1,539 research outputs found

    Language Design for Reactive Systems: On Modal Models, Time, and Object Orientation in Lingua Franca and SCCharts

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    Reactive systems play a crucial role in the embedded domain. They continuously interact with their environment, handle concurrent operations, and are commonly expected to provide deterministic behavior to enable application in safety-critical systems. In this context, language design is a key aspect, since carefully tailored language constructs can aid in addressing the challenges faced in this domain, as illustrated by the various concurrency models that prevent the known pitfalls of regular threads. Today, many languages exist in this domain and often provide unique characteristics that make them specifically fit for certain use cases. This thesis evolves around two distinctive languages: the actor-oriented polyglot coordination language Lingua Franca and the synchronous statecharts dialect SCCharts. While they take different approaches in providing reactive modeling capabilities, they share clear similarities in their semantics and complement each other in design principles. This thesis analyzes and compares key design aspects in the context of these two languages. For three particularly relevant concepts, it provides and evaluates lean and seamless language extensions that are carefully aligned with the fundamental principles of the underlying language. Specifically, Lingua Franca is extended toward coordinating modal behavior, while SCCharts receives a timed automaton notation with an efficient execution model using dynamic ticks and an extension toward the object-oriented modeling paradigm

    Introduction to Riemannian Geometry and Geometric Statistics: from basic theory to implementation with Geomstats

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    International audienceAs data is a predominant resource in applications, Riemannian geometry is a natural framework to model and unify complex nonlinear sources of data.However, the development of computational tools from the basic theory of Riemannian geometry is laborious.The work presented here forms one of the main contributions to the open-source project geomstats, that consists in a Python package providing efficient implementations of the concepts of Riemannian geometry and geometric statistics, both for mathematicians and for applied scientists for whom most of the difficulties are hidden under high-level functions. The goal of this monograph is two-fold. First, we aim at giving a self-contained exposition of the basic concepts of Riemannian geometry, providing illustrations and examples at each step and adopting a computational point of view. The second goal is to demonstrate how these concepts are implemented in Geomstats, explaining the choices that were made and the conventions chosen. The general concepts are exposed and specific examples are detailed along the text.The culmination of this implementation is to be able to perform statistics and machine learning on manifolds, with as few lines of codes as in the wide-spread machine learning tool scikit-learn. We exemplify this with an introduction to geometric statistics

    Engineering Blockchain Based Software Systems: Foundations, Survey, and Future Directions

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    Many scientific and practical areas have shown increasing interest in reaping the benefits of blockchain technology to empower software systems. However, the unique characteristics and requirements associated with Blockchain Based Software (BBS) systems raise new challenges across the development lifecycle that entail an extensive improvement of conventional software engineering. This article presents a systematic literature review of the state-of-the-art in BBS engineering research from a software engineering perspective. We characterize BBS engineering from the theoretical foundations, processes, models, and roles and discuss a rich repertoire of key development activities, principles, challenges, and techniques. The focus and depth of this survey not only gives software engineering practitioners and researchers a consolidated body of knowledge about current BBS development but also underpins a starting point for further research in this field

    Synergies between Numerical Methods for Kinetic Equations and Neural Networks

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    The overarching theme of this work is the efficient computation of large-scale systems. Here we deal with two types of mathematical challenges, which are quite different at first glance but offer similar opportunities and challenges upon closer examination. Physical descriptions of phenomena and their mathematical modeling are performed on diverse scales, ranging from nano-scale interactions of single atoms to the macroscopic dynamics of the earth\u27s atmosphere. We consider such systems of interacting particles and explore methods to simulate them efficiently and accurately, with a focus on the kinetic and macroscopic description of interacting particle systems. Macroscopic governing equations describe the time evolution of a system in time and space, whereas the more fine-grained kinetic description additionally takes the particle velocity into account. The study of discretizing kinetic equations that depend on space, time, and velocity variables is a challenge due to the need to preserve physical solution bounds, e.g. positivity, avoiding spurious artifacts and computational efficiency. In the pursuit of overcoming the challenge of computability in both kinetic and multi-scale modeling, a wide variety of approximative methods have been established in the realm of reduced order and surrogate modeling, and model compression. For kinetic models, this may manifest in hybrid numerical solvers, that switch between macroscopic and mesoscopic simulation, asymptotic preserving schemes, that bridge the gap between both physical resolution levels, or surrogate models that operate on a kinetic level but replace computationally heavy operations of the simulation by fast approximations. Thus, for the simulation of kinetic and multi-scale systems with a high spatial resolution and long temporal horizon, the quote by Paul Dirac is as relevant as it was almost a century ago. The first goal of the dissertation is therefore the development of acceleration strategies for kinetic discretization methods, that preserve the structure of their governing equations. Particularly, we investigate the use of convex neural networks, to accelerate the minimal entropy closure method. Further, we develop a neural network-based hybrid solver for multi-scale systems, where kinetic and macroscopic methods are chosen based on local flow conditions. Furthermore, we deal with the compression and efficient computation of neural networks. In the meantime, neural networks are successfully used in different forms in countless scientific works and technical systems, with well-known applications in image recognition, and computer-aided language translation, but also as surrogate models for numerical mathematics. Although the first neural networks were already presented in the 1950s, the scientific discipline has enjoyed increasing popularity mainly during the last 15 years, since only now sufficient computing capacity is available. Remarkably, the increasing availability of computing resources is accompanied by a hunger for larger models, fueled by the common conception of machine learning practitioners and researchers that more trainable parameters equal higher performance and better generalization capabilities. The increase in model size exceeds the growth of available computing resources by orders of magnitude. Since 20122012, the computational resources used in the largest neural network models doubled every 3.43.4 months\footnote{\url{https://openai.com/blog/ai-and-compute/}}, opposed to Moore\u27s Law that proposes a 22-year doubling period in available computing power. To some extent, Dirac\u27s statement also applies to the recent computational challenges in the machine-learning community. The desire to evaluate and train on resource-limited devices sparked interest in model compression, where neural networks are sparsified or factorized, typically after training. The second goal of this dissertation is thus a low-rank method, originating from numerical methods for kinetic equations, to compress neural networks already during training by low-rank factorization. This dissertation thus considers synergies between kinetic models, neural networks, and numerical methods in both disciplines to develop time-, memory- and energy-efficient computational methods for both research areas

    Applications of Molecular Dynamics simulations for biomolecular systems and improvements to density-based clustering in the analysis

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    Molecular Dynamics simulations provide a powerful tool to study biomolecular systems with atomistic detail. The key to better understand the function and behaviour of these molecules can often be found in their structural variability. Simulations can help to expose this information that is otherwise experimentally hard or impossible to attain. This work covers two application examples for which a sampling and a characterisation of the conformational ensemble could reveal the structural basis to answer a topical research question. For the fungal toxin phalloidin—a small bicyclic peptide—observed product ratios in different cyclisation reactions could be rationalised by assessing the conformational pre-organisation of precursor fragments. For the C-type lectin receptor langerin, conformational changes induced by different side-chain protonations could deliver an explanation of the pH-dependency in the protein’s calcium-binding. The investigations were accompanied by the continued development of a density-based clustering protocol into a respective software package, which is generally well applicable for the use case of extracting conformational states from Molecular Dynamics data

    Synthesizing FDIR Recovery Strategies for Space Systems

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    Dynamic Fault Trees (DFTs) are powerful tools to drive the design of fault tolerant systems. However, semantic pitfalls limit their practical utility for interconnected systems that require complex recovery strategies to maximize their reliability. This thesis discusses the shortcomings of DFTs in the context of analyzing Fault Detection, Isolation and Recovery (FDIR) concepts with a particular focus on the needs of space systems. To tackle these shortcomings, we introduce an inherently non-deterministic model for DFTs. Deterministic recovery strategies are synthesized by transforming these non-deterministic DFTs into Markov automata that represent all possible choices between recovery actions. From the corresponding scheduler, optimized to maximize a given RAMS (Reliability, Availability, Maintainability and Safety) metric, an optimal recovery strategy can then be derived and represented by a model we call recovery automaton. We discuss dedicated techniques for reducing the state space of this recovery automaton and analyze their soundness and completeness. Moreover, modularized approaches to handle the complexity added by the state-based transformation approach are discussed. Furthermore, we consider the non-deterministic approach in a partially observable setting and propose an approach to lift the model for the fully observable case. We give an implementation of our approach within the Model-Based Systems Engineering (MBSE) framework Virtual Satellite. Finally, the implementation is evaluated based on the FFORT benchmark. The results show that basic non-deterministic DFTs generally scale well. However, we also found that semantically enriched non-deterministic DFTs employing repair or delayed observability mechanisms pose a challenge

    Understanding the Code of Life: Holistic Conceptual Modeling of the Genome

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    [ES] En las últimas décadas, los avances en la tecnología de secuenciación han producido cantidades significativas de datos genómicos, hecho que ha revolucionado nuestra comprensión de la biología. Sin embargo, la cantidad de datos generados ha superado con creces nuestra capacidad para interpretarlos. Descifrar el código de la vida es un gran reto. A pesar de los numerosos avances realizados, nuestra comprensión del mismo sigue siendo mínima, y apenas estamos empezando a descubrir todo su potencial, por ejemplo, en áreas como la medicina de precisión o la farmacogenómica. El objetivo principal de esta tesis es avanzar en nuestra comprensión de la vida proponiendo una aproximación holística mediante un enfoque basado en modelos que consta de tres artefactos: i) un esquema conceptual del genoma, ii) un método para su aplicación en el mundo real, y iii) el uso de ontologías fundacionales para representar el conocimiento del dominio de una forma más precisa y explícita. Las dos primeras contribuciones se han validado mediante la implementación de sistemas de información genómicos basados en modelos conceptuales. La tercera contribución se ha validado mediante experimentos empíricos que han evaluado si el uso de ontologías fundacionales conduce a una mejor comprensión del dominio genómico. Los artefactos generados ofrecen importantes beneficios. En primer lugar, se han generado procesos de gestión de datos más eficientes, lo que ha permitido mejorar los procesos de extracción de conocimientos. En segundo lugar, se ha logrado una mejor comprensión y comunicación del dominio.[CA] En les últimes dècades, els avanços en la tecnologia de seqüenciació han produït quantitats significatives de dades genòmiques, fet que ha revolucionat la nostra comprensió de la biologia. No obstant això, la quantitat de dades generades ha superat amb escreix la nostra capacitat per a interpretar-los. Desxifrar el codi de la vida és un gran repte. Malgrat els nombrosos avanços realitzats, la nostra comprensió del mateix continua sent mínima, i a penes estem començant a descobrir tot el seu potencial, per exemple, en àrees com la medicina de precisió o la farmacogenómica. L'objectiu principal d'aquesta tesi és avançar en la nostra comprensió de la vida proposant una aproximació holística mitjançant un enfocament basat en models que consta de tres artefactes: i) un esquema conceptual del genoma, ii) un mètode per a la seua aplicació en el món real, i iii) l'ús d'ontologies fundacionals per a representar el coneixement del domini d'una forma més precisa i explícita. Les dues primeres contribucions s'han validat mitjançant la implementació de sistemes d'informació genòmics basats en models conceptuals. La tercera contribució s'ha validat mitjançant experiments empírics que han avaluat si l'ús d'ontologies fundacionals condueix a una millor comprensió del domini genòmic. Els artefactes generats ofereixen importants beneficis. En primer lloc, s'han generat processos de gestió de dades més eficients, la qual cosa ha permés millorar els processos d'extracció de coneixements. En segon lloc, s'ha aconseguit una millor comprensió i comunicació del domini.[EN] Over the last few decades, advances in sequencing technology have produced significant amounts of genomic data, which has revolutionised our understanding of biology. However, the amount of data generated has far exceeded our ability to interpret it. Deciphering the code of life is a grand challenge. Despite our progress, our understanding of it remains minimal, and we are just beginning to uncover its full potential, for instance, in areas such as precision medicine or pharmacogenomics. The main objective of this thesis is to advance our understanding of life by proposing a holistic approach, using a model-based approach, consisting of three artifacts: i) a conceptual schema of the genome, ii) a method for its application in the real-world, and iii) the use of foundational ontologies to represent domain knowledge in a more unambiguous and explicit way. The first two contributions have been validated by implementing genome information systems based on conceptual models. The third contribution has been validated by empirical experiments assessing whether using foundational ontologies leads to a better understanding of the genomic domain. The artifacts generated offer significant benefits. First, more efficient data management processes were produced, leading to better knowledge extraction processes. Second, a better understanding and communication of the domain was achieved.Las fructíferas discusiones y los resultados derivados de los proyectos INNEST2021 /57, MICIN/AEI/10.13039/501100011033, PID2021-123824OB-I00, CIPROM/2021/023 y PDC2021- 121243-I00 han contribuido en gran medida a la calidad final de este tesis.García Simón, A. (2022). Understanding the Code of Life: Holistic Conceptual Modeling of the Genome [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/19143
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