Forward and Backward Bisimulations for Chemical Reaction Networks

We present two quantitative behavioral equivalences over species of a chemical reaction network (CRN) with semantics based on ordinary differential equations. Forward CRN bisimulation identifies a partition where each equivalence class represents the exact sum of the concentrations of the species belonging to that class. Backward CRN bisimulation relates species that have the identical solutions at all time points when starting from the same initial conditions. Both notions can be checked using only CRN syntactical information, i.e., by inspection of the set of reactions. We provide a unified algorithm that computes the coarsest refinement up to our bisimulations in polynomial time. Further, we give algorithms to compute quotient CRNs induced by a bisimulation. As an application, we find significant reductions in a number of models of biological processes from the literature. In two cases we allow the analysis of benchmark models which would be otherwise intractable due to their memory requirements.Comment: Extended version of the CONCUR 2015 pape

Sigref – A Symbolic Bisimulation Tool Box

We present a uniform signature-based approach to compute the most popular bisimulations. Our approach is implemented symbolically using BDDs, which enables the handling of very large transition systems. Signatures for the bisimulations are built up from a few generic building blocks, which naturally correspond to efficient BDD operations. Thus, the definition of an appropriate signature is the key for a rapid development of algorithms for other types of bisimulation. We provide experimental evidence of the viability of this approach by presenting computational results for many bisimulations on real-world instances. The experiments show cases where our framework can handle state spaces efficiently that are far too large to handle for any tool that requires an explicit state space description. This work was partly supported by the German Research Council (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS). See www.avacs.org for more information

Probabilistic Bisimulations for PCTL Model Checking of Interval MDPs

Verification of PCTL properties of MDPs with convex uncertainties has been investigated recently by Puggelli et al. However, model checking algorithms typically suffer from state space explosion. In this paper, we address probabilistic bisimulation to reduce the size of such an MDPs while preserving PCTL properties it satisfies. We discuss different interpretations of uncertainty in the models which are studied in the literature and that result in two different definitions of bisimulations. We give algorithms to compute the quotients of these bisimulations in time polynomial in the size of the model and exponential in the uncertain branching. Finally, we show by a case study that large models in practice can have small branching and that a substantial state space reduction can be achieved by our approach.Comment: In Proceedings SynCoP 2014, arXiv:1403.784

Language-based Abstractions for Dynamical Systems

Ordinary differential equations (ODEs) are the primary means to modelling dynamical systems in many natural and engineering sciences. The number of equations required to describe a system with high heterogeneity limits our capability of effectively performing analyses. This has motivated a large body of research, across many disciplines, into abstraction techniques that provide smaller ODE systems while preserving the original dynamics in some appropriate sense. In this paper we give an overview of a recently proposed computer-science perspective to this problem, where ODE reduction is recast to finding an appropriate equivalence relation over ODE variables, akin to classical models of computation based on labelled transition systems.Comment: In Proceedings QAPL 2017, arXiv:1707.0366

The Glory of the Past and Geometrical Concurrency

This paper contributes to the general understanding of the geometrical model of concurrency that was named higher dimensional automata (HDAs) by Pratt. In particular we investigate modal logics for such models and their expressive power in terms of the bisimulation that can be captured. The geometric model of concurrency is interesting from two main reasons: its generality and expressiveness, and the natural way in which autoconcurrency and action refinement are captured. Logics for this model, though, are not well investigated, where a simple, yet adequate, modal logic over HDAs was only recently introduced. As this modal logic, with two existential modalities, during and after, captures only split bisimulation, which is rather low in the spectrum of van Glabbeek and Vaandrager, the immediate question was what small extension of this logic could capture the more fine-grained hereditary history preserving bisimulation (hh)? In response, the work in this paper provides several insights. One is the fact that the geometrical aspect of HDAs makes it possible to use for capturing the hh-bisimulation, a standard modal logic that does not employ event variables, opposed to the two logics (over less expressive models) that we compare with. The logic that we investigate here uses standard past modalities and extends the previously introduced logic (called HDML) that had only forward, action-labelled, modalities. Besides, we try to understand better the above issues by introducing a related model that we call ST-configuration structures, which extend the configuration structures of van Glabbeek and Plotkin. We relate this model to HDAs, and redefine and prove the earlier results in the light of this new model. These offer a different view on why the past modalities and geometrical concurrency capture the hereditary history preserving bisimulation. Additional correlating insights are also gained.Comment: 17 pages, 7 figure

Challenges in Quantitative Abstractions for Collective Adaptive Systems

Like with most large-scale systems, the evaluation of quantitative properties of collective adaptive systems is an important issue that crosscuts all its development stages, from design (in the case of engineered systems) to runtime monitoring and control. Unfortunately it is a difficult problem to tackle in general, due to the typically high computational cost involved in the analysis. This calls for the development of appropriate quantitative abstraction techniques that preserve most of the system's dynamical behaviour using a more compact representation. This paper focuses on models based on ordinary differential equations and reviews recent results where abstraction is achieved by aggregation of variables, reflecting on the shortcomings in the state of the art and setting out challenges for future research.Comment: In Proceedings FORECAST 2016, arXiv:1607.0200

On Bisimulations for Description Logics

We study bisimulations for useful description logics. The simplest among the considered logics is $\mathcal{ALC}_{reg}$ (a variant of PDL). The others extend that logic with inverse roles, nominals, quantified number restrictions, the universal role, and/or the concept constructor for expressing the local reflexivity of a role. They also allow role axioms. We give results about invariance of concepts, TBoxes and ABoxes, preservation of RBoxes and knowledge bases, and the Hennessy-Milner property w.r.t. bisimulations in the considered description logics. Using the invariance results we compare the expressiveness of the considered description logics w.r.t. concepts, TBoxes and ABoxes. Our results about separating the expressiveness of description logics are naturally extended to the case when instead of $\mathcal{ALC}_{reg}$ we have any sublogic of $\mathcal{ALC}_{reg}$ that extends $\mathcal{ALC}$. We also provide results on the largest auto-bisimulations and quotient interpretations w.r.t. such equivalence relations. Such results are useful for minimizing interpretations and concept learning in description logics. To deal with minimizing interpretations for the case when the considered logic allows quantified number restrictions and/or the constructor for the local reflexivity of a role, we introduce a new notion called QS-interpretation, which is needed for obtaining expected results. By adapting Hopcroft's automaton minimization algorithm and the Paige-Tarjan algorithm, we give efficient algorithms for computing the partition corresponding to the largest auto-bisimulation of a finite interpretation.Comment: 42 page

Reverse Bisimulations on Stable Configuration Structures

The relationships between various equivalences on configuration structures, including interleaving bisimulation (IB), step bisimulation (SB) and hereditary history-preserving (HH) bisimulation, have been investigated by van Glabbeek and Goltz (and later Fecher). Since HH bisimulation may be characterised by the use of reverse as well as forward transitions, it is of interest to investigate forms of IB and SB where both forward and reverse transitions are allowed. We give various characterisations of reverse SB, showing that forward steps do not add extra power. We strengthen Bednarczyk's result that, in the absence of auto-concurrency, reverse IB is as strong as HH bisimulation, by showing that we need only exclude auto-concurrent events at the same depth in the configuration

A coalgebraic semantics for causality in Petri nets

In this paper we revisit some pioneering efforts to equip Petri nets with compact operational models for expressing causality. The models we propose have a bisimilarity relation and a minimal representative for each equivalence class, and they can be fully explained as coalgebras on a presheaf category on an index category of partial orders. First, we provide a set-theoretic model in the form of a a causal case graph, that is a labeled transition system where states and transitions represent markings and firings of the net, respectively, and are equipped with causal information. Most importantly, each state has a poset representing causal dependencies among past events. Our first result shows the correspondence with behavior structure semantics as proposed by Trakhtenbrot and Rabinovich. Causal case graphs may be infinitely-branching and have infinitely many states, but we show how they can be refined to get an equivalent finitely-branching model. In it, states are equipped with symmetries, which are essential for the existence of a minimal, often finite-state, model. The next step is constructing a coalgebraic model. We exploit the fact that events can be represented as names, and event generation as name generation. Thus we can apply the Fiore-Turi framework: we model causal relations as a suitable category of posets with action labels, and generation of new events with causal dependencies as an endofunctor on this category. Then we define a well-behaved category of coalgebras. Our coalgebraic model is still infinite-state, but we exploit the equivalence between coalgebras over a class of presheaves and History Dependent automata to derive a compact representation, which is equivalent to our set-theoretical compact model. Remarkably, state reduction is automatically performed along the equivalence.Comment: Accepted by Journal of Logical and Algebraic Methods in Programmin