BLOCKS, a Component Framework with Checking Facilities for Knowledge-Based Systems

équipe PULSARInternational audienceBLOCKS is an answer to the software engineering needs of the design of knowledge-based system engines. It is a framework composed of reusable and adaptable software components. However , its safe and correct use is complex and we supply formal models and associated tools to assist using it. These models and tools are based on behavioral description of components and on model checking techniques. They ensure a safe reuse of the components, especially when extending them through inheritance, owing to the notion of behavioral refinement

Towards Formalizing Behavorial Substitutability in Component Frameworks

International audienceWhen using a component framework, developers need to respect the behavior implemented by the components. Static information about the component interface is not sufficient. Dynamic information such as the description of valid sequences of operations is required. In this paper we propose a mathematical model and a formal language to describe the knowledge about behavior. We rely on a hierarchical model of deterministic finite state-machines. The execution model of these state-machines follows the Synchronous Paradigm. We focus on extension of components, owing to the notion of behavioral substitutability. A formal semantics for the language is defined and a composition-ality result allows us to get modular model-checking facilities. From the language and the model, we can draw practical design rules that are sufficient to preserve behavorial substitutability. Associated tools may ensure correct (re)use of components, as well as automatic simulation and verification , code generation, and run-time checks

A Behavioral Model of Component Frameworks

When using a component framework developers need to respect the behavior implemented by the components. Static information about the component interface is not sufficient. Dynamic information such as the description of valid sequences of operations is required. Instead of being in some external documentation, this information should be formally represented and embedded within the components themselves, so that it can be used by automatic tools. We propose a mathematical model and a formal language to describe the knowledge about behavior. We rely on a hierarchical model of deterministic finite state-machines. The communication between the machines follows the Synchronous Paradigm. We favor a structural approach allowing incremental simulation, automatic verification, code generation, and run-time checks. Associated tools may ensure correct and safe reuse of the components. We focus on extension of components through inheritance (in the sense of sub-typing), owing to the notion of behavioral refinement

Une approche synchrone pour la reconnaissance d'activités

International audienceActivity Recognition aims at recognizing and understanding sequences of actions and movements of mobile objects (human beings, animals or artefacts), that follow the predefined model of an activity. We propose to describe activities as a series of actions, triggered and driven by environmental events. Due to the large range of application domains (surveillance, safety, health care...), we propose a generic approach to design activity recognition systems that interact continously with their environment and react to its stimuli at run-time. In our target applications, the data coming from sensors (video-cameras, etc.) are first processed to recognize and track objects and to detect low-level events. This low-level information is collected and transformed into higher level inputs to our activity recognition system. Such recognition systems must satisfy stringent requirements: dependability, real time, cost effectiveness , security and safety, correctness, completeness... To enforce most of these properties our approach is to base the configuration of the system as well as its execution on formal techniques. We chose the synchronous approach which provides formal bases to perform static analysis, verification and validation, but also direct implementation. Several synchronous languages such as Lustre, Esterel, Scade and Signal [2] have been defined to describe synchronous automata. These languages are for expert users. We propose a new user-oriented language , named ADeL (Activity Description Language) to express activities and to automatically generate recognition automata. This language is easier to understand and to use by non computer scientists (e.g., physicians) while relying on formal semantics

Semantic Studies of a Synchronous Approach to Activity Recognition

International audienceMany important and critical applications such as surveillance or healthcare require some form of (human) activity recognition. Activities are usually represented by a series of actions driven and triggered by events. Recognition systems have to be real time, reactive, correct, complete, and dependable. These stringent requirements justify the use of formal methods to describe, analyze, verify, and generate effective recognition systems. Due to the large number of possible application domains, the researchers aim at building a generic recognition system. They choose the synchronous approach because it has a well-founded semantics and it ensures determinism and safe parallel composition. They propose a new language to represent activities as synchronous automata and they supply it with two complementary formal semantics. First a behavioral semantics gives a reference definition of program behavior using rewriting rules. Second, an equational semantics describes the behavior in a constructive way and can be directly implemented. This paper focuses on the description of these two semantics and their relation

An Activity Description Language for Activity Recognition

International audienceActivity recognition aims at recognizing and understanding the movements, actions, and objectives of mobile objects. These objects can be humans, animals, or simple artefacts. Many important and critical applications such as surveillance or health care require some form of (human) activity recognition. Existing languages can be used to describe models of activities, but they are difficult to master by non computer scientists (ex: doctors). In this paper, we present a new language dedicated to end users, to describe their activities. We call it ADeL (Activity Description Language). This language is intended to be part of a complete recognition system. Such a system has to be real time, reactive, correct, and dependable. We choose the synchronous approach because it respects these characteristics, it ensures determinism and safe parallel composition, and it allows verification of systems using model-checking. Relying on the synchronous approach, we supply our language with two complementary formal semantics and we provide it with two formats: textual and graphical. This paper focuses on the description of the ADeL language

A food web model for the Baffin Bay coastal and shelf ecosystem. Part 1 : Ecopath Technical Report

This work was undertaken as part of a multidisciplinary research project funded by the Marine Observation Prediction and Assessment Network - MEOPAR (at ULaval), Canadian Institute of Health Research – CIHR (at University of Ottawa), and Sentinel North (at ULaval), and hosted at Université Laval, in Canada. The objective of the overall project is to support the food security (i.e., the availability and access to sufficient, safe, nutritious food that meets dietary preference) of Inuit communities of the Eastern Canadian Arctic, as well as to explore ways to adapt to effects of climate change. Inuit fish and hunt local marine species, from invertebrates to fish and marine mammals, which make a large part of their diet and are central to their food security. With temperatures increasing twice as fast as the global average and sea ice becoming thinner and forming later, climate change effects on the distribution and abundance of Arctic marine species are already taking place. To better understand the effects of climate change in important subsistence species, a multi-species model (Ecopath with Ecosim) will be used to inform the development of an integrated ecosystem assessment. The model will be used as a tool to co-create scenarios of ecosystem change with the community of Qikiqtarjuaq, Nunavut, to inform adaptation strategies regarding food security (e.g., potential of new fisheries in the region). This report describes the development of an Ecopath model of the Baffin Bay coastal and shelf ecosystem. The methodology, data used to construct the model, data gaps and limitations are described

A TALEN Genome-Editing System for Generating Human Stem Cell-Based Disease Models

SummaryTranscription activator-like effector nucleases (TALENs) are a new class of engineered nucleases that are easier to design to cleave at desired sites in a genome than previous types of nucleases. We report here the use of TALENs to rapidly and efficiently generate mutant alleles of 15 genes in cultured somatic cells or human pluripotent stem cells, the latter for which we differentiated both the targeted lines and isogenic control lines into various metabolic cell types. We demonstrate cell-autonomous phenotypes directly linked to disease—dyslipidemia, insulin resistance, hypoglycemia, lipodystrophy, motor-neuron death, and hepatitis C infection. We found little evidence of TALEN off-target effects, but each clonal line nevertheless harbors a significant number of unique mutations. Given the speed and ease with which we were able to derive and characterize these cell lines, we anticipate TALEN-mediated genome editing of human cells becoming a mainstay for the investigation of human biology and disease

White-to-brown metabolic conversion of human adipocytes by JAK inhibition

The rising incidence of obesity and related disorders such as diabetes and heart disease has focused considerable attention on the discovery of novel therapeutics. One promising approach has been to increase the number or activity of brown-like adipocytes in white adipose depots, as this has been shown to prevent diet-induced obesity and reduce the incidence and severity of type 2 diabetes. Thus, the conversion of fat-storing cells into metabolically active thermogenic cells has become an appealing therapeutic strategy to combat obesity. Here, we report a screening platform for the identification of small molecules capable of promoting a white-to-brown metabolic conversion in human adipocytes. We identified two inhibitors of Janus Kinase (JAK) activity with no precedent in adipose tissue biology that stably confer brown-like metabolic activity to white adipocytes. Importantly, these metabolically converted adipocytes exhibit elevated UCP1 expression and increased mitochondrial activity. We further found that repression of interferon signalling and activation of hedgehog signalling in JAK-inactivated adipocytes contributes to the metabolic conversion observed in these cells. Our findings highlight a novel role for the JAK/STAT pathway in the control of adipocyte function and establish a platform to identify compounds for the treatment of obesity

A TALEN Genome-Editing System for Generating Human Stem Cell-Based Disease Models

Transcription activator-like effector nucleases (TALENs) are a new class of engineered nucleases that are easier to design to cleave at desired sites in a genome than previous types of nucleases. We report here the use of TALENs to rapidly and efficiently generate mutant alleles of 15 genes in cultured somatic cells or human pluripotent stem cells, the latter for which we differentiated both the targeted lines and isogenic control lines into various metabolic cell types. We demonstrate cell-autonomous phenotypes directly linked to disease—dyslipidemia, insulin resistance, hypoglycemia, lipodystrophy, motor-neuron death, and hepatitis C infection. We found little evidence of TALEN off-target effects, but each clonal line nevertheless harbors a significant number of unique mutations. Given the speed and ease with which we were able to derive and characterize these cell lines, we anticipate TALEN-mediated genome editing of human cells becoming a mainstay for the investigation of human biology and disease.Stem Cell and Regenerative Biolog