Algebra, coalgebra, and minimization in polynomial differential equations

We consider reasoning and minimization in systems of polynomial ordinary differential equations (ode's). The ring of multivariate polynomials is employed as a syntax for denoting system behaviours. We endow this set with a transition system structure based on the concept of Lie-derivative, thus inducing a notion of L-bisimulation. We prove that two states (variables) are L-bisimilar if and only if they correspond to the same solution in the ode's system. We then characterize L-bisimilarity algebraically, in terms of certain ideals in the polynomial ring that are invariant under Lie-derivation. This characterization allows us to develop a complete algorithm, based on building an ascending chain of ideals, for computing the largest L-bisimulation containing all valid identities that are instances of a user-specified template. A specific largest L-bisimulation can be used to build a reduced system of ode's, equivalent to the original one, but minimal among all those obtainable by linear aggregation of the original equations. A computationally less demanding approximate reduction and linearization technique is also proposed.Comment: 27 pages, extended and revised version of FOSSACS 2017 pape

Efficient and Modular Coalgebraic Partition Refinement

We present a generic partition refinement algorithm that quotients coalgebraic systems by behavioural equivalence, an important task in system analysis and verification. Coalgebraic generality allows us to cover not only classical relational systems but also, e.g. various forms of weighted systems and furthermore to flexibly combine existing system types. Under assumptions on the type functor that allow representing its finite coalgebras in terms of nodes and edges, our algorithm runs in time $\mathcal{O}(m\cdot \log n)$ where $n$ and $m$ are the numbers of nodes and edges, respectively. The generic complexity result and the possibility of combining system types yields a toolbox for efficient partition refinement algorithms. Instances of our generic algorithm match the run-time of the best known algorithms for unlabelled transition systems, Markov chains, deterministic automata (with fixed alphabets), Segala systems, and for color refinement.Comment: Extended journal version of the conference paper arXiv:1705.08362. Beside reorganization of the material, the introductory section 3 is entirely new and the other new section 7 contains new mathematical result

Coalgebra Encoding for Efficient Minimization

Recently, we have developed an efficient generic partition refinement algorithm, which computes behavioural equivalence on a state-based system given as an encoded coalgebra, and implemented it in the tool CoPaR. Here we extend this to a fully fledged minimization algorithm and tool by integrating two new aspects: (1) the computation of the transition structure on the minimized state set, and (2) the computation of the reachable part of the given system. In our generic coalgebraic setting these two aspects turn out to be surprisingly non-trivial requiring us to extend the previous theory. In particular, we identify a sufficient condition on encodings of coalgebras, and we show how to augment the existing interface, which encapsulates computations that are specific for the coalgebraic type functor, to make the above extensions possible. Both extensions have linear run time

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

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/

Conditional Transition Systems with Upgrades

We introduce a variant of transition systems, where activation of transitions depends on conditions of the environment and upgrades during runtime potentially create additional transitions. Using a cornerstone result in lattice theory, we show that such transition systems can be modelled in two ways: as conditional transition systems (CTS) with a partial order on conditions, or as lattice transition systems (LaTS), where transitions are labelled with the elements from a distributive lattice. We define equivalent notions of bisimilarity for both variants and characterise them via a bisimulation game. We explain how conditional transition systems are related to featured transition systems for the modelling of software product lines. Furthermore, we show how to compute bisimilarity symbolically via BDDs by defining an operation on BDDs that approximates an element of a Boolean algebra into a lattice. We have implemented our procedure and provide runtime results

Efficient Coalgebraic Partition Refinement

We present a generic partition refinement algorithm that quotients coalgebraic systems by behavioural equivalence, an important task in reactive verification; coalgebraic generality implies in particular that we cover not only classical relational systems but also various forms of weighted systems. Under assumptions on the type functor that allow representing its finite coalgebras in terms of nodes and edges, our algorithm runs in time O(m log n) where n and m are the numbers of nodes and edges, respectively. Instances of our generic algorithm thus match the runtime of the best known algorithms for unlabelled transition systems, Markov chains, and deterministic automata (with fixed alphabets), and improve the best known algorithms for Segala systems