1,789 research outputs found

    CONJURE: automatic generation of constraint models from problem specifications

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    Funding: Engineering and Physical Sciences Research Council (EP/V027182/1, EP/P015638/1), Royal Society (URF/R/180015).When solving a combinatorial problem, the formulation or model of the problem is critical tothe efficiency of the solver. Automating the modelling process has long been of interest because of the expertise and time required to produce an effective model of a given problem. We describe a method to automatically produce constraint models from a problem specification written in the abstract constraint specification language Essence. Our approach is to incrementally refine the specification into a concrete model by applying a chosen refinement rule at each step. Any nontrivial specification may be refined in multiple ways, creating a space of models to choose from. The handling of symmetries is a particularly important aspect of automated modelling. Many combinatorial optimisation problems contain symmetry, which can lead to redundant search. If a partial assignment is shown to be invalid, we are wasting time if we ever consider a symmetric equivalent of it. A particularly important class of symmetries are those introduced by the constraint modelling process: modelling symmetries. We show how modelling symmetries may be broken automatically as they enter a model during refinement, obviating the need for an expensive symmetry detection step following model formulation. Our approach is implemented in a system called Conjure. We compare the models producedby Conjure to constraint models from the literature that are known to be effective. Our empirical results confirm that Conjure can reproduce successfully the kernels of the constraint models of 42 benchmark problems found in the literature.Publisher PDFPeer reviewe

    When rule-based models need to count

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    Rule-based modelers dislike direct enumeration of cases when more efficient means of enumeration are available. We present an extension of the Kappa language which attaches to agents a notion of level. We detail two encodings that are more concise than the former practice

    Rule-based Modelling and Tunable Resolution

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    We investigate the use of an extension of rule-based modelling for cellular signalling to create a structured space of model variants. This enables the incremental development of rule sets that start from simple mechanisms and which, by a gradual increase in agent and rule resolution, evolve into more detailed descriptions

    An Intuitive Automated Modelling Interface for Systems Biology

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    We introduce a natural language interface for building stochastic pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and transformation. This language thus allows us to model biochemical systems modularly by describing their dynamics in a narrative-style language, while making amendments, refinements and extensions on the models easy. We demonstrate the language on a model of Fc-gamma receptor phosphorylation during phagocytosis. We provide a tool implementation of the translation into a stochastic pi calculus language, Microsoft Research's SPiM

    Exploiting Symmetries When Proving Equivalence Properties for Security Protocols

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    International audienceVerification of privacy-type properties for cryptographic protocols in an active adversarial environment, modelled as a behavioural equivalence in concurrent-process calculi, exhibits a high computational complexity. While undecidable in general, for some classes of common cryptographic primitives the problem is coNEXP-complete when the number of honest participants is bounded.In this paper we develop optimisation techniques for verifying equivalences, exploiting symmetries between the two processes under study. We demonstrate that they provide a significant (several orders of magnitude) speed-up in practice, thus increasing the size of the protocols that can be analysed fully automatically

    Thermodynamic graph-rewriting

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    We develop a new thermodynamic approach to stochastic graph-rewriting. The ingredients are a finite set of reversible graph-rewriting rules called generating rules, a finite set of connected graphs P called energy patterns and an energy cost function. The idea is that the generators define the qualitative dynamics, by showing which transformations are possible, while the energy patterns and cost function specify the long-term probability π\pi of any reachable graph. Given the generators and energy patterns, we construct a finite set of rules which (i) has the same qualitative transition system as the generators; and (ii) when equipped with suitable rates, defines a continuous-time Markov chain of which π\pi is the unique fixed point. The construction relies on the use of site graphs and a technique of `growth policy' for quantitative rule refinement which is of independent interest. This division of labour between the qualitative and long-term quantitative aspects of the dynamics leads to intuitive and concise descriptions for realistic models (see the examples in S4 and S5). It also guarantees thermodynamical consistency (AKA detailed balance), otherwise known to be undecidable, which is important for some applications. Finally, it leads to parsimonious parameterizations of models, again an important point in some applications

    Discovering Knowledge using a Constraint-based Language

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    Discovering pattern sets or global patterns is an attractive issue from the pattern mining community in order to provide useful information. By combining local patterns satisfying a joint meaning, this approach produces patterns of higher level and thus more useful for the data analyst than the usual local patterns, while reducing the number of patterns. In parallel, recent works investigating relationships between data mining and constraint programming (CP) show that the CP paradigm is a nice framework to model and mine such patterns in a declarative and generic way. We present a constraint-based language which enables us to define queries addressing patterns sets and global patterns. The usefulness of such a declarative approach is highlighted by several examples coming from the clustering based on associations. This language has been implemented in the CP framework.Comment: 12 page
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