Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors

In this paper, we survey five different computational modeling methods. For comparison, we use the activation cycle of G-proteins that regulate cellular signaling events downstream of G-protein-coupled receptors (GPCRs) as a driving example. Starting from an existing Ordinary Differential Equations (ODEs) model, we implement the G-protein cycle in the stochastic Pi-calculus using SPiM, as Petri-nets using Cell Illustrator, in the Kappa Language using Cellucidate, and in Bio-PEPA using the Bio-PEPA eclipse plug in. We also provide a high-level notation to abstract away from communication primitives that may be unfamiliar to the average biologist, and we show how to translate high-level programs into stochastic Pi-calculus processes and chemical reactions.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Interaction and Depth against Nondeterminism in Proof Search

Deep inference is a proof theoretic methodology that generalizes the standard notion of inference of the sequent calculus, whereby inference rules become applicable at any depth inside logical expressions. Deep inference provides more freedom in the design of deductive systems for different logics and a rich combinatoric analysis of proofs. In particular, construction of exponentially shorter analytic proofs becomes possible, however with the cost of a greater nondeterminism than in the sequent calculus. In this paper, we show that the nondeterminism in proof search can be reduced without losing the shorter proofs and without sacrificing proof theoretic cleanliness. For this, we exploit an interaction and depth scheme in the logical expressions. We demonstrate our method on deep inference systems for multiplicative linear logic and classical logic, discuss its proof complexity and its relation to focusing, and present implementations

Nondeterminism and Language Design in Deep Inference

This thesis studies the design of deep-inference deductive systems. In the systems with deep inference, in contrast to traditional proof-theoretic systems, inference rules can be applied at any depth inside logical expressions. Deep applicability of inference rules provides a rich combinatorial analysis of proofs. Deep inference also makes it possible to design deductive systems that are tailored for computer science applications and otherwise provably not expressible. By applying the inference rules deeply, logical expressions can be manipulated starting from their sub-expressions. This way, we can simulate analytic proofs in traditional deductive formalisms. Furthermore, we can also construct much shorter analytic proofs than in these other formalisms. However, deep applicability of inference rules causes much greater nondeterminism in proof construction. This thesis attacks the problem of dealing with nondeterminism in proof search while preserving the shorter proofs that are available thanks to deep inference. By redesigning the deep inference deductive systems, some redundant applications of the inference rules are prevented. By introducing a new technique which reduces nondeterminism, it becomes possible to obtain a more immediate access to shorter proofs, without breaking certain proof theoretical properties such as cutelimination. Different implementations presented in this thesis allow to perform experiments on the techniques that we developed and observe the performance improvements. Within a computation-as-proof-search perspective, we use deepinference deductive systems to develop a common proof-theoretic language to the two fields of planning and concurrency

Labelled Event Structure Semantics of Linear Logic Planning

Labelled event structures is a model of concurrency, where causality between actions is expressed by a partial order and the nondeterminism is expressed by a conflict relation on actions. We present a new approach to linear logic planning where computation is performed as cutfree proof search. We provide a labelled event structure semantics for the planning problems, and establish an explicit correspondence between the cut-free proofs of the planning problems and partial order plans that we extract from proofs. This results in a concurrency theoretic semantics of planning problems. As the underlying formalism, we employ the recently developed calculus of structures. This way, additional proof theoretical properties, that are not available in the sequent calculus presentation of linear logic, become available. We provide an implementation of our approach, and argue that this work is a crucial step for using the methods of concurrency for establishing a meaningful notion of plan equivalence

Reducing Nondeterminism in the Calculus of Structures

The calculus of structures is a proof theoretical formalism which generalizes the sequent calculus with the feature of deep inference: in contrast to the sequent calculus, inference rules can be applied at any depth inside a formula, bringing shorter proofs than all other formalisms supporting analytical proofs. However, deep applicability of inference rules causes greater nondeterminism than in the sequent calculus regarding proof search. In this paper, we introduce a new technique which reduces nondeterminism without breaking proof theoretical properties, and provides a more immediate access to shorter proofs. We present our technique on system BV, the smallest technically non-trivial system in the calculus of structures, extending multiplicative linear logic with the rules mix, nullary mix and a self dual, non-commutative logical operator. Since our technique exploits a scheme common to all the systems in the calculus of structures, we argue that it generalizes to these systems for classical logic, linear logic and modal logics

Reducing Nondeterminism in the Calculus of Structures

The calculus of structures is a proof theoretical formalism which generalizes the sequent calculus with the feature of deep inference: in contrast to the sequent calculus, inference rules can be applied at any depth inside a formula, bringing shorter proofs than all other formalisms supporting analytical proofs. However, deep applicability of inference rules causes greater nondeterminism than in the sequent calculus regarding proof search. In this paper, we introduce a new technique which reduces nondeterminism without breaking proof theoretical properties, and provides a more immediate access to shorter proofs. We present this technique on system BV, the smallest technically non-trivial system in the calculus of structures, extending multiplicative linear logic with the rules mix, nullary mix and a self dual, non-commutative logical operator

Implementing System BV of the Calculus of Structures in Maude

System BV is an extension of multiplicative linear logic with a non-commutative self-dual operator. We first map derivations of system BV of the calculus of structures to rewritings in a term rewriting system modulo equality, and then express this rewriting system as a Maude system module. This results in an automated proof search implementation for this system, and provides a recipe for implementing existing calculus of structures systems for other logics. Our result is interesting from the view of applications, specially, where sequentiality is essential, e.g., planning and natural language processing. In particular, we argue that we can express plans as logical formulae by using the sequential operator of BV and reason on them in a purely logical way

Plans as Formulae with a Non-commutative Logical Operator - Planning as Concurrency

System NEL is a conservative extension of multiplicative exponential linear logic with a self-dual, non-commutative operator. In this paper, we express plans as logical formulae by using this sequential operator

Reducing the Nondeterminism in the Calculus of Structures

The calculus of structures is a proof theoretical formalism which generalizes the sequent calculus with the feature of deep inference: in contrast to the sequent calculus, inference rules can be applied at any depth inside a formula, bringing shorter proofs than all other formalisms supporting analytical proofs. However, deep applicability of inference rules causes greater nondeterminism than in the sequent calculus regarding proof search. In this paper, we introduce a new technique which reduces nondeterminism without breaking proof theoretical properties, and provides a more immediate access to shorter proofs. We present our technique on system BV, the smallest technically non-trivial system in the calculus of structures, extending multiplicative linear logic with the rules mix, nullary mix and a self dual, non-commutative logical operator. Since our technique exploits a scheme common to all the systems in the calculus of structures, we argue that it generalizes to these systems for classical logic, linear logic and modal logics