Exhaustive analysis of dynamical properties of Biological Regulatory Networks with Answer Set Programming

International audienceThe combination of numerous simple influences between the components of a Biological Regulatory Network (BRN) often leads to behaviors that cannot be grasped intuitively. They thus call for the development of proper mathematical methods to delineate their dynamical properties. As a consequence , formal methods and computer tools for the modeling and simulation of BRNs become essential. Our recently introduced discrete formalism called the Process Hitting (PH), a restriction of synchronous automata networks, is notably suitable to such study. In this paper, we propose a new logical approach to perform model-checking of dynamical properties of BRNs modeled in PH. Our work here focuses on state reachability properties on the one hand, and on the identification of fixed points on the other hand. The originality of our model-checking approach relies in the exhaustive enumeration of all possible simulations verifying the dynamical properties thanks to the use of Answer Set Programming

Every normal logic program has a 2-valued semantics: theory, extensions, applications, implementations

Trabalho apresentado no âmbito do Doutoramento em Informática, como requisito parcial para obtenção do grau de Doutor em InformáticaAfter a very brief introduction to the general subject of Knowledge Representation and Reasoning with Logic Programs we analyse the syntactic structure of a logic program and how it can influence the semantics. We outline the important properties of a 2-valued semantics for Normal Logic Programs, proceed to define the new Minimal Hypotheses semantics with those properties and explore how it can be used to benefit some knowledge representation and reasoning mechanisms. The main original contributions of this work, whose connections will be detailed in the sequel, are: • The Layering for generic graphs which we then apply to NLPs yielding the Rule Layering and Atom Layering — a generalization of the stratification notion; • The Full shifting transformation of Disjunctive Logic Programs into (highly nonstratified)NLPs; • The Layer Support — a generalization of the classical notion of support; • The Brave Relevance and Brave Cautious Monotony properties of a 2-valued semantics; • The notions of Relevant Partial Knowledge Answer to a Query and Locally Consistent Relevant Partial Knowledge Answer to a Query; • The Layer-Decomposable Semantics family — the family of semantics that reflect the above mentioned Layerings; • The Approved Models argumentation approach to semantics; • The Minimal Hypotheses 2-valued semantics for NLP — a member of the Layer-Decomposable Semantics family rooted on a minimization of positive hypotheses assumption approach; • The definition and implementation of the Answer Completion mechanism in XSB Prolog — an essential component to ensure XSB’s WAM full compliance with the Well-Founded Semantics; • The definition of the Inspection Points mechanism for Abductive Logic Programs;• An implementation of the Inspection Points workings within the Abdual system [21] We recommend reading the chapters in this thesis in the sequence they appear. However, if the reader is not interested in all the subjects, or is more keen on some topics rather than others, we provide alternative reading paths as shown below. 1-2-3-4-5-6-7-8-9-12 Definition of the Layer-Decomposable Semantics family and the Minimal Hypotheses semantics (1 and 2 are optional) 3-6-7-8-10-11-12 All main contributions – assumes the reader is familiarized with logic programming topics 3-4-5-10-11-12 Focus on abductive reasoning and applications.FCT-MCTES (Fundação para a Ciência e Tecnologia do Ministério da Ciência,Tecnologia e Ensino Superior)- (no. SFRH/BD/28761/2006

OpenUP/MDRE: A Model-Driven Requirements Engineering Approach for Health-Care Systems

The domains and problems for which it would be desirable to introduce information systems are currently very complex and the software development process is thus of the same complexity. One of these domains is health-care. Model-Driven Development (MDD) and Service-Oriented Architecture (SOA) are software development approaches that raise to deal with complexity, to reduce time and cost of development, augmenting flexibility and interoperability. However, many techniques and approaches that have been introduced are of little use when not provided under a formalized and well-documented methodological umbrella. A methodology gives the process a well-defined structure that helps in fast and efficient analysis and design, trouble-free implementation, and finally results in the software product improved quality. While MDD and SOA are gaining their momentum toward the adoption in the software industry, there is one critical issue yet to be addressed before its power is fully realized. It is beyond dispute that requirements engineering (RE) has become a critical task within the software development process. Errors made during this process may have negative effects on subsequent development steps, and on the quality of the resulting software. For this reason, the MDD and SOA development approaches should not only be taken into consideration during design and implementation as usually occurs, but also during the RE process. The contribution of this dissertation aims at improving the development process of health-care applications by proposing OpenUP/MDRE methodology. The main goal of this methodology is to enrich the development process of SOA-based health-care systems by focusing on the requirements engineering processes in the model-driven context. I believe that the integration of those two highly important areas of software engineering, gathered in one consistent process, will provide practitioners with many benets. It is noteworthy that the approach presented here was designed for SOA-based health-care applications, however, it also provides means to adapt it to other architectural paradigms or domains. The OpenUP/MDRE approach is an extension of the lightweight OpenUP methodology for iterative, architecture-oriented and model-driven software development. The motivation for this research comes from the experience I gained as a computer science professional working on the health-care systems. This thesis also presents a comprehensive study about: i) the requirements engineering methods and techniques that are being used in the context of the model-driven development, ii) known generic but flexible and extensible methodologies, as well as approaches for service-oriented systems development, iii) requirements engineering techniques used in the health-care industry. Finally, OpenUP/MDRE was applied to a concrete industrial health-care project in order to show the feasibility and accuracy of this methodological approach.Loniewski, G. (2010). OpenUP/MDRE: A Model-Driven Requirements Engineering Approach for Health-Care Systems. http://hdl.handle.net/10251/11652Archivo delegad

DRUM-II : efficient model based diagnosis of technical systems

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Expanding the Horizons of Manufacturing: Towards Wide Integration, Smart Systems and Tools

This research topic aims at enterprise-wide modeling and optimization (EWMO) through the development and application of integrated modeling, simulation and optimization methodologies, and computer-aided tools for reliable and sustainable improvement opportunities within the entire manufacturing network (raw materials, production plants, distribution, retailers, and customers) and its components. This integrated approach incorporates information from the local primary control and supervisory modules into the scheduling/planning formulation. That makes it possible to dynamically react to incidents that occur in the network components at the appropriate decision-making level, requiring fewer resources, emitting less waste, and allowing for better responsiveness in changing market requirements and operational variations, reducing cost, waste, energy consumption and environmental impact, and increasing the benefits. More recently, the exploitation of new technology integration, such as through semantic models in formal knowledge models, allows for the capture and utilization of domain knowledge, human knowledge, and expert knowledge toward comprehensive intelligent management. Otherwise, the development of advanced technologies and tools, such as cyber-physical systems, the Internet of Things, the Industrial Internet of Things, Artificial Intelligence, Big Data, Cloud Computing, Blockchain, etc., have captured the attention of manufacturing enterprises toward intelligent manufacturing systems

Attention-based machine perception for intelligent cyber-physical systems

Cyber-physical systems (CPS) fundamentally change the way of how information systems interact with the physical world. They integrate the sensing, computing, and communication capabilities on heterogeneous platforms and infrastructures. Efficient and effective perception of the environment lays the foundation of proper operations in other CPS components (e.g., planning and control). Recent advances in artificial intelligence (AI) have unprecedentedly changed the way of how cyber systems extract knowledge from the collected sensing data, and understand the physical surroundings. This novel data-to-knowledge transformation capability pushes a wide spectrum of recognition tasks (e.g., visual object detection, speech recognition, and sensor-based human activity recognition) to a higher level, and opens an new era of intelligent cyber-physical systems. However, the state-of-the-art neural perception models are typically computation-intensive and sensitive to data noises, which induce significant challenges when they are deployed on resources-limited embedded platforms. This dissertation works on optimizing both the efficiency and efficacy of deep-neural- network (DNN)-based machine perception in intelligent cyber-physical systems. We extensively exploit and apply the design philosophy of attention, originated from cognitive psychology field, from multiple perspectives of machine perception. It generally means al- locating different degrees of concentration to different perceived stimuli. Specifically, we address the following five research questions: First, can we run the computation-intensive neural perception models in real-time by only looking at (i.e., scheduling) the important parts of the perceived scenes, with the cueing from an external sensor? Second, can we eliminate the dependency on the external cueing and make the scheduling framework a self- cueing system? Third, how to distribute the workloads among cameras in a distributed (visual) perception system, where multiple cameras can observe the same parts of the environment? Fourth, how to optimize the achieved perception quality when sensing data from heterogeneous locations and sensor types are collected and utilized? Fifth, how to handle sensor failures in a distributed sensing system, when the deployed neural perception models are sensitive to missing data? We formulate the above problems, and introduce corresponding attention-based solutions for each, to construct the fundamental building blocks for envisioning an attention-based machine perception system in intelligent CPS with both efficiency and efficacy guarantees