A guided tour of asynchronous cellular automata

Research on asynchronous cellular automata has received a great amount of attention these last years and has turned to a thriving field. We survey the recent research that has been carried out on this topic and present a wide state of the art where computing and modelling issues are both represented.Comment: To appear in the Journal of Cellular Automat

An Individual-based Probabilistic Model for Fish Stock Simulation

We define an individual-based probabilistic model of a sole (Solea solea) behaviour. The individual model is given in terms of an Extended Probabilistic Discrete Timed Automaton (EPDTA), a new formalism that is introduced in the paper and that is shown to be interpretable as a Markov decision process. A given EPDTA model can be probabilistically model-checked by giving a suitable translation into syntax accepted by existing model-checkers. In order to simulate the dynamics of a given population of soles in different environmental scenarios, an agent-based simulation environment is defined in which each agent implements the behaviour of the given EPDTA model. By varying the probabilities and the characteristic functions embedded in the EPDTA model it is possible to represent different scenarios and to tune the model itself by comparing the results of the simulations with real data about the sole stock in the North Adriatic sea, available from the recent project SoleMon. The simulator is presented and made available for its adaptation to other species.Comment: In Proceedings AMCA-POP 2010, arXiv:1008.314

Multiple verification in computational modeling of bone pathologies

We introduce a model checking approach to diagnose the emerging of bone pathologies. The implementation of a new model of bone remodeling in PRISM has led to an interesting characterization of osteoporosis as a defective bone remodeling dynamics with respect to other bone pathologies. Our approach allows to derive three types of model checking-based diagnostic estimators. The first diagnostic measure focuses on the level of bone mineral density, which is currently used in medical practice. In addition, we have introduced a novel diagnostic estimator which uses the full patient clinical record, here simulated using the modeling framework. This estimator detects rapid (months) negative changes in bone mineral density. Independently of the actual bone mineral density, when the decrease occurs rapidly it is important to alarm the patient and monitor him/her more closely to detect insurgence of other bone co-morbidities. A third estimator takes into account the variance of the bone density, which could address the investigation of metabolic syndromes, diabetes and cancer. Our implementation could make use of different logical combinations of these statistical estimators and could incorporate other biomarkers for other systemic co-morbidities (for example diabetes and thalassemia). We are delighted to report that the combination of stochastic modeling with formal methods motivate new diagnostic framework for complex pathologies. In particular our approach takes into consideration important properties of biosystems such as multiscale and self-adaptiveness. The multi-diagnosis could be further expanded, inching towards the complexity of human diseases. Finally, we briefly introduce self-adaptiveness in formal methods which is a key property in the regulative mechanisms of biological systems and well known in other mathematical and engineering areas.Comment: In Proceedings CompMod 2011, arXiv:1109.104

Frontiers of Membrane Computing: Open Problems and Research Topics

This is a list of open problems and research topics collected after the Twelfth Conference on Membrane Computing, CMC 2012 (Fontainebleau, France (23 - 26 August 2011), meant initially to be a working material for Tenth Brainstorming Week on Membrane Computing, Sevilla, Spain (January 30 - February 3, 2012). The result was circulated in several versions before the brainstorming and then modified according to the discussions held in Sevilla and according to the progresses made during the meeting. In the present form, the list gives an image about key research directions currently active in membrane computing

DEVELOPMENT OF A MIXED-FLOW OPTIMIZATION SYSTEM FOR EMERGENCY EVACUATION IN URBAN NETWORKS

In most metropolitan areas, an emergency evacuation may demand a potentially large number of evacuees to use transit systems or to walk over some distance to access their passenger cars. In the process of approaching designated pick-up points for evacuation, the massive number of pedestrians often incurs tremendous burden to vehicles in the roadway network. Hence, one critical issue in a multi-modal evacuation planning is the effective coordination of the vehicle and pedestrian flows by considering their complex interactions. The purpose of this research is to develop an integrated system that is capable of generating the optimal evacuation plan and reflecting the real-world network traffic conditions caused by the conflicts of these two types of flows. The first part of this research is an integer programming model designed to optimize the control plans for massive mixed pedestrian-vehicle flows within the evacuation zone. The proposed model, integrating the pedestrian and vehicle networks, can effectively account for their potential conflicts during the evacuation. The model can generate the optimal routing strategies to guide evacuees moving toward either their pick-up locations or parking areas and can also produce a responsive plan to accommodate the massive pedestrian movements. The second part of this research is a mixed-flow simulation tool that can capture the conflicts between pedestrians, between vehicles, and between pedestrians and vehicles in an evacuation network. The core logic of this simulation model is the Mixed-Cellular Automata (MCA) concept, which, with some embedded components, offers a realistic mechanism to reflect the competing and conflicting interactions between vehicle and pedestrian flows. This study is expected to yield the following contributions * Design of an effective framework for planning a multi-modal evacuation within metropolitan areas; * Development of an integrated mixed-flow optimization model that can overcome various modeling and computing difficulties in capturing the mixed-flow dynamics in urban network evacuation; * Construction and calibration of a new mixed-flow simulation model, based on the Cellular Automaton concept, to reflect various conflicting patterns between vehicle and pedestrian flows in an evacuation network

Cyber-Physical Modeling of Implantable Cardiac Medical Devices

The design of bug-free and safe medical device software is challenging, especially in complex implantable devices that control and actuate organs in unanticipated contexts. Safety recalls of pacemakers and implantable cardioverter defibrillators between 1990 and 2000 affected over 600,000 devices. Of these, 200,000 or 41%, were due to firmware issues and their effect continues to increase in frequency. There is currently no formal methodology or open experimental platform to test and verify the correct operation of medical device software within the closed-loop context of the patient. To this effect, a real-time Virtual Heart Model (VHM) has been developed to model the electrophysiological operation of the functioning and malfunctioning (i.e., during arrhythmia) heart. By extracting the timing properties of the heart and pacemaker device, we present a methodology to construct a timed-automata model for functional and formal testing and verification of the closed-loop system. The VHM\u27s capability of generating clinically-relevant response has been validated for a variety of common arrhythmias. Based on a set of requirements, we describe a closed-loop testing environment that allows for interactive and physiologically relevant model-based test generation for basic pacemaker device operations such as maintaining the heart rate, atrial-ventricle synchrony and complex conditions such as pacemaker-mediated tachycardia. This system is a step toward a testing and verification approach for medical cyber-physical systems with the patient-in-the-loop

High-Confidence Medical Device Software Development

The design of bug-free and safe medical device software is challenging, especially in complex implantable devices. This is due to the device\u27s closed-loop interaction with the patient\u27s organs, which are stochastic physical environments. The life-critical nature and the lack of existing industry standards to enforce software validation make this an ideal domain for exploring design automation challenges for integrated functional and formal modeling with closed-loop analysis. The primary goal of high-confidence medical device software is to guarantee the device will never drive the patient into an unsafe condition even though we do not have complete understanding of the physiological plant. There are two major differences between modeling physiology and modeling man-made systems: first, physiology is much more complex and less well-understood than man-made systems like cars and airplanes, and spans several scales from the molecular to the entire human body. Secondly, the variability between humans is orders of magnitude larger than that between two cars coming off the assembly line. Using the implantable cardiac pacemaker as an example of closed-loop device, and the heart as the organ to be modeled, we present several of the challenges and early results in model-based device validation. We begin with detailed timed automata model of the pacemaker, based on the specifications and algorithm descriptions from Boston Scientific. For closed-loop evaluation, a real-time Virtual Heart Model (VHM) has been developed to model the electrophysiological operation of the functioning and malfunctioning (i.e., during arrhythmia) hearts. By extracting the timing properties of the heart and pacemaker device, we present a methodology to construct timed-automata models for formal model checking and functional testing of the closed-loop system. The VHM\u27s capability of generating clinically-relevant response has been validated for a variety of common arrhythmias. Based on a set of requirements, we describe a framework of Abstraction Trees that allows for interactive and physiologically relevant closed-loop model checking and testing for basic pacemaker device operations such as maintaining the heart rate, atrial-ventricle synchrony and complex conditions such as avoiding pacemaker-mediated tachycardia. Through automatic model translation of abstract models to simulation-based testing and code generation for platform-level testing, this model-based design approach ensures the closed-loop safety properties are retained through the design toolchain and facilitates the development of verified software from verified models. This system is a step toward a validation and testing approach for medical cyber-physical systems with the patient-in-the-loop

Heart Rhythm Insights Into Structural Remodeling in Atrial Tissue: Timed Automata Approach

The heart rhythm of a person following heart transplantation (HTX) is assumed to display an intrinsic cardiac rhythm because it is significantly less influenced by the autonomic nervous system—the main source of heart rate variability in healthy people. Therefore, such a rhythm provides evidence for arrhythmogenic processes developing, usually silently, in the cardiac tissue. A model is proposed to simulate alterations in the cardiac tissue and to observe the effects of these changes on the resulting heart rhythm. The hybrid automata framework used makes it possible to represent reliably and simulate efficiently both the electrophysiology of a cardiac cell and the tissue organization. The curve fitting method used in the design of the hybrid automaton cycle follows the well-recognized physiological phases of the atrial myocyte membrane excitation. Moreover, knowledge of the complex architecture of the right atrium, the ability of the almost free design of intercellular connections makes the automata approach the only one possible. Two particular aspects are investigated: impairment of the impulse transmission between cells and structural changes in intercellular connections. The first aspect models the observed fatigue of cells due to specific cardiac tissue diseases. The second aspect simulates the increase in collagen deposition with aging. Finally, heart rhythms arising from the model are validated with the sinus heart rhythms recorded in HTX patients. The modulation in the impairment of the impulse transmission between cells reveals qualitatively the abnormally high heart rate variability observed in patients living long after HTX