Analysis of signalling pathways using the prism model checker

We describe a new modelling and analysis approach for signal transduction networks in the presence of incomplete data. We illustrate the approach with an example, the RKIP inhibited ERK pathway [1]. Our models are based on high level descriptions of continuous time Markov chains: reactions are modelled as synchronous processes and concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis of queries such as if a concentration reaches a certain level, will it remain at that level thereafter? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable

Learning flexible representations of stochastic processes on graphs

Graph convolutional networks adapt the architecture of convolutional neural networks to learn rich representations of data supported on arbitrary graphs by replacing the convolution operations of convolutional neural networks with graph-dependent linear operations. However, these graph-dependent linear operations are developed for scalar functions supported on undirected graphs. We propose a class of linear operations for stochastic (time-varying) processes on directed (or undirected) graphs to be used in graph convolutional networks. We propose a parameterization of such linear operations using functional calculus to achieve arbitrarily low learning complexity. The proposed approach is shown to model richer behaviors and display greater flexibility in learning representations than product graph methods

On the Catalyzing Effect of Randomness on the Per-Flow Throughput in Wireless Networks

This paper investigates the throughput capacity of a flow crossing a multi-hop wireless network, whose geometry is characterized by general randomness laws including Uniform, Poisson, Heavy-Tailed distributions for both the nodes' densities and the number of hops. The key contribution is to demonstrate \textit{how} the \textit{per-flow throughput} depends on the distribution of 1) the number of nodes $N_j$ inside hops' interference sets, 2) the number of hops $K$, and 3) the degree of spatial correlations. The randomness in both $N_j$'s and $K$ is advantageous, i.e., it can yield larger scalings (as large as $\Theta(n)$) than in non-random settings. An interesting consequence is that the per-flow capacity can exhibit the opposite behavior to the network capacity, which was shown to suffer from a logarithmic decrease in the presence of randomness. In turn, spatial correlations along the end-to-end path are detrimental by a logarithmic term

Model checking probabilistic and stochastic extensions of the pi-calculus

We present an implementation of model checking for probabilistic and stochastic extensions of the pi-calculus, a process algebra which supports modelling of concurrency and mobility. Formal verification techniques for such extensions have clear applications in several domains, including mobile ad-hoc network protocols, probabilistic security protocols and biological pathways. Despite this, no implementation of automated verification exists. Building upon the pi-calculus model checker MMC, we first show an automated procedure for constructing the underlying semantic model of a probabilistic or stochastic pi-calculus process. This can then be verified using existing probabilistic model checkers such as PRISM. Secondly, we demonstrate how for processes of a specific structure a more efficient, compositional approach is applicable, which uses our extension of MMC on each parallel component of the system and then translates the results into a high-level modular description for the PRISM tool. The feasibility of our techniques is demonstrated through a number of case studies from the pi-calculus literature

Analysis of signalling pathways using continuous time Markov chains

We describe a quantitative modelling and analysis approach for signal transduction networks. We illustrate the approach with an example, the RKIP inhibited ERK pathway [CSK+03]. Our models are high level descriptions of continuous time Markov chains: proteins are modelled by synchronous processes and reactions by transitions. Concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis such as what is the probability that if a concentration reaches a certain level, it will remain at that level thereafter? or how does varying a given reaction rate affect that probability? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable

Fractional calculus ties the microscopic and macroscopic scales of complex network dynamics

A two-state master equation based decision making model has been shown to generate phase transitions, to be topologically complex and to manifest temporal complexity through an inverse power-law probability distribution function in the switching times between the two critical states of consensus. These properties are entailed by the fundamental assumption that the network elements in the decision making model imperfectly imitate one another. The process of subordination establishes that a single network element can be described by a fractional master equation whose analytic solution yields the observed inverse power-law probability distribution obtained by numerical integration of the two-state master equation to a high degree of accuracy

A Stochastic Broadcast Pi-Calculus

In this paper we propose a stochastic broadcast PI-calculus which can be used to model server-client based systems where synchronization is always governed by only one participant. Therefore, there is no need to determine the joint synchronization rates. We also take immediate transitions into account which is useful to model behaviors with no impact on the temporal properties of a system. Since immediate transitions may introduce non-determinism, we will show how these non-determinism can be resolved, and as result a valid CTMC will be obtained finally. Also some practical examples are given to show the application of this calculus.Comment: In Proceedings QAPL 2011, arXiv:1107.074

Process Calculi Abstractions for Biology

Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri Nets theory, and some other by stochastic processes. A most recent approach consists in interpreting the living entities as terms of process calculi where the behavior of the represented systems can be inferred by applying syntax-driven rules. A comprehensive picture of the state of the art of the process calculi approach to biological modeling is still missing. This paper goes in the direction of providing such a picture by presenting a comparative survey of the process calculi that have been used and proposed to describe the behavior of living entities. This is the preliminary version of a paper that was published in Algorithmic Bioprocesses. The original publication is available at http://www.springer.com/computer/foundations/book/978-3-540-88868-