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Computing Descent Direction of MTL Robustness for NonLinear Systems
"... Abstract—The automatic analysis of transient properties of nonlinear dynamical systems is a challenging problem. The problem is even more challenging when complex statespace and timing requirements must be satisfied by the system. Such complex requirements can be captured by Metric Temporal Logic ( ..."
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Abstract—The automatic analysis of transient properties of nonlinear dynamical systems is a challenging problem. The problem is even more challenging when complex statespace and timing requirements must be satisfied by the system. Such complex requirements can be captured by Metric Temporal Logic (MTL) specifications. The problem of finding system behaviors that do not satisfy an MTL specification is referred to as MTL falsification. This paper presents an approach for improving stochastic MTL falsification methods by performing local search in the set of initial conditions. In particular, MTL robustness quantifies how correct or wrong is a system trajectory with respect to an MTL specification. Positive values indicate satisfaction of the property while negative values indicate falsification. A stochastic falsification method attempts to minimize the system’s robustness with respect to the MTL property. Given some arbitrary initial state, this paper presents a method to compute a descent direction in the set of initial conditions, such that the new system trajectory gets closer to the unsafe set of behaviors. This technique can be iterated in order to converge to a local minimum of the robustness landscape. The paper demonstrates the applicability of the method on some challenging nonlinear systems from the literature. I.
A ModelBased Approach to Synthesizing Insulin Infusion Pump Usage Parameters for Diabetic Patients
"... Abstract — We present a modelbased approach to synthesizing insulin infusion pump usage parameters against varying meal scenarios and physiological conditions. Insulin infusion pumps are commonly used by type1 diabetic patients to control their blood glucose levels. The amounts of insulin to be in ..."
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Abstract — We present a modelbased approach to synthesizing insulin infusion pump usage parameters against varying meal scenarios and physiological conditions. Insulin infusion pumps are commonly used by type1 diabetic patients to control their blood glucose levels. The amounts of insulin to be infused are calculated based on parameters such as insulintocarbohydrate ratios and correction factors that need to be calibrated carefully for each patient. Frequent and careful calibration of these parameters is essential for avoiding complications such as hypoglycemia and hyperglycemia. In this paper, we propose to synthesize optimal parameters for meal bolus calculation starting from models of the patient’s insulinglucose regulatory system and the infusion pump. Various offtheshelf global optimization techniques are used to search for parameter values that minimize a penalty function defined over the predicted glucose sensor readings. The penalty function “rewards ” glucose levels that lie within the prescribed ranges and “penalizes ” the occurrence of hypoglycemia and hyperglycemia. We evaluate our approach using a model of the insulinglucose regulatory system proposed by Dalla Man et al. Using this model, we compare various strategies for optimizing pump usage parameters for a virtual population of insilico patients. I.
RobustnessGuided Temporal Logic Testing and Verification for Stochastic CyberPhysical Systems
"... Abstract—We present a framework for automatic specificationguided testing for Stochastic CyberPhysical Systems (SCPS). The framework utilizes the theory of robustness of Metric Temporal Logic (MTL) specifications to quantify how robustly an SCPS satisfies a specification in MTL. The goal of the te ..."
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Abstract—We present a framework for automatic specificationguided testing for Stochastic CyberPhysical Systems (SCPS). The framework utilizes the theory of robustness of Metric Temporal Logic (MTL) specifications to quantify how robustly an SCPS satisfies a specification in MTL. The goal of the testing framework is to detect system operating conditions that cause the system to exhibit the worst expected specification robustness. The resulting expected robustness minimization problem is solved using Markov chain Monte Carlo algorithms. This also allows us to use finitetime guarantees, which quantify the quality of the solution after a finite number of simulations. In a ModelBased Design (MBD) process, our framework can be combined with Statistical Model Checking (SMC). Finally, we present a case study on a high fidelity engine model where the goal is to verify EPA standards on the airtofuel ratio. I.
Edinburgh Research Explorer
"... A logic of behaviour in context Citation for published version: ..."
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Computational Modeling, Formal Analysis, and Tools for Systems Biology
, 2016
"... As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biolo ..."
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As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science.
Synthesis of Biological Models from Mutation Experiments
"... Executable biology presents new challenges to formal methods. This paper addresses two problems that cell biologists face when developing formally analyzable models. First, we show how to automatically synthesize a concurrent insilico model for cell development given invivo experiments of how part ..."
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Executable biology presents new challenges to formal methods. This paper addresses two problems that cell biologists face when developing formally analyzable models. First, we show how to automatically synthesize a concurrent insilico model for cell development given invivo experiments of how particular mutations influence the experiment outcome. The problem of synthesis under mutations is unique because mutations may produce nondeterministic outcomes (presumably by introducing races between competing signaling pathways in the cells) and the synthesized model must be able to replay all these outcomes in order to faithfully describe the modeled cellular processes. In contrast, a “regular ” concurrent program is correct if it picks any outcome allowed by the nondeterministic specification. We developed synthesis algorithms and synthesized a model of cell fate determination
2.2. Highlight: Model Reductions as Subgraph Epimorphisms 2
"... c t i v it y e p o r t 2010 Table of contents ..."
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Parameter Synthesis Through Temporal Logic Specifications?
"... Abstract. Parameters are often used to tune mathematical models and capture nondeterminism and uncertainty in physical and engineering systems. This paper is concerned with parametric nonlinear dynamical systems and the problem of determining the parameter values that are consistent with some expect ..."
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Abstract. Parameters are often used to tune mathematical models and capture nondeterminism and uncertainty in physical and engineering systems. This paper is concerned with parametric nonlinear dynamical systems and the problem of determining the parameter values that are consistent with some expected properties. In our previous works, we proposed a parameter synthesis algorithm limited to safety properties and demonstrated its applications for biological systems. Here we consider more general properties specified by a fragment of STL (Signal Temporal Logic), which allows us to deal with complex behavioral patterns that biological processes exhibit. We propose an algorithm for parameter synthesis w.r.t. a property specified using the considered logic. It exploits reachable set computations and forward refinements. We instantiate our algorithm in the case of polynomial dynamical systems exploiting Bernstein coefficients and we illustrate it on an epidemic model.
Cells as Machines: Towards Deciphering Biochemical Programs in the Cell
"... Abstract. Systems biology aims at understanding complex biological processes in terms of their basic mechanisms at the molecular level in cells. The bet of applying theoretical computer science concepts and software engineering methods to the analysis of distributed biochemical reaction systems in t ..."
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Abstract. Systems biology aims at understanding complex biological processes in terms of their basic mechanisms at the molecular level in cells. The bet of applying theoretical computer science concepts and software engineering methods to the analysis of distributed biochemical reaction systems in the cell, designed by natural evolution, has led to interesting challenges in computer science, and new modelbased insights in biology. In this paper, we review the development over the last decade of the biochemical abstract machine (Biocham) software environment for modeling cell biology molecular reaction systems, reasoning about them at different levels of abstraction, formalizing biological behaviors in temporal logic with numerical constraints, and using them to infer nonmeasurable kinetic parameter values, evaluate robustness, decipher natural biochemical processes and implement new programs in synthetic biology. 1