Formal Modeling Framework Research Articles

Statistical Agent-Based Models for Discrete Spatio-Temporal Systems

Agent-based models have been used to mimic natural processes in a variety of fields, from biology to social science. By specifying mechanistic models that describe how small-scale processes function and then scaling them up, agent-based approaches can result in very complicated large-scale behavior while often relying on only a small set of initial conditions and intuitive rules. Although many agent-based models are used strictly in a simulation context, statistical implementations are less common. To characterize complex dynamic processes, such as the spread of epidemics, we present a hierarchical Bayesian framework for formal statistical agent-based modeling using spatiotemporal binary data. Our approach is based on an intuitive parameterization of the system dynamics and can explicitly accommodate directionally varying dispersal, long distance dispersal, and spatial heterogeneity.

Modeling and Simulation of Nuclear Medicine Patient Service Management in DEVS

Increased demand for specialized healthcare services has been identified as one of the causes of increased healthcare costs in the US. Nuclear medicine, a sub-specialty of radiology, uses relatively new technology to diagnose and treat patients. Procedures (tests) in nuclear medicine require the use of radiopharmaceuticals with a limited half-life and involve several steps that are constrained by strict time windows and require multiple resources for completion. Consequently, managing patient service in nuclear medicine is a very challenging problem that has received very little research attention. In this paper, we present a discrete event system specification (DEVS) simulation model for nuclear medicine patient service management that considers both patient and management perspectives. DEVS is a formal modeling and simulation framework based on dynamical systems theory and provides well-defined concepts for coupling components, hierarchical and modular model construction, and an object-oriented substrate supporting repository reuse. We report on simulation results based on historical data using both patient and management performance measures. The results provide useful insights regarding the management of patient service in nuclear medicine. While this work focuses on nuclear medicine, results will find generality in other healthcare settings.

Using improved resource interfaces to formally describe adaptability in embedded systems

In embedded systems, timing and resource utilization are vital aspects, having impacts on the deployed software. In this paper, an extensible formal framework for modeling of resource usage and adaptability of software components is introduced. The formalism explicitly supports modeling resources of various types and in different ways; and the timing requirements that applications have. The models can be used as a basis for quantitative analysis, and in the extension as a basis for system synthesis. An example of usage of the formalism is given.

A Formal Framework for Stochastic Discrete Event System Specification Modeling and Simulation

We introduce an extension of the classic Discrete Event System Specification (DEVS) formalism that includes stochastic features. Based on the use of the probability spaces theory we define the stochastic DEVS (STDEVS) specification, which provides a formal framework for modeling and simulation of general non-deterministic discrete event systems. The main theoretical properties of the STDEVS framework are treated, including a new definition of legitimacy of models in the stochastic context and a proof of STDEVS closure under coupling. We also illustrate the new stochastic modeling capabilities introduced by STDEVS and their relation with those found in classic DEVS. Practical simulation examples are given involving performance analysis of computer systems and hybrid modeling of networked control systems, applications where the modeling of stochastic components is vital.

An entity-based integration framework for modeling and evaluating data enhancement products

This paper describes ongoing research to develop a comprehensive, formal framework for modeling and analyzing information products derived through multi-source, entity-based integration. It describ...

A Generic P/T Net Model and Framework for Concurrent Integrated Design and Planning of Electromechanical Assemblies

This paper describes a new unified formal modeling framework based on generic place/transition nets (PTNs) for concurrent integrated design and planning of electromechanical assemblies. First, a generic PTN model is defined as an abstract (meta)class of all types of PTNs. Then, an integrated object modeling framework is proposed for capturing and representing information and knowledge in the assembly design and planning processes based on the defined generic PTN modeling language and formalisms. The proposed integrated assembly model with the generic PTNs can uniformly represent the causal relations at the assembly level, the operation level, and the feature-based single-part level through the data abstraction of components and connectors on various levels of integrated assembly design and planning. An assembly model compatible with the STandard for the Exchange of Product model data (STEP, officially ISO 10303) is also built with the generic PTNs. To validate the proposed modeling framework, a prototype system has been developed, and a case study on gearbox assembly design and planning is provided.

Reliability analysis of programmable mechatronics system using Bayesian approach

In this modern digital age, software based Mechatronics is an emerging technology which is widely used in manufacturing industries. A Programmable Mechatronics system should contain high quality software and hardware components. To achieve a high quality system, reliability prediction of its components is an important initial process in the early design stage. Nowadays, software based Electro pneumatic systems are used in many manufacturing industries. The reliability analyses of various components involved in electro pneumatic system is necessary to initiate a smooth operation in application area. The Bayesian technique is a consistent formal modelling framework based on Bayesian statistics. It considers the uncertainties of unknown parameters. In this paper, Bayesian model is used to analyse the reliability of the software based electro pneumatic system in a systematic way. This attempt is helped to take a decision about the reliability of the system and also provides a sufficient confidence about the systems.

A Dynamic Model of Stress in the G-DEVS Formalism

This paper presents a model of stress based on theories and data originating from psychology, physiology and human factors literature. Our goal is to provide a formal framework for modeling and simulation of behavior moderators. G-DEVS offers a basis for specifying formal models and a clean simulation semantics. The presented model can be utilized in the context of cognitive simulation, jointly with a cognitive architecture to reflect the impact of stress on performance.

Process-oriented organisation modelling and analysis

This paper presents a formal framework for process-oriented modelling and analysis of organisations. The high expressivity of the sorted predicate logic language used for specification allows representing a wide range of process-related concepts (e.g. tasks, processes, resources), characteristics and relations, which are described in the paper. Furthermore, for every organisation, structural and behavioural constraints on process-related concepts can be identified. Some of them should always be fulfilled by the organisation (e.g. physical world constraints), whereas others allow some degree of organisational flexibility (e.g. some domain specific constraints). An organisational specification is correct if it satisfies a set of relevant organisational constraints. This paper describes automated formal techniques for establishing correctness of organisational specifications with respect to a set of diverse constraint types. The introduced framework is a part of a general framework for organisation modelling and analysis.

On deducing causality in metabolic networks

BackgroundMetabolic networks present a complex interconnected structure, whose understanding is in general a non-trivial task. Several formal approaches have been developed to support the investigation of such networks. One of the relevant problems in this context is the comprehension of causality dependencies amongst the molecules involved in the metabolic process.ResultsWe apply techniques from formal methods and computational logic to develop an abstract qualitative model of metabolic networks in order to determine possible causal dependencies. Keeping in mind both expressiveness and ease of use, we aimed at providing: i) a minimal notation to represent causality in biochemical interactions, and ii) an automated tool allowing human experts to easily vary conditions of in silico experiments. We exploit a reading of chemical reactions in terms of logical implications: starting from a description of a metabolic network in terms of reaction rules and initial conditions, chains of reactions, causally depending one from the another, can be automatically deduced. Both the components of the initial state and the clauses ruling reactions can be easily varied and a new trial of the experiment started, according to a what-if investigation strategy. Our approach aims at exploiting computational logic as a formal modeling framework, amongst the several available, that is naturally close to human reasoning. It directly leads to executable implementations and may support, in perspective, various reasoning schemata. Indeed, our abstractions are supported by a computational counterpart, based on a Prolog implementation, which allows for a representation language closely correspondent to the adopted chemical abstract notation. The proposed approach has been validated by results regarding gene knock-out and essentiality for a model of the metabolic network of Escherichia coli K12, which show a relevant coherence with available wet-lab experimental data.ConclusionsStarting from the presented work, our goal is to provide an effective analysis toolkit, supported by an efficient full-fledged computational counterpart, with the aim of fruitfully driving in vitro experiments by effectively pruning non promising directions.

A High-Level Petri Net Framework for Genetic Regulatory Networks

Summary To understand the function of genetic regulatory networks in the development of cellular systems, we must not only realise the individual network entities, but also the manner by which they interact. Multi-valued networks are a promising qualitative approach for modelling such genetic regulatory networks, however, at present they have limited formal analysis techniques and tools. We present a flexible formal framework for modelling and analysing multi-valued genetic regulatory networks using high-level Petri nets and logic minimization techniques. We demonstrate our approach with a detailed case study in which part of the genetic regulatory network responsible for the carbon starvation stress response in Escherichia coli is modelled and analysed. We then compare and contrast this multivalued model to a corresponding Boolean model and consider their formal relationship.

PARALLEL ALGORITHMS FOR CELLULAR MODELS SIMULATION

DEVS is a sound formal modeling and simulation (M&S) framework based on generic dynamic system concepts. Cell-DEVS is a formalism for cell-shaped models based on DEVS. This work presents a new simulation technique for execution of DEVS and Cell-DEVS models in parallel environments. These techniques are modifications to the original Time Warp mechanism offered by WARPED kernel. Time Warp functionalities are revised to include two new algorithms namely, Local Rollback Frequency Model (LRFM) and Global Rollback Frequency Model (GRFM). The resulting simulator is used as new simulation engine for CD++, an M&S toolkit that implements DEVS and Cell-DEVS theories. The results obtained allowed us to achieve considerable speedups due to the reductions that LRFM and GRFM protocols perform on number of rollbacks and anti-messages.

A framework for formal modeling and analysis of organizations

A new, formal, role-based, framework for modeling and analyzing both real world and artificial organizations is introduced. It exploits static and dynamic properties of the organizational model and includes the (frequently ignored) environment. The transition is described from a generic framework of an organization to its deployed model and to the actual agent allocation. For verification and validation of the proposed model, a set of dedicated techniques is introduced. Moreover, where most computational models can handle only two or three layered organizational structures, our framework can handle any arbitrary number of organizational layers. Henceforth, real-world organizations can be modeled and analyzed, as illustrated by a case study, within the DEAL project line

SEXUAL TENSION: DOES CONFLICT LEAD TO COSTLY MATE CHOICE?1

SEXUAL TENSION: DOES CONFLICT LEAD TO COSTLY MATE CHOICE?1

Performance modeling and analysis of workflow

Workflow model analysis is performed at logic, temporal, and performance levels. This paper mainly deals with the performance level issues. Workflow net (WF-net) is extended with time information to the timing workflow net (TWF-net). To provide a formal framework for modeling and analyzing workflow, this paper proposes a multidimension workflow net (MWF-net) that include multiple TWF-nets and the organization and resource information. The algorithm to decompose a free-choice and acyclic Petri nets (PN) into a set of T-components is extended to a TWF-net containing iteration structures. Then, resource availability and workload analysis is performed. A method for computing the lower bound of average turnaround time of transaction instances processed in a MWF-net is proposed. Finally a case study is used to show that the proposed method can be effectively utilized in practice.

JDEVS: an implementation of a DEVS based formal framework for environmental modelling

The development of models using multiple modelling paradigms is necessary to formulate and study current problems in environmental science. To simplify the coupling of those models, a formal basis for a high-level specification of such models must be set up. In this paper, we propose a discrete event system specification (DEVS) based modelling framework as a formal basis in environmental modelling. The formal framework ensures that the models are reusable and interoperable components with well defined interfaces. Moreover, a wide variety of modelling paradigms can be expressed in the DEVS formalism. We also extend the modelling paradigms that can be expressed in the DEVS framework with two techniques: Feedback-DEVS for the specification of supervised-learning models and Vector-DEVS for the specification of models in vector space. JDEVS is the Java implementation of the framework. It enables discrete event, general purpose, object oriented, component based, GIS connected, collaborative, visual simulation model development and execution. A Feedback-DEVS neural-network model and a cellular infiltration model are described as experiments using JDEVS. Those models are later coupled to show the new modelling scenarios enabled by the use of a formal framework and the flexibility of the software.

Integration of simulation and optimization for solving complex decision making problems

This paper represents an on-going research and concerns the development of an unified formal modeling framework designed to provide for model sharing, reusability and integration of simulation and optimization methods to allow decision-makers to master the dynamics of complex discrete systems. It should be pointed out that the different steps of problem identification, modeling and application generation use the same integrated formalism and environment.

A framework for testing special-purpose memories

Current memory testing methods rely on fault models that are inadequate to accurately represent potential defects that occur in modern, often specialized, memories. To remedy this, the authors present a formal framework for modeling and testing special-purpose memories. Their approach uses three models: the transistor circuit, the event-sequence model, and finite-state machines. The methodology is explained using the example of a content-addressable memory (CAM). The fault model they describe comprises input stuck-at, transistor, and bridging faults. The authors show that functional tests can reliably detect all input stuck-at faults, most transistor faults (including all stuck-open faults), and about 50% of bridging faults. The remaining faults are detectable by parametric tests. A test of length 7n+2l+9 that detects all the reliably testable faults in an n-word by l-bit CAM is presented. A CAM test by Giles & Hunter is evaluated with respect to the input stuck-at faults. It is shown that this test fails to detect certain faults; it can be modified to achieve full coverage at the cost of increased length.

A formal framework for business process modelling and design

We present a formal framework for enterprise and business process modelling. The concepts of our framework (objectives and goals, roles and actors, actions and processes, responsibilities and constraints) allow business analysts to capture enterprise knowledge in a way that is both intuitive and mathematically formal. We also outline the basic steps of a methodology that allows business analysts to produce detailed, formal specifications of business processes from high-level enterprise objectives. The use of a formal language permits us to verify that the specifications possess certain correctness properties, namely that the responsibilities assigned to roles are fulfilled, and that constraints are maintained as a result of process execution.

Extending IDEF1X to model fuzzy data

IDEF1X has provided a formal framework for consistent modeling of the data necessary for the integration of various functional areas in computer integrated manufacturing (CIM). The basic idea has been extensively applied in current manufacturing industry. Imprecise and uncertain information, however, is generally involved in many engineering activities. It is especially true for constructing intelligent manufacturing systems. This paper provides extensions to the IDEF1X, which makes it possible to represent fuzzy information.