29,151 research outputs found
Modeling biological systems with delays in Bio-PEPA
Delays in biological systems may be used to model events for which the
underlying dynamics cannot be precisely observed, or to provide abstraction of
some behavior of the system resulting more compact models. In this paper we
enrich the stochastic process algebra Bio-PEPA, with the possibility of
assigning delays to actions, yielding a new non-Markovian process algebra:
Bio-PEPAd. This is a conservative extension meaning that the original syntax of
Bio-PEPA is retained and the delay specification which can now be associated
with actions may be added to existing Bio-PEPA models. The semantics of the
firing of the actions with delays is the delay-as-duration approach, earlier
presented in papers on the stochastic simulation of biological systems with
delays. These semantics of the algebra are given in the Starting-Terminating
style, meaning that the state and the completion of an action are observed as
two separate events, as required by delays. Furthermore we outline how to
perform stochastic simulation of Bio-PEPAd systems and how to automatically
translate a Bio-PEPAd system into a set of Delay Differential Equations, the
deterministic framework for modeling of biological systems with delays. We end
the paper with two example models of biological systems with delays to
illustrate the approach.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005
Reductions of Hidden Information Sources
In all but special circumstances, measurements of time-dependent processes
reflect internal structures and correlations only indirectly. Building
predictive models of such hidden information sources requires discovering, in
some way, the internal states and mechanisms. Unfortunately, there are often
many possible models that are observationally equivalent. Here we show that the
situation is not as arbitrary as one would think. We show that generators of
hidden stochastic processes can be reduced to a minimal form and compare this
reduced representation to that provided by computational mechanics--the
epsilon-machine. On the way to developing deeper, measure-theoretic foundations
for the latter, we introduce a new two-step reduction process. The first step
(internal-event reduction) produces the smallest observationally equivalent
sigma-algebra and the second (internal-state reduction) removes sigma-algebra
components that are redundant for optimal prediction. For several classes of
stochastic dynamical systems these reductions produce representations that are
equivalent to epsilon-machines.Comment: 12 pages, 4 figures; 30 citations; Updates at
http://www.santafe.edu/~cm
Process algebra for performance evaluation
This paper surveys the theoretical developments in the field of stochastic process algebras, process algebras where action occurrences may be subject to a delay that is determined by a random variable. A huge class of resource-sharing systems – like large-scale computers, client–server architectures, networks – can accurately be described using such stochastic specification formalisms. The main emphasis of this paper is the treatment of operational semantics, notions of equivalence, and (sound and complete) axiomatisations of these equivalences for different types of Markovian process algebras, where delays are governed by exponential distributions. Starting from a simple actionless algebra for describing time-homogeneous continuous-time Markov chains, we consider the integration of actions and random delays both as a single entity (like in known Markovian process algebras like TIPP, PEPA and EMPA) and as separate entities (like in the timed process algebras timed CSP and TCCS). In total we consider four related calculi and investigate their relationship to existing Markovian process algebras. We also briefly indicate how one can profit from the separation of time and actions when incorporating more general, non-Markovian distributions
GSOS for non-deterministic processes with quantitative aspects
Recently, some general frameworks have been proposed as unifying theories for
processes combining non-determinism with quantitative aspects (such as
probabilistic or stochastically timed executions), aiming to provide general
results and tools. This paper provides two contributions in this respect.
First, we present a general GSOS specification format (and a corresponding
notion of bisimulation) for non-deterministic processes with quantitative
aspects. These specifications define labelled transition systems according to
the ULTraS model, an extension of the usual LTSs where the transition relation
associates any source state and transition label with state reachability weight
functions (like, e.g., probability distributions). This format, hence called
Weight Function SOS (WFSOS), covers many known systems and their bisimulations
(e.g. PEPA, TIPP, PCSP) and GSOS formats (e.g. GSOS, Weighted GSOS,
Segala-GSOS, among others).
The second contribution is a characterization of these systems as coalgebras
of a class of functors, parametric on the weight structure. This result allows
us to prove soundness of the WFSOS specification format, and that
bisimilarities induced by these specifications are always congruences.Comment: In Proceedings QAPL 2014, arXiv:1406.156
Process algebra modelling styles for biomolecular processes
We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed
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