A Value-Based Approach for Reasoning with Goal Models

Goal models are used to represent stakeholders’ intentions regarding the system to be developed and the alternative means to achieve those intentions. Goal-oriented analysis techniques have been proposed to help analysts reason when employing goal models. These techniques can be used to identify conflicts among goals, to choose between alternatives or to check the satisfiability of the model. Unfortunately, most of these techniques consider that stakeholders their intentions are equally important. This paper presents a value-based approach that and allows stakeholders to assign a relative importance to the elements in a goal model. It then propagates that importance by means of their relationships (dependencies, contributions and decompositions) in order to determine which elements are more valuable. Fisher’s weighted distribution and multi-criteria decision analysis techniques are used to deal with the propagation of the importance among the goals. The contribution is the alignment of information system with stakeholders and organizational goals

Integrating requirements prioritization and selection into goal models

Requirements engineering is the first main activity in software development process. It must address the individual goals of the organization. The inadequate, inconsistent, incomplete and ambiguous requirements are main obstacles on the quality of software systems. Goal Oriented Requirements Engineering (GORE) starts with abstracts high level goals. These goals are refined to lower levels until they are assignable to agents. During GORE analysis, decisions need to be made among alternatives at various positions. Decisions involve different stakeholders which may contradict with each other based on certain criteria. In the context of GORE, the support for identifying and managing the criteria for requirements selection process is required. The criteria are based on stakeholders needs and preferences and therefore stakeholders opinions need to be involved in selection process. It helps to identify the importance of requirement according to stakeholders understandings and needs. It also helps in the understanding of interaction between system and stakeholders (stakeholders involvement in making important decisions) and by documenting the stakeholder preferences early in GORE, helps to identify inconsistencies early in the requirements engineering. Software quality requirements are essential part for the success of software development. Defined and guaranteed quality in software development requires identifying, refining, and predicting quality properties by appropriate means. Goal models and quality models are useful for modelling of functional goals as well as for quality goals. This thesis presents the integration of goal models with quality models, which helps to involve stakeholders opinions and the representation of dependencies among goals and quality models. The integration of goal models and quality models helps in the derivation of customized quality models. The integrated goal-quality model representing the functional requirements and quality requirements is used to rank each functional requirement arising from functional goals and quality requirement arising from quality goals. Triangular Fuzzy Numbers (TFN) are used to represent stakeholder opinions for prioritizing requirements. By defuzzification process on TFN, stakeholders opinions are quantified. TFN and defuzzification process is also used to prioritize the identified relationships among functional and non-functional requirements. In the last step development constraints are used to re-prioritize the requirements. After final prioritization, a selection algorithm helps to select the requirements based on benefit over cost ratio. The algorithm makes sure that maximum number of requirements are selected while fulfilling the upper cost limit. Thus the whole process helps in the selection of requirements based on stakeholders opinions, goal-quality models interaction and development constraints. The thesis also presents an integrative model of influence factors to tailor product line development processes according to different project needs, organizational goals, individual goals of the developers or constraints of the environment. Tailoring is realized with prioritized attributes, with which the resulting elements of the product, process and project analysed are ranked. An integrative model for the description of stakeholder needs and goals in relation to the development process artefacts and the development environment specifics is needed, to be able to analyse potential influences of changing goals early in the project development. The proposed tailoring meta-model includes goal models, SPEM models and requirements to development processes. With this model stakeholder specific goals can be used to support binding a variable part of the development process. This support addresses soft factors as well as concrete requirements.Requirements Engineering ist der erste Schritt im Softwareentwicklungsprozess. Er dient zur Aufnahme organisationsabhängiger Ziele und Anforderungen. Unangemessene, inkonsistente, unvollständige oder mehrdeutige Anforderungen können die Qualität von Softwaresystem stark negativ beeinflussen. Goal Oriented Requirements Engineering (GORE) beginnt mit der Entwicklung von übergeordneter Zielen, welche in weiteren Entwicklungsstufen verfeinert werden, bis sie einer verantwortlichen Person zugewiesen werden können. Während einer GORE Analyse werden an verschiedenen Stellen Entscheidungen über Alternativen getroffen. Diese Entscheidungen betreffen unterschiedliche Akteure, die sich in ihren Ansichten widersprechen können. Im Rahmen von GORE wird die Unterstützung zur Identifizierung und Verwaltung von Kriterien zur Auswahl von Anforderungen benötigt. Diese Kriterien basieren auf den Vorstellungen und Vorlieben von Stakeholdern, daher ist eine Integration aller Stakeholder in den Auswahlprozess erforderlich. Dies soll dabei helfen, die Bedeutung bestimmter Anforderungen auf Basis der betroffenen Personen zu identifizieren und aufzuarbeiten. Darüber hinaus hilft GORE bei der Kommunikation zwischen System und Akteuren durch ihren Einbezug in wichtige Entscheidungen. Durch frühzeitige Dokumentation des tatsächlichen Stakholderbedarfs können Inkonsistenzen im Requirements Engineering frühzeitig ermittelt werden. Die Bestimmung von Software Qualitätsmerkmalen ist wesentlicher Erfolgsfaktor in der Software Entwicklung. Zur Gewährleistung einer qualitativen Softwareentwicklung und eines entsprechenden Produktes sind die Identifizierung, die Verfeinerung und die Vorhersage von Qualitätseigenschaften jederzeit durch geeignete Maßnahmen erforderlich. Goal Models und Quality Models sind wertvolle Werkzeuge zur Ermittlung und Modellierung funktionaler und nicht-funktionaler Anforderungen und Ziele. Diese Arbeit enthält einen Lösungsansatz zur Integration von Goal Models und Quality Models, der dazu beitragen soll, Stakeholder und Abhängigkeiten zwischen Goal und Quality Models einzubeziehen und sichtbar zu machen. Die Integration von Goal Models und Quality Models soll zur Ableitung spezifischer Quality Models beitragen. Somit kann das integrierte Goal-Quality Model, welches die funktionalen Anforderungen und die Qualitätsanforderungen vereint, zur Priorisierung aller funktionalen Anforderung, die sich aus den funktionalen Zielen ergeben, und aller Qualitätsanforderungen, die aus Qualitätszielen resultieren, dienen. Zur Priorisierung der Anforderung auf Basis der Stakeholderbedarfe werden Triangular Fuzzy Numbers (TFN) verwendet. Nach der endgültigen Priorisierung dient ein spezieller Algorithmus zur Einschätzung und Auswahl der Anforderungen auf Basis einer Kosten-Nutzen-Analyse. Dieser Algorithmus stellt sicher, dass unter Einhaltung einer von der Organisation gewählten Kostenobergrenze die maximale Anzahl der Anforderungen umgesetzt werden kann. Der gesamte Prozess dient demnach zur Anforderungsanalyse unter Berücksichtigung verschiedener Interessengruppen, Abhängigkeiten, sowie durch den Einbezug von Grenzen, die sich beim Zusammenspiel von Goal-Quality Models und der Softwareentwicklung ergeben können. Darüber hinaus enthält die Arbeit ein integratives Modell, um Entwicklungsprozesse während der Erstellung von Produktlinien an Einflussfaktoren, wie Projektbedürfnisse, Organisationsziele, individuelle Ziele von Entwicklern oder an Umweltbedingungen anzupassen. Dieses sogenannte Tailoring wird durch Priorisierung von Attributen erreicht, welche verschiedene Elemente des zu erzeugende Produktes, des Prozesses oder des Projektes analysieren und nach Bedeutung sortieren. Ein integratives Modell zur Beschreibung von Stakeholderbedürfnissen und -zielen in Bezug auf die Artefakte des Entwicklungsprozesses und die Besonderheiten einer Entwicklungsumgebung wird benötigt, um potenzielle Einflüsse sich verändernder Ziele frühzeitig während der Projektentwicklung zu analysieren. Das hier vorgestellte Tailoring-Meta-Model beinhaltet Goal-Models, SPEM Models und Requirements hinsichtlich Entwicklungsprozesse. Mithilfe dieses Modells können stakeholderspezifische Ziele dazu verwendet werden, um einen variablen Teil eines Entwicklungsprozesses projektbezogen zu gestalten. Auf diese Weise können weiche Faktoren genauso integriert werden, wie konkrete Anforderungen

A framework for the definition of metrics for actor-dependency models

Actor-dependency models are a formalism aimed at providing intentional descriptions of processes as a network of dependency relationships among actors. This kind of models is currently widely used in the early phase of requirements engineering as well as in other contexts such as organizational analysis and business process reengineering. In this paper, we are interested in the definition of a framework for the formulation of metrics over these models. These metrics are used to analyse the models with respect to some properties that are interesting for the system being modelled, such as security, efficiency or accuracy. The metrics are defined in terms of the actors and dependencies of the model. We distinguish three different kinds of metrics that are formally defined, and then we apply the framework at two different layers of a meeting scheduler system.Postprint (published version

Bioinformatics Techniques for Studying Drug Resistance In HIV and Staphylococcus Aureus

The worldwide HIV/AIDS pandemic has been partly controlled and treated by antivirals targeting HIV protease, integrase and reverse transcriptase, however, drug resistance has become a serious problem. HIV-1 drug resistance to protease inhibitors evolves by mutations in the PR gene. The resistance mutations can alter protease catalytic activity, inhibitor binding, and stability. Different machine learning algorithms (restricted boltzmann machines, clustering, etc.) have been shown to be effective machine learning tools for classification of genomic and resistance data. Application of restricted boltzmann machine produced highly accurate and robust classification of HIV protease resistance. They can also be used to compare resistance profiles of different protease inhibitors. HIV drug resistance has also been studied by enzyme kinetics and X-ray crystallography. Triple mutant HIV-1 protease with resistance mutations V32I, I47V and V82I has been used as a model for the active site of HIV-2 protease. The effects of four investigational antiviral inhibitors was measured for Triple mutant. The tested compounds had significantly worse inhibition of triple mutant with Ki values of 17-40 nM compared to 2-10 pM for wild type protease. The crystal structure of triple mutant in complex with GRL01111 was solved and showed few changes in protease interactions with inhibitor. These new inhibitors are not expected to be effective for HIV-2 protease or HIV-1 protease with changes V32I, I47V and V82I. Methicillin-resistant Staphylococcus aureus (MRSA) is an opportunistic pathogen that causes hospital and community-acquired infections. Antibiotic resistance occurs because of newly acquired low-affinity penicillin-binding protein (PBP2a). Transcriptome analysis was performed to determine how MuM (mutated PBP2 gene) responds to spermine and how Mu50 (wild type) responds to spermine and spermine–β-lactam synergy. Exogenous spermine and oxacillin were found to alter some significant gene expression patterns with major biochemical pathways (iron, sigB regulon) in MRSA with mutant PBP2 protein

Understanding and Predicting the Dynamics, Folding and Binding of Proteins

Proteins are involved in all processes of life and their shapes, interactions and functions are governed by physical forces. A model with atomic resolution is pivotal for the understanding of their mechanisms and how mutations perturb these. However, given the large variation of proteins and the limitations of experimental methods, in-silico approaches are the only viable solution. Presented here are a number of computational methods to predict their structure and binary interactions with atomic detail. Firstly, a machine-learning method was developed that models the recognition process of protein-protein binding to improve the identification of near-native binding sites. Secondly, a refinement method was developed to improve the structural accuracy of predicted monomers. An intra reside-residue contact map space was defined to perform more directed conformational exploration with metadynamics in order to find solutions that better resemble the native state. This method was extended to perform refinement of pre-docked heterodimers in order to predict the conformational transition from unbound to bound. Here, an inter residue-residue contact map space was defined between the interface of a receptor and a ligand. Following this extensive sampling of protein conformations by simulation, a recurrent neural network was defined and trained to predict the state changes during the sampling such that improved quality conformations can be identified. Finally, extensive in-silico biophysical experiments were performed to understand the mechanism of auto-phosphorylation for RET-kinase in wild-type and its deregulation by an oncogenic mutation

Quality Goal Oriented Architectural Design and Traceability for Evolvable Software Systems

Softwaresysteme werden heute z.B. aufgrund sich ändernder Geschäftsprozesse oder Technologien mit häufigen Veränderungen konfrontiert. Die Software und speziell ihre Architektur muss diese Änderungen zur dauerhaften Nutzbarkeit ermöglichen.Während der Software-Evolution können Änderungen zu einer Verschlechterung der Architektur führen, der Architekturerosion. Dies erschwert oder verhindert weitere Änderungen wegen Inkonsistenz oder fehlendem Programmverstehen. Zur Erosionsvermeidung müssen Qualitätsziele wie Weiterentwickelbarkeit, Performanz oder Usability sowie die Nachvollziehbarkeit von Architekturentwurfsentscheidungen berücksichtigt werden. Dies wird jedoch oft vernachlässigt.Existierende Entwurfsmethoden unterstützen den Übergang von Qualitätzielen zu geeigneten Architekturlösungen nur unzureichend aufgrund einer Lücke zwischen Methoden des Requirements Engineering und des Architekturentwurfs. Insbesondere gilt dies für Weiterentwickelbarkeit und die Nachvollziehbarkeit von Entwurfsentscheidungen durch explizite Modellabhängigkeiten.Diese Arbeit präsentiert ein neues Konzept, genannt Goal Solution Scheme, das Qualitätsziele über Architekturprinzipien auf Lösungsinstrumente durch explizite Abhängigkeiten abbildet. Es hilft somit, Architekturlösungen entsprechend ihrem Einfluss auf Qualitätsziele auszuwählen. Das Schema wird speziell hinsichtlich Weiterentwickelbarkeit diskutiert und ist in ein zielorientiertes Vorgehen eingebettet, das etablierte Methoden und Konzepte des Requirements Engineering und Architekturentwurfs verbessert und integriert. Dies wird ergänzt durch ein Traceability-Konzept, welches einen regelbasierten Ansatz mit Techniken des Information Retrieval verbindet. Dies ermöglicht eine (halb-) automatische Erstellung von Traceability Links mit spezifischen Linktypen und Attributen für eine reichhaltige Semantik sowie mit hoher Genauigkeit und Trefferquote.Die Realisierbarkeit des Ansatzes wird an einer Fallstudie einer Software für mobile Serviceroboter gezeigt. Das Werkzeug EMFTrace wurde als eine erweiterbare Plattform basierend auf Eclipse-Technologie implementiert, um die Anwendbarkeit der Konzepte zu zeigen. Es integriert Entwurfsmodelle von externen CASE-Tools mittels XML-Technologie in einem gemeinsamen Modell-Repository, wendet Regeln zur Linkerstellung an und bietet Validierungsfunktionen für Regeln und Links.Today software systems are frequently faced with demands for changes, for example, due to changing business processes or technologies. The software and especially its architecture has to cope with those frequent changes to permanently remain usable.During software evolution changes can lead to a deterioration of the structure of software architectures called architectural erosion, which hampers or even inhibits further changes because of inconsistencies or lacking program comprehension. To support changes and avoid erosion, especially quality goals, such as evolvability, performance, or usability, and the traceability of design decisions have to be considered during architectural design. This however often is neglected.Existing design methods do not sufficiently support the transition from the quality goals to appropriate architectural solutions because there is still a gap between requirements engineering and architectural design methods. Particularly support is lacking for the goal evolvability and for the traceability of design decisions by explicit model dependencies.This thesis presents a new concept called Goal Solution Scheme, which provides a mapping from goals via architectural principles to solution instruments by explicit dependencies. Thus it helps to select appropriate architectural solutions according to their influence on quality goals. The scheme is discussed especially regarding evolvability, and it is embedded in a goal-oriented architectural design method, which enhances and integrates established methods and concepts from requirements engineering as well as architectural design. This is supplemented by a traceability concept, which combines a rule-based approach with information retrieval techniques for a (semi-) automated establishment of links with specific link types and attributes for rich semantics and a high precision and recall.The feasibility of the design approach has been evaluated in a case study of a software platform for mobile robots. A prototype tool suite called EMFTrace was implemented as an extensible platform based on Eclipse technology to show the practicability of the thesis' concept. It integrates design models from external CASE tools in a joint model repository by means of XML technology, applies rules for link establishment, and provides validation capabilities for rules and links

Molecular Mechanisms of Resistance and Structure-Based Drug Design in Homodimeric Viral Proteases

Drug resistance is a global health threat costing society billions of dollars and impacting millions of lives each year. Current drug design strategies are inadequate because they focus on disrupting target activity and not restricting the evolutionary pathways to resistance. Improved strategies would exploit the structural and dynamic changes in the enzyme–inhibitor system integrating data from many inhibitors and variants. Using HIV-1 protease as a model system, I aimed to elucidate the underlying resistance mechanisms, characterize conserved protease-inhibitor interactions, and generate more robust inhibitors by applying these insights. For primary mechanisms of resistance, comparing interactions at the protease–inhibitor interface showed how specific modifications affected potency. For mutations distal to the active site, molecular dynamics simulations were necessary to elucidate how changes propagated to reduce inhibitor binding. These insights informed inhibitor design to improve potency against highly resistant variants by optimizing hydrogen bonding. A series of hybrid inhibitors was also designed that showed excellent potency by combining key moieties of multiple FDA-approved inhibitors. I characterized the structural basis for alterations in binding affinity in HIV-1 protease both from mutations and inhibitors. I applied these strategies to HTLV-1 protease, a potential drug target. I identified the HIV-1 inhibitor darunavir as a viable scaffold and evaluated analogues, leading to a low-nanomolar compound with potential for optimization. Hopefully, insights from this thesis will lead to the development of potent HTLV-1 protease inhibitors. More broadly, these inhibitor design strategies are applicable to other rapidly evolving targets, thereby reducing drug resistance rates in the future

Pedestrian Attribute Recognition: A Survey

Recognizing pedestrian attributes is an important task in computer vision community due to it plays an important role in video surveillance. Many algorithms has been proposed to handle this task. The goal of this paper is to review existing works using traditional methods or based on deep learning networks. Firstly, we introduce the background of pedestrian attributes recognition (PAR, for short), including the fundamental concepts of pedestrian attributes and corresponding challenges. Secondly, we introduce existing benchmarks, including popular datasets and evaluation criterion. Thirdly, we analyse the concept of multi-task learning and multi-label learning, and also explain the relations between these two learning algorithms and pedestrian attribute recognition. We also review some popular network architectures which have widely applied in the deep learning community. Fourthly, we analyse popular solutions for this task, such as attributes group, part-based, \emph{etc}. Fifthly, we shown some applications which takes pedestrian attributes into consideration and achieve better performance. Finally, we summarized this paper and give several possible research directions for pedestrian attributes recognition. The project page of this paper can be found from the following website: \url{https://sites.google.com/view/ahu-pedestrianattributes/}.Comment: Check our project page for High Resolution version of this survey: https://sites.google.com/view/ahu-pedestrianattributes