Extended Differential Aggregations in Process Algebra for Performance and Biology

We study aggregations for ordinary differential equations induced by fluid semantics for Markovian process algebra which can capture the dynamics of performance models and chemical reaction networks. Whilst previous work has required perfect symmetry for exact aggregation, we present approximate fluid lumpability, which makes nearby processes perfectly symmetric after a perturbation of their parameters. We prove that small perturbations yield nearby differential trajectories. Numerically, we show that many heterogeneous processes can be aggregated with negligible errors.Comment: In Proceedings QAPL 2014, arXiv:1406.156

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

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

Syntactic Markovian Bisimulation for Chemical Reaction Networks

In chemical reaction networks (CRNs) with stochastic semantics based on continuous-time Markov chains (CTMCs), the typically large populations of species cause combinatorially large state spaces. This makes the analysis very difficult in practice and represents the major bottleneck for the applicability of minimization techniques based, for instance, on lumpability. In this paper we present syntactic Markovian bisimulation (SMB), a notion of bisimulation developed in the Larsen-Skou style of probabilistic bisimulation, defined over the structure of a CRN rather than over its underlying CTMC. SMB identifies a lumpable partition of the CTMC state space a priori, in the sense that it is an equivalence relation over species implying that two CTMC states are lumpable when they are invariant with respect to the total population of species within the same equivalence class. We develop an efficient partition-refinement algorithm which computes the largest SMB of a CRN in polynomial time in the number of species and reactions. We also provide an algorithm for obtaining a quotient network from an SMB that induces the lumped CTMC directly, thus avoiding the generation of the state space of the original CRN altogether. In practice, we show that SMB allows significant reductions in a number of models from the literature. Finally, we study SMB with respect to the deterministic semantics of CRNs based on ordinary differential equations (ODEs), where each equation gives the time-course evolution of the concentration of a species. SMB implies forward CRN bisimulation, a recently developed behavioral notion of equivalence for the ODE semantics, in an analogous sense: it yields a smaller ODE system that keeps track of the sums of the solutions for equivalent species.Comment: Extended version (with proofs), of the corresponding paper published at KimFest 2017 (http://kimfest.cs.aau.dk/

Fluid aggregations for Markovian process algebra

Quantitative analysis by means of discrete-state stochastic processes is hindered by the well-known phenomenon of state-space explosion, whereby the size of the state space may have an exponential growth with the number of objects in the model. When the stochastic process underlies a Markovian process algebra model, this problem may be alleviated by suitable notions of behavioural equivalence that induce lumping at the underlying continuous-time Markov chain, establishing an exact relation between a potentially much smaller aggregated chain and the original one. However, in the modelling of massively distributed computer systems, even aggregated chains may be still too large for efficient numerical analysis. Recently this problem has been addressed by fluid techniques, where the Markov chain is approximated by a system of ordinary differential equations (ODEs) whose size does not depend on the number of the objects in the model. The technique has been primarily applied in the case of massively replicated sequential processes with small local state space sizes. This thesis devises two different approaches that broaden the scope of applicability of efficient fluid approximations. Fluid lumpability applies in the case where objects are composites of simple objects, and aggregates the potentially massive, naively constructed ODE system into one whose size is independent from the number of composites in the model. Similarly to quasi and near lumpability, we introduce approximate fluid lumpability that covers ODE systems which can be aggregated after a small perturbation in the parameters. The technique of spatial aggregation, instead, applies to models whose objects perform a random walk on a two-dimensional lattice. Specifically, it is shown that the underlying ODE system, whose size is proportional to the number of the regions, converges to a system of partial differential equations of constant size as the number of regions goes to infinity. This allows for an efficient analysis of large-scale mobile models in continuous space like ad hoc networks and multi-agent systems

An Aggregation Technique for Large-Scale PEPA Models with Non-Uniform Populations

Performance analysis based on modelling consists of two major steps: model construction and model analysis. Formal modelling techniques significantly aid model construction but can exacerbate model analysis. In particular, here we consider the analysis of large-scale systems which consist of one or more entities replicated many times to form large populations. The replication of entities in such models can cause their state spaces to grow exponentially to the extent that their exact stochastic analysis becomes computationally expensive or even infeasible. In this paper, we propose a new approximate aggregation algorithm for a class of large-scale PEPA models. For a given model, the method quickly checks if it satisfies a syntactic condition, indicating that the model may be solved approximately with high accuracy. If so, an aggregated CTMC is generated directly from the model description. This CTMC can be used for efficient derivation of an approximate marginal probability distribution over some of the model's populations. In the context of a large-scale client-server system, we demonstrate the usefulness of our method

Symbolic Computation of Differential Equivalences

Ordinary differential equations (ODEs) are widespread in manynatural sciences including chemistry, ecology, and systems biology,and in disciplines such as control theory and electrical engineering. Building on the celebrated molecules-as-processes paradigm, they have become increasingly popular in computer science, with high-level languages and formal methods such as Petri nets, process algebra, and rule-based systems that are interpreted as ODEs. We consider the problem of comparing and minimizing ODEs automatically. Influenced by traditional approaches in the theory of programming, we propose differential equivalence relations. We study them for a basic intermediate language, for which we have decidability results, that can be targeted by a class of high-level specifications. An ODE implicitly represents an uncountable state space, hence reasoning techniques cannot be borrowed from established domains such as probabilistic programs with finite-state Markov chain semantics. We provide novel symbolic procedures to check an equivalence and compute the largest one via partition refinement algorithms that use satisfiability modulo theories. We illustrate the generality of our framework by showing that differential equivalences include (i) well-known notions for the minimization of continuous-time Markov chains (lumpability),(ii) bisimulations for chemical reaction networks recently proposedby Cardelli et al., and (iii) behavioral relations for process algebra with ODE semantics. With a prototype implementation we are able to detect equivalences in biochemical models from the literature thatcannot be reduced using competing automatic techniques

Fluid aggregations for Markovian process algebra

Quantitative analysis by means of discrete-state stochastic processes is hindered by the well-known phenomenon of state-space explosion, whereby the size of the state space may have an exponential growth with the number of objects in the model. When the stochastic process underlies a Markovian process algebra model, this problem may be alleviated by suitable notions of behavioural equivalence that induce lumping at the underlying continuous-time Markov chain, establishing an exact relation between a potentially much smaller aggregated chain and the original one. However, in the modelling of massively distributed computer systems, even aggregated chains may be still too large for efficient numerical analysis. Recently this problem has been addressed by fluid techniques, where the Markov chain is approximated by a system of ordinary differential equations (ODEs) whose size does not depend on the number of the objects in the model. The technique has been primarily applied in the case of massively replicated sequential processes with small local state space sizes. This thesis devises two different approaches that broaden the scope of applicability of efficient fluid approximations. Fluid lumpability applies in the case where objects are composites of simple objects, and aggregates the potentially massive, naively constructed ODE system into one whose size is independent from the number of composites in the model. Similarly to quasi and near lumpability, we introduce approximate fluid lumpability that covers ODE systems which can be aggregated after a small perturbation in the parameters. The technique of spatial aggregation, instead, applies to models whose objects perform a random walk on a two-dimensional lattice. Specifically, it is shown that the underlying ODE system, whose size is proportional to the number of the regions, converges to a system of partial differential equations of constant size as the number of regions goes to infinity. This allows for an efficient analysis of large-scale mobile models in continuous space like ad hoc networks and multi-agent systems

On approximating the stochastic behaviour of Markovian process algebra models

Markov chains offer a rigorous mathematical framework to describe systems that exhibit stochastic behaviour, as they are supported by a plethora of methodologies to analyse their properties. Stochastic process algebras are high-level formalisms, where systems are represented as collections of interacting components. This compositional approach to modelling allows us to describe complex Markov chains using a compact high-level specification. There is an increasing need to investigate the properties of complex systems, not only in the field of computer science, but also in computational biology. To explore the stochastic properties of large Markov chains is a demanding task in terms of computational resources. Approximating the stochastic properties can be an effective way to deal with the complexity of large models. In this thesis, we investigate methodologies to approximate the stochastic behaviour of Markovian process algebra models. The discussion revolves around two main topics: approximate state-space aggregation and stochastic simulation. Although these topics are different in nature, they are both motivated by the need to efficiently handle complex systems. Approximate Markov chain aggregation constitutes the formulation of a smaller Markov chain that approximates the behaviour of the original model. The principal hypothesis is that states that can be characterised as equivalent can be adequately represented as a single state. We discuss different notions of approximate state equivalence, and how each of these can be used as a criterion to partition the state-space accordingly. Nevertheless, approximate aggregation methods typically require an explicit representation of the transition matrix, a fact that renders them impractical for large models. We propose a compositional approach to aggregation, as a means to efficiently approximate complex Markov models that are defined in a process algebra specification, PEPA in particular. Regarding our contributions to Markov chain simulation, we propose an accelerated method that can be characterised as almost exact, in the sense that it can be arbitrarily precise. We discuss how it is possible to sample from the trajectory space rather than the transition space. This approach requires fewer random samples than a typical simulation algorithm. Most importantly, our approach does not rely on particular assumptions with respect to the model properties, in contrast to otherwise more efficient approaches