collection of units, dimensions, and/or objects to which a variable or model constituent refers. To date, models that primarily use continuous mathematics rely heavily on absolute grounding, whereas those that primarily use discrete software paradigms (e.g., object-oriented, agent-based, actor) typically employ relational grounding. We review grounding issues and identify strategies to address them. We maintain that grounding issues should be addressed at the start of any MSM project and should be reevaluated throughout the model development process. We make the following points. Grounding decisions influence model flexibility, adaptability, and thus reusability. Grounding choices should be influenced by measures, uncertainty, system information, and the nature of available validation data. Absolute grounding complicates the process of combining models to form larger models unless all are grounded absolutely. Relational grounding facilitates referent knowledge embodiment within computational mechanisms but requires separate model-to-referent mappings. Absolute grounding can simplify integration by forcing common units and, hence, a common integration target, but context change may require model reengineering. Relational grounding enables synthesis of large, composite (multi-module) models that can be robust to context changes. Because biological components have varying degrees of autonomy, corresponding components in MSMs need to do the same. Relational grounding facilitates achieving such autonomy. Biomimetic analogues designed to facilitate translational research and development must have long lifecycles. Exploring mechanisms of normal-to-disease transition requires model components that are grounded relationally. Multi-paradigm modeling requires both hyperspatial and relational grounding

Integration of e-business strategy for multi-lifecycle production systems

Internet use has grown exponentially on the last few years becoming a global communication and business resource. Internet-based business, or e-Business will truly affect every sector of the economy in ways that today we can only imagine. The manufacturing sector will be at the forefront of this change. This doctoral dissertation provides a scientific framework and a set of novel decision support tools for evaluating, modeling, and optimizing the overall performance of e-Business integrated multi-lifecycle production systems. The characteristics of this framework include environmental lifecycle study, environmental performance metrics, hyper-network model of integrated e-supply chain networks, fuzzy multi-objective optimization method, discrete-event simulation approach, and scalable enterprise environmental management system design. The dissertation research reveals that integration of e-Business strategy into production systems can alter current industry practices along a pathway towards sustainability, enhancing resource productivity, improving cost efficiencies and reducing lifecycle environmental impacts. The following research challenges and scholarly accomplishments have been addressed in this dissertation: Identification and analysis of environmental impacts of e-Business. A pioneering environmental lifecycle study on the impact of e-Business is conducted, and fuzzy decision theory is further applied to evaluate e-Business scenarios in order to overcome data uncertainty and information gaps; Understanding, evaluation, and development of environmental performance metrics. Major environmental performance metrics are compared and evaluated. A universal target-based performance metric, developed jointly with a team of industry and university researchers, is evaluated, implemented, and utilized in the methodology framework; Generic framework of integrated e-supply chain network. The framework is based on the most recent research on large complex supply chain network model, but extended to integrate demanufacturers, recyclers, and resellers as supply chain partners. Moreover, The e-Business information network is modeled as a overlaid hypernetwork layer for the supply chain; Fuzzy multi-objective optimization theory and discrete-event simulation methods. The solution methods deal with overall system parameter trade-offs, partner selections, and sustainable decision-making; Architecture design for scalable enterprise environmental management system. This novel system is designed and deployed using knowledge-based ontology theory, and XML techniques within an agent-based structure. The implementation model and system prototype are also provided. The new methodology and framework have the potential of being widely used in system analysis, design and implementation of e-Business enabled engineering systems

Dependency Management 2.0 – A Semantic Web Enabled Approach

Software development and evolution are highly distributed processes that involve a multitude of supporting tools and resources. Application programming interfaces are commonly used by software developers to reduce development cost and complexity by reusing code developed by third-parties or published by the open source community. However, these application programming interfaces have also introduced new challenges to the Software Engineering community (e.g., software vulnerabilities, API incompatibilities, and software license violations) that not only extend beyond the traditional boundaries of individual projects but also involve different software artifacts. As a result, there is the need for a technology-independent representation of software dependency semantics and the ability to seamlessly integrate this representation with knowledge from other software artifacts. The Semantic Web and its supporting technology stack have been widely promoted to model, integrate, and support interoperability among heterogeneous data sources. This dissertation takes advantage of the Semantic Web and its enabling technology stack for knowledge modeling and integration. The thesis introduces five major contributions: (1) We present a formal Software Build System Ontology – SBSON, which captures concepts and properties for software build and dependency management systems. This formal knowledge representation allows us to take advantage of Semantic Web inference services forming the basis for a more flexibility API dependency analysis compared to traditional proprietary analysis approaches. (2) We conducted a user survey which involved 53 open source developers to allow us to gain insights on how actual developers manage API breaking changes. (3) We introduced a novel approach which integrates our SBSON model with knowledge about source code usage and changes within the Maven ecosystem to support API consumers and producers in managing (assessing and minimizing) the impacts of breaking changes. (4) A Security Vulnerability Analysis Framework (SV-AF) is introduced, which integrates builds system, source code, versioning system, and vulnerability ontologies to trace and assess the impact of security vulnerabilities across project boundaries. (5) Finally, we introduce an Ontological Trustworthiness Assessment Model (OntTAM). OntTAM is an integration of our build, source code, vulnerability and license ontologies which supports a holistic analysis and assessment of quality attributes related to the trustworthiness of libraries and APIs in open source systems. Several case studies are presented to illustrate the applicability and flexibility of our modelling approach, demonstrating that our knowledge modeling approach can seamlessly integrate and reuse knowledge extracted from existing build and dependency management systems with other existing heterogeneous data sources found in the software engineering domain. As part of our case studies, we also demonstrate how this unified knowledge model can enable new types of project dependency analysis

Enhancing Trust –A Unified Meta-Model for Software Security Vulnerability Analysis

Over the last decade, a globalization of the software industry has taken place which has facilitated the sharing and reuse of code across existing project boundaries. At the same time, such global reuse also introduces new challenges to the Software Engineering community, with not only code implementation being shared across systems but also any vulnerabilities it is exposed to as well. Hence, vulnerabilities found in APIs no longer affect only individual projects but instead might spread across projects and even global software ecosystem borders. Tracing such vulnerabilities on a global scale becomes an inherently difficult task, with many of the resources required for the analysis not only growing at unprecedented rates but also being spread across heterogeneous resources. Software developers are struggling to identify and locate the required data to take full advantage of these resources. The Semantic Web and its supporting technology stack have been widely promoted to model, integrate, and support interoperability among heterogeneous data sources. This dissertation introduces four major contributions to address these challenges: (1) It provides a literature review of the use of software vulnerabilities databases (SVDBs) in the Software Engineering community. (2) Based on findings from this literature review, we present SEVONT, a Semantic Web based modeling approach to support a formal and semi-automated approach for unifying vulnerability information resources. SEVONT introduces a multi-layer knowledge model which not only provides a unified knowledge representation, but also captures software vulnerability information at different abstract levels to allow for seamless integration, analysis, and reuse of the modeled knowledge. The modeling approach takes advantage of Formal Concept Analysis (FCA) to guide knowledge engineers in identifying reusable knowledge concepts and modeling them. (3) A Security Vulnerability Analysis Framework (SV-AF) is introduced, which is an instantiation of the SEVONT knowledge model to support evidence-based vulnerability detection. The framework integrates vulnerability ontologies (and data) with existing Software Engineering ontologies allowing for the use of Semantic Web reasoning services to trace and assess the impact of security vulnerabilities across project boundaries. Several case studies are presented to illustrate the applicability and flexibility of our modelling approach, demonstrating that the presented knowledge modeling approach cannot only unify heterogeneous vulnerability data sources but also enables new types of vulnerability analysis

New Fundamental Technologies in Data Mining

The progress of data mining technology and large public popularity establish a need for a comprehensive text on the subject. The series of books entitled by "Data Mining" address the need by presenting in-depth description of novel mining algorithms and many useful applications. In addition to understanding each section deeply, the two books present useful hints and strategies to solving problems in the following chapters. The contributing authors have highlighted many future research directions that will foster multi-disciplinary collaborations and hence will lead to significant development in the field of data mining

Interim research assessment 2003-2005 - Computer Science

This report primarily serves as a source of information for the 2007 Interim Research Assessment Committee for Computer Science at the three technical universities in the Netherlands. The report also provides information for others interested in our research activities

New IR & Ranking Algorithm for Top-K Keyword Search on Relational Databases ‘Smart Search’

Database management systems are as old as computers, and the continuous research and development in databases is huge and an interest of many database venders and researchers, as many researchers work in solving and developing new modules and frameworks for more efficient and effective information retrieval based on free form search by users with no knowledge of the structure of the database. Our work as an extension to previous works, introduces new algorithms and components to existing databases to enable the user to search for keywords with high performance and effective top-k results. Work intervention aims at introducing new table structure for indexing of keywords, which would help algorithms to understand the semantics of keywords and generate only the correct CN‟s (Candidate Networks) for fast retrieval of information with ranking of results according to user‟s history, semantics of keywords, distance between keywords and match of keywords. In which a three modules where developed for this purpose. We implemented our three proposed modules and created the necessary tables, with the development of a web search interface called „Smart Search‟ to test our work with different users. The interface records all user interaction with our „Smart Search‟ for analyses, as the analyses of results shows improvements in performance and effective results returned to the user. We conducted hundreds of randomly generated search terms with different sizes and multiple users; all results recorded and analyzed by the system were based on different factors and parameters. We also compared our results with previous work done by other researchers on the DBLP database which we used in our research. Our final result analysis shows the importance of introducing new components to the database for top-k keywords search and the performance of our proposed system with high effective results.نظم إدارة قواعد البيانات قديمة مثل أجيزة الكمبيوتر، و البحث والتطوير المستمر في قواعد بيانات ضخم و ىنالك اىتمام من العديد من مطوري قواعد البيانات والباحثين، كما يعمل العديد من الباحثين في حل وتطوير وحدات جديدة و أطر السترجاع المعمومات بطرق أكثر كفاءة وفعالية عمى أساس نموذج البحث الغير مقيد من قبل المستخدمين الذين ليس لدييم معرفة في بنية قاعدة البيانات. ويأتي عممنا امتدادا لألعمال السابقة، ويدخل الخوارزميات و مكونات جديدة لقواعد البيانات الموجودة لتمكين المستخدم من البحث عن الكممات المفتاحية )search Keyword )مع األداء العالي و نتائج فعالة في الحصول عمى أعمى ترتيب لمبيانات .)Top-K( وييدف ىذا العمل إلى تقديم بنية جديدة لفيرسة الكممات المفتاحية )Table Keywords Index ،)والتي من شأنيا أن تساعد الخوارزميات المقدمة في ىذا البحث لفيم معاني الكممات المفتاحية المدخمة من قبل المستخدم وتوليد فقط الشبكات المرشحة (s’CN (الصحيحة السترجاع سريع لممعمومات مع ترتيب النتائج وفقا ألوزان مختمفة مثل تاريخ البحث لممستخدم، ترتيب الكمات المفتاحية في النتائج والبعد بين الكممات المفتاحية في النتائج بالنسبة لما قام المستخدم بأدخالو. قمنا بأقتراح ثالث مكونات جديدة )Modules )وتنفيذىا من خالل ىذه االطروحة، مع تطوير واجية البحث عمى شبكة اإلنترنت تسمى "البحث الذكي" الختبار عممنا مع المستخدمين. وتتضمن واجية البحث مكونات تسجل تفاعل المستخدمين وتجميع تمك التفاعالت لمتحميل والمقارنة، وتحميالت النتائج تظير تحسينات في أداء استرجاع البينات و النتائج ذات صمة ودقة أعمى. أجرينا مئات عمميات البحث بأستخدام جمل بحث تم أنشائيا بشكل عشوائي من مختمف األحجام، باالضافة الى االستعانة بعدد من المستخدمين ليذه الغاية. واستندت جميع النتائج المسجمة وتحميميا بواسطة واجية البحث عمى عوامل و معايير مختمفة .وقمنا بالنياية بعمل مقارنة لنتائجنا مع االعمال السابقة التي قام بيا باحثون آخرون عمى نفس قاعدة البيانات (DBLP (الشييرة التي استخدمناىا في أطروحتنا. وتظير نتائجنا النيائية مدى أىمية أدخال بنية جديدة لفيرسة الكممات المفتاحية الى قواعد البيانات العالئقية، وبناء خوارزميات استنادا الى تمك الفيرسة لمبحث بأستخدام كممات مفتاحية فقط والحصول عمى نتائج أفضل ودقة أعمى، أضافة الى التحسن في وقت البحث