From examples to knowledge in model-driven engineering : a holistic and pragmatic approach

Le Model-Driven Engineering (MDE) est une approche de développement logiciel qui propose d’élever le niveau d’abstraction des langages afin de déplacer l’effort de conception et de compréhension depuis le point de vue des programmeurs vers celui des décideurs du logiciel. Cependant, la manipulation de ces représentations abstraites, ou modèles, est devenue tellement complexe que les moyens traditionnels ne suffisent plus à automatiser les différentes tâches. De son côté, le Search-Based Software Engineering (SBSE) propose de reformuler l’automatisation des tâches du MDE comme des problèmes d’optimisation. Une fois reformulé, la résolution du problème sera effectuée par des algorithmes métaheuristiques. Face à la pléthore d’études sur le sujet, le pouvoir d’automatisation du SBSE n’est plus à démontrer. C’est en s’appuyant sur ce constat que la communauté du Example-Based MDE (EBMDE) a commencé à utiliser des exemples d’application pour alimenter la reformulation SBSE du problème d’apprentissage de tâche MDE. Dans ce contexte, la concordance de la sortie des solutions avec les exemples devient un baromètre efficace pour évaluer l’aptitude d’une solution à résoudre une tâche. Cette mesure a prouvé être un objectif sémantique de choix pour guider la recherche métaheuristique de solutions. Cependant, s’il est communément admis que la représentativité des exemples a un impact sur la généralisabilité des solutions, l'étude de cet impact souffre d’un manque de considération flagrant. Dans cette thèse, nous proposons une formulation globale du processus d'apprentissage dans un contexte MDE incluant une méthodologie complète pour caractériser et évaluer la relation qui existe entre la généralisabilité des solutions et deux propriétés importantes des exemples, leur taille et leur couverture. Nous effectuons l’analyse empirique de ces deux propriétés et nous proposons un plan détaillé pour une analyse plus approfondie du concept de représentativité, ou d’autres représentativités.Model-Driven Engineering (MDE) is a software development approach that proposes to raise the level of abstraction of languages in order to shift the design and understanding effort from a programmer point of view to the one of decision makers. However, the manipulation of these abstract representations, or models, has become so complex that traditional techniques are not enough to automate its inherent tasks. For its part, the Search-Based Software Engineering (SBSE) proposes to reformulate the automation of MDE tasks as optimization problems. Once reformulated, the problem will be solved by metaheuristic algorithms. With a plethora of studies on the subject, the power of automation of SBSE has been well established. Based on this observation, the Example-Based MDE community (EB-MDE) started using application examples to feed the reformulation into SBSE of the MDE task learning problem. In this context, the concordance of the output of the solutions with the examples becomes an effective barometer for evaluating the ability of a solution to solve a task. This measure has proved to be a semantic goal of choice to guide the metaheuristic search for solutions. However, while it is commonly accepted that the representativeness of the examples has an impact on the generalizability of the solutions, the study of this impact suffers from a flagrant lack of consideration. In this thesis, we propose a thorough formulation of the learning process in an MDE context including a complete methodology to characterize and evaluate the relation that exists between two important properties of the examples, their size and coverage, and the generalizability of the solutions. We perform an empirical analysis, and propose a detailed plan for further investigation of the concept of representativeness, or of other representativities

SEIS: Insight's Seismic Experiment for Internal Structure of Mars.

By the end of 2018, 42 years after the landing of the two Viking seismometers on Mars, InSight will deploy onto Mars' surface the SEIS (Seismic Experiment for Internal Structure) instrument; a six-axes seismometer equipped with both a long-period three-axes Very Broad Band (VBB) instrument and a three-axes short-period (SP) instrument. These six sensors will cover a broad range of the seismic bandwidth, from 0.01 Hz to 50 Hz, with possible extension to longer periods. Data will be transmitted in the form of three continuous VBB components at 2 sample per second (sps), an estimation of the short period energy content from the SP at 1 sps and a continuous compound VBB/SP vertical axis at 10 sps. The continuous streams will be augmented by requested event data with sample rates from 20 to 100 sps. SEIS will improve upon the existing resolution of Viking's Mars seismic monitoring by a factor of ∼ 2500 at 1 Hz and ∼ 200 000 at 0.1 Hz. An additional major improvement is that, contrary to Viking, the seismometers will be deployed via a robotic arm directly onto Mars' surface and will be protected against temperature and wind by highly efficient thermal and wind shielding. Based on existing knowledge of Mars, it is reasonable to infer a moment magnitude detection threshold of M w ∼ 3 at 40 ∘ epicentral distance and a potential to detect several tens of quakes and about five impacts per year. In this paper, we first describe the science goals of the experiment and the rationale used to define its requirements. We then provide a detailed description of the hardware, from the sensors to the deployment system and associated performance, including transfer functions of the seismic sensors and temperature sensors. We conclude by describing the experiment ground segment, including data processing services, outreach and education networks and provide a description of the format to be used for future data distribution.Electronic supplementary materialThe online version of this article (10.1007/s11214-018-0574-6) contains supplementary material, which is available to authorized users

A framework for evaluating the quality of modelling languages in MDE environments

This thesis presents the Multiple Modelling Quality Evaluation Framework method (hereinafter MMQEF), which is a conceptual, methodological, and technological framework for evaluating quality issues in modelling languages and modelling elements by the application of a taxonomic analysis. It derives some analytic procedures that support the detection of quality issues in model-driven projects, such as the suitability of modelling languages, traces between abstraction levels, specification for model transformations, and integration between modelling proposals. MMQEF also suggests metrics to perform analytic procedures based on the classification obtained for the modelling languages and artifacts under evaluation. MMQEF uses a taxonomy that is extracted from the Zachman framework for Information Systems (Zachman, 1987; Sowa and Zachman, 1992), which proposed a visual language to classify elements that are part of an Information System (IS). These elements can be from organizational to technical artifacts. The visual language contains a bi-dimensional matrix for classifying IS elements (generally expressed as models) and a set of seven rules to perform the classification. As an evaluation method, MMQEF defines activities in order to derive quality analytics based on the classification applied on modelling languages and elements. The Zachman framework was chosen because it was one of the first and most precise proposals for a reference architecture for IS, which is recognized by important standards such as the ISO 42010 (612, 2011). This thesis presents the conceptual foundation of the evaluation framework, which is based on the definition of quality for model-driven engineering (MDE). The methodological and technological support of MMQEF is also described. Finally, some validations for MMQEF are reported.Esta tesis presenta el método MMQEF (Multiple Modelling Quality Evaluation Framework), el cual es un marco de trabajo conceptual, metodológico y tecnológico para evaluar aspectos de calidad sobre lenguajes y elementos de modelado mediante la aplicación de análisis taxonómico. El método deriva procedimientos analíticos que soportan la detección de aspectos de calidad en proyectos model-driven tales como: idoneidad de lenguajes de modelado, trazabilidad entre niveles de abstracción, especificación de transformación de modelos, e integración de propuestas de modelado. MMQEF también sugiere métricas para ejecutar procedimientos analíticos basados en la clasificación obtenida para los lenguajes y artefactos de modelado bajo evaluación. MMQEF usa una taxonomía para Sistemas de Información basada en el framework Zachman (Zachman, 1987; Sowa and Zachman, 1992). Dicha taxonomía propone un lenguaje visual para clasificar elementos que hacen parte de un Sistema de Información. Los elementos pueden ser artefactos asociados a niveles desde organizacionales hasta técnicos. El lenguaje visual contiene una matriz bidimensional para clasificar elementos de Sistemas de Información, y un conjunto de siete reglas para ejecutar la clasificación. Como método de evaluación MMEQF define actividades para derivar analíticas de calidad basadas en la clasificación aplicada sobre lenguajes y elementos de modelado. El marco Zachman fue seleccionado debido a que éste fue una de las primeras y más precisas propuestas de arquitectura de referencia para Sistemas de Información, siendo ésto reconocido por destacados estándares como ISO 42010 (612, 2011). Esta tesis presenta los fundamentos conceptuales del método de evaluación basado en el análisis de la definición de calidad en la ingeniería dirigida por modelos (MDE). Posteriormente se describe el soporte metodológico y tecnológico de MMQEF, y finalmente se reportan validaciones.Aquesta tesi presenta el mètode MMQEF (Multiple Modelling Quality Evaluation Framework), el qual és un marc de treball conceptual, metodològic i tecnològic per avaluar aspectes de qualitat sobre llenguatges i elements de modelatge mitjançant l'aplicació d'anàlisi taxonòmic. El mètode deriva procediments analítics que suporten la detecció d'aspectes de qualitat en projectes model-driven com ara: idoneïtat de llenguatges de modelatge, traçabilitat entre nivells d'abstracció, especificació de transformació de models, i integració de propostes de modelatge. MMQEF també suggereix mètriques per executar procediments analítics basats en la classificació obtinguda pels llenguatges i artefactes de mode-lat avaluats. MMQEF fa servir una taxonomia per a Sistemes d'Informació basada en el framework Zachman (Zachman, 1987; Sowa and Zachman, 1992). Aquesta taxonomia proposa un llenguatge visual per classificar elements que fan part d'un Sistema d'Informació. Els elements poden ser artefactes associats a nivells des organitzacionals fins tècnics. El llenguatge visual conté una matriu bidimensional per classificar elements de Sistemes d'Informació, i un conjunt de set regles per executar la classificació. Com a mètode d'avaluació MMEQF defineix activitats per derivar analítiques de qualitat basades en la classificació aplicada sobre llenguatges i elements de modelatge. El marc Zachman va ser seleccionat a causa de que aquest va ser una de les primeres i més precises propostes d'arquitectura de referència per a Sistemes d'Informació, sent això reconegut per destacats estàndards com ISO 42010 (612, 2011). Aquesta tesi presenta els fonaments conceptuals del mètode d'avaluació basat en l'anàlisi de la definició de qualitat en l'enginyeria dirigida per models (MDE). Posteriorment es descriu el suport metodològic i tecnològic de MMQEF, i finalment es reporten validacions.Giraldo Velásquez, FD. (2017). A framework for evaluating the quality of modelling languages in MDE environments [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/90628TESI

Engineering secure systems: Models, patterns and empirical validation

Several development approaches have been proposed to handle the growing complexity of software system design. The most popular methods use models as the main artifacts to construct and maintain. The desired role of such models is to facilitate, systematize and standardize the construction of software-based systems. In our work, we propose a model-driven engineering (MDE) methodological approach associated with a pattern-based approach to support the development of secure software systems. We address the idea of using patterns to describe solutions for security as recurring security problems in specific design contexts and present a well-proven generic scheme for their solutions. The proposed approach is based on metamodeling and model transformation techniques to define patterns at different levels of abstraction and generate different representations according to the target domain concerns, respectively. Moreover, we describe an operational architecture for development tools to support the approach. Finally, an empirical evaluation of the proposed approach is presented through a practical application to a use case in the metrology domain with strong security requirements, which is followed by a description of a survey performed among domain experts to better understand their perceptions regarding our approach

A Data-Driven Approach for Modeling Agents

Agents are commonly created on a set of simple rules driven by theories, hypotheses, and assumptions. Such modeling premise has limited use of real-world data and is challenged when modeling real-world systems due to the lack of empirical grounding. Simultaneously, the last decade has witnessed the production and availability of large-scale data from various sensors that carry behavioral signals. These data sources have the potential to change the way we create agent-based models; from simple rules to driven by data. Despite this opportunity, the literature has neglected to offer a modeling approach to generate granular agent behaviors from data, creating a gap in the literature. This dissertation proposes a novel data-driven approach for modeling agents to bridge the research gap. The approach is composed of four detailed steps including data preparation, attribute model creation, behavior model creation, and integration. The connection between and within each step is established using data flow diagrams. The practicality of the approach is demonstrated with a human mobility model that uses millions of location footprints collected from social media. In this model, the generation of movement behavior is tested with five machine learning/statistical modeling techniques covering a large number of model/data configurations. Results show that Random Forest-based learning is the most effective for the mobility use case. Furthermore, agent attribute values are obtained/generated with machine learning and translational assignment techniques. The proposed approach is evaluated in two ways. First, the use case model is compared to another model which is developed using a state-of-the-art data-driven approach. The model’s prediction performance is comparable to the state-of-the-art model. The plausibility of behaviors and model structure in the use case model is found to be closer to real-world than the state-of-the-art model. This outcome indicates that the proposed approach produces realistic results. Second, a standard mobility dataset is used for driving the mobility model in place of social media data. Despite its small size, the data and model resembled the results gathered from the primary use case indicating the possibility of using different datasets with the proposed approach

Molecular mechanism of poly(ADP-ribosyl)ation catalyzed by human poly(ADP-ribose) polymerase-1

Human poly(ADP-ribose) polymerase-1 (PARP-1) is an abundant nuclear enzyme which catalyzes protein poly(ADP-ribosyl)ation upon binding to DNA. NAD+ is used as a co-substrate in the reaction via iterative transfer of its ADP-ribose moiety to acceptor proteins including PARP-1 itself, yielding elongated and branched poly(ADP-ribose) (PAR) polymers. This type of protein posttranslational modification has been demonstrated in the regulation of diverse biological processes including DNA repair, gene expression, cell cycle, etc. Therefore, elucidating the catalytic mechanism of PARP-1 would not only advance our understanding of how its enzymatic activity is regulated under physiological and pathophysiological conditions, but also greatly benefit the development of novel therapeutics involving pharmacological manipulation of PARP-1. In this dissertation, the molecular mechanism of DNA-dependent poly(ADP-ribosyl)ation by human PARP-1 was addressed from an enzymological perspective in terms of the allosteric ligand DNA, the substrate NAD+, and the PARP-1 protein–DNA complex as a whole. By site-specific labeling of the DNA-binding domain AB of PARP-1 and DNA ligands with fluorophores, quantitative binding kinetics of AB with DNA was investigated by single-molecule fluorescence spectroscopy. Two binding modes, one involving a strongly-associated protein–DNA complex and the other being transient, were suggested by the experimental data. To probe the catalytic mechanism of the initiation, elongation, and branching step of poly(ADP-ribosyl)ation with regard to NAD+ substrate scope, analogues of NAD+ with fluoro-substituted ribose ring were synthesized chemoenzymatically and employed as substrates. The results are consistent with the proposed mechanism that the ADP-ribosyl transfer reaction proceeds through an oxocarbenium-like transition state. Mass spectrometry and biochemical approaches were utilized to decipher the poly(ADP-ribosyl)ation sites on PARP-1 and the chemical nature of PAR–protein linkages. The data confirm the existence of automodification sites beyond domain D, and lysine could be the targeted residue for poly(ADP-ribosyl)ation, either enzymatically or nonenzymatically. The macromolecular mechanism of DNA-dependent PARP-1 automodification was established by an in vitro radioactivity-based poly(ADP-ribosyl)ation assay using structurally distinguishable PARP-1 mutants. The data support the model of an intermolecular process. Top-down MS analysis and crosslinking assay bolster the monomeric structure of domain C in solution and its participation in interdomain contacts during PARP-1 catalysis. Taken together, these mechanistic studies provide further insight into the catalytic strategies exploited by human PARP-1 complementary to recent reports of structural characterization, and may help discover better therapeutic agents modulating poly(ADP-ribosyl)ation.Pharmaceutical Science

RESTful Web Services Development with a Model-Driven Engineering Approach

A RESTful web service implementation requires following the constrains inherent to Representational State Transfer (REST) architectural style, which, being a non-trivial task, often leads to solutions that do not fulfill those requirements properly. Model-driven techniques have been proposed to improve the development of complex applications. In model-driven software development, software is not implemented manually based on informal descriptions, but partial or completely generated from formal models derived from metamodels. A model driven approach, materialized in a domain specific language that integrates the OpenAPI specification, an emerging standard for describing REST services, allows developers to use a design first approach in the web service development process, focusing in the definition of resources and their relationships, leaving the repetitive code production process to the automation provided by model-driven engineering techniques. This also allows to shift the creative coding process to the resolution of the complex business rules, instead of the tiresome and error-prone create, read, update, and delete operations. The code generation process covers the web service flow, from the establishment and exposure of the endpoints to the definition of database tables.A implementação de serviços web RESTful requer que as restrições inerentes ao estilo arquitetónico “Representational State Transfer” (REST) sejam cumpridas, o que, sendo usualmente uma tarefa não trivial, geralmente leva a soluções que não atendem a esses requisitos adequadamente. Técnicas orientadas a modelos têm sido propostas para melhorar o desenvolvimento de aplicações complexas. No desenvolvimento de software orientado a modelos, o software não é implementado manualmente com base em descrições informais, mas parcial ou completamente gerado a partir de modelos formais derivados de meta-modelos. Uma abordagem orientada a modelos, materializada através de uma linguagem específica do domínio que integra a especificação OpenAPI, um padrão emergente para descrever serviços REST, permite aos desenvolvedores usar uma primeira abordagem de design no processo de desenvolvimento de serviços da Web, concentrando-se na definição dos recursos e das suas relações, deixando o processo de produção de código repetitivo para a automação fornecida por técnicas de engenharia orientadas a modelos. Isso também permite focar o processo de codificação criativo na resolução e implementação das regras de negócios mais complexas, em vez de nas operações mais repetitivas e propensas a erros: criação, leitura, atualização e remoção de dados. O processo de geração de código abrange o fluxo do serviço web desde o estabelecimento e exposição dos caminhos para os serviços disponíveis até à definição de tabelas de base de dados

Enhancing Biomechanical Function through Development and Testing of Assistive Devices for Shoulder Impairment and Total Limb Amputation

Assistive devices serve as a potential for restoring sensorimotor function to impaired individuals. My research focuses on two assistive devices: a passive shoulder exoskeleton and a muscle-driven endoprosthesis (MDE). Previous passive shoulder exoskeletons have focused on testing during static loading conditions in the shoulder. However, activities of daily living are based on dynamic tasks. My research for passive shoulder exoskeletons analyzes the effect that a continuous passive assistance has on shoulder biomechanics. In my research I showed that passive assistance decreases the muscular activation in muscles responsible for positive shoulder exoskeleton. An MDE has the potential to have accurate and precise control of movement as well as restore a sense of proprioception to the user. Such a transformative and invasive device has never previously been tested. Therefore, my research focused on analyzing fundamental principles of the MDE in an in-vivo rabbit model. The two concepts I tested in my research were the feasibility of implanting an orthopedic device underneath the skin at the distal end of a limb following amputation and the locomotor restorative capabilities of an artificial tendon used for muscle-device connection. In my work I proved the feasibility of implanting fully-footed rigid endoprostheses underneath the skin and isolated the primary factors for a successful surgery and recovery. In addition, my research showed that although artificial tendons have the potential to restore locomotor function, proper in-situ tendon lengths must be achieved for optimal movement. This research informed the design and testing of a fully jointed muscle-driven endoprosthesis prototype