Bisimulation of Labelled State-to-Function Transition Systems Coalgebraically

Labeled state-to-function transition systems, FuTS for short, are characterized by transitions which relate states to functions of states over general semirings, equipped with a rich set of higher-order operators. As such, FuTS constitute a convenient modeling instrument to deal with process languages and their quantitative extensions in particular. In this paper, the notion of bisimulation induced by a FuTS is addressed from a coalgebraic point of view. A correspondence result is established stating that FuTS-bisimilarity coincides with behavioural equivalence of the associated functor. As generic examples, the equivalences underlying substantial fragments of major examples of quantitative process algebras are related to the bisimilarity of specific FuTS. The examples range from a stochastic process language, PEPA, to a language for Interactive Markov Chains, IML, a (discrete) timed process language, TPC, and a language for Markov Automata, MAL. The equivalences underlying these languages are related to the bisimilarity of their specific FuTS. By the correspondence result coalgebraic justification of the equivalences of these calculi is obtained. The specific selection of languages, besides covering a large variety of process interaction models and modelling choices involving quantities, allows us to show different classes of FuTS, namely so-called simple FuTS, combined FuTS, nested FuTS, and general FuTS

Logical Characterization of Bisimulation for Transition Relations over Probability Distributions with Internal Actions

In recent years the study of probabilistic transition systems has shifted to transition relations over distributions to allow for a smooth adaptation of the standard non-probabilistic apparatus. In this paper we study transition relations over probability distributions in a setting with internal actions. We provide new logics that characterize probabilistic strong, weak and branching bisimulation. Because these semantics may be considered too strong in the probabilistic context, Eisentraut et al. recently proposed weak distribution bisimulation. To show the flexibility of our approach based on the framework of van Glabbeek for the non-deterministic setting, we provide a novel logical characterization for the latter probabilistic equivalence as well

Rooted branching bisimulation as a congruence for probabilistic transition systems

Ponencia presentada en el 13 International Workshop on Quantitative Aspects of Programming Languages and Systems. London, United Kingdom, April 11-12, 2015.We propose a probabilistic transition system specification format, referred to as probabilistic RBB safe, for which rooted branching bisimulation is a congruence. The congruence theorem is based on the approach of Fokkink for the qualitative case. For this to work, the theory of transition system specifications in the setting of labeled transition systems needs to be extended to deal with probability distributions, both syntactically and semantically. We provide a scheduler-free characterization of probabilistic branching bisimulation as adapted from work of Andova et al. for the alternating model. Counter examples are given to justify the various conditions required by the format.Fil: Lee, Matías David. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomía y Física; Argentina.Fil: De Vink, Erik P. Eindhoven University of Technology; The Netherlands.Fil: De Vink, Erik P. Centrum Wiskunde & Informatica; The Netherlands.Ciencias de la Computació

Modelling and analysing software in mCRL2

Model checking is an effective way to design correct software.Making behavioural models of software, formulating correctness properties using modal formulas, and verifying these using finite state analysis techniques, is a very efficient way to obtain the required insight in the software. We illustrate this on four common but tricky examples

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

Programmable models of growth and mutation of cancer-cell populations

In this paper we propose a systematic approach to construct mathematical models describing populations of cancer-cells at different stages of disease development. The methodology we propose is based on stochastic Concurrent Constraint Programming, a flexible stochastic modelling language. The methodology is tested on (and partially motivated by) the study of prostate cancer. In particular, we prove how our method is suitable to systematically reconstruct different mathematical models of prostate cancer growth - together with interactions with different kinds of hormone therapy - at different levels of refinement.Comment: In Proceedings CompMod 2011, arXiv:1109.104

A Study of the PDGF Signaling Pathway with PRISM

In this paper, we apply the probabilistic model checker PRISM to the analysis of a biological system -- the Platelet-Derived Growth Factor (PDGF) signaling pathway, demonstrating in detail how this pathway can be analyzed in PRISM. We show that quantitative verification can yield a better understanding of the PDGF signaling pathway.Comment: In Proceedings CompMod 2011, arXiv:1109.104

Decoupled execution of synchronous coordination models via behavioural automata

Synchronous coordination systems allow the exchange of data by logically indivisible actions involving all coordinated entities. This paper introduces behavioural automata, a logically synchronous coordination model based on the Reo coordination language, which focuses on relevant aspects for the concurrent evolution of these systems. We show how our automata model encodes the Reo and Linda coordination models and how it introduces an explicit predicate that captures the concurrent evolution, distinguishing local from global actions, and lifting the need of most synchronous models to involve all entities at each coordination step, paving the way to more scalable implementations.Comment: In Proceedings FOCLASA 2011, arXiv:1107.584

Endothelial Surface Layer Degradation by Chronic Hyaluronidase Infusion Induces Proteinuria in Apolipoprotein E-Deficient Mice

Functional studies show that disruption of endothelial surface layer (ESL) is accompanied by enhanced sensitivity of the vasculature towards atherogenic stimuli. However, relevance of ESL disruption as causal mechanism for vascular dysfunction remains to be demonstrated. We examined if loss of ESL through enzymatic degradation would affect vascular barrier properties in an atherogenic model. Eight week old male apolipoprotein E deficient mice on Western-type diet for 10 weeks received continuous active or heat-inactivated hyaluronidase (10 U/hr, i.v.) through an osmotic minipump during 4 weeks. Blood chemistry and anatomic changes in both macrovasculature and kidneys were examined. Infusion with active hyaluronidase resulted in decreased ESL (0.32±0.22 mL) and plasma volume (1.03±0.18 mL) compared to inactivated hyaluronidase (0.52±0.29 mL and 1.28±0.08 mL, p<0.05 respectively).Active hyaluronidase increased proteinuria compared to inactive hyaluronidase (0.27±0.02 vs. 0.15±0.01 µg/µg protein/creatinin, p<0.05) without changes in glomerular morphology or development of tubulo-interstitial inflammation. Atherosclerotic lesions in the aortic branches showed increased matrix production (collagen, 32±5 vs. 18±3%; glycosaminoglycans, 11±5 vs. 0.1±0.01%, active vs. inactive hyaluronidase, p<0.05). ESL degradation in apoE deficient mice contributes to reduced increased urinary protein excretion without significant changes in renal morphology. Second, the induction of compositional changes in atherogenic plaques by hyaluronidase point towards increased plaque vulnerability. These findings support further efforts to evaluate whether ESL restoration is a valuable target to prevent (micro) vascular disease progressio