Simulation-based model selection for dynamical systems in systems and population biology

Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not straightforward. We therefore require suitable statistical tools that allow us to choose rationally between different mechanistic models of e.g. signal transduction or gene regulation networks. This is particularly challenging in systems biology where only a small number of molecular species can be assayed at any given time and all measurements are subject to measurement uncertainty. Here we develop such a model selection framework based on approximate Bayesian computation and employing sequential Monte Carlo sampling. We show that our approach can be applied across a wide range of biological scenarios, and we illustrate its use on real data describing influenza dynamics and the JAK-STAT signalling pathway. Bayesian model selection strikes a balance between the complexity of the simulation models and their ability to describe observed data. The present approach enables us to employ the whole formal apparatus to any system that can be (efficiently) simulated, even when exact likelihoods are computationally intractable.Comment: This article is in press in Bioinformatics, 2009. Advance Access is available on Bioinformatics webpag

Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living things. Mathematical idealisations of biochemically reacting systems must be able to capture stochastic phenomena. While robust theory exists to describe such stochastic models, the computational challenges in exploring these models can be a significant burden in practice since realistic models are analytically intractable. Determining the expected behaviour and variability of a stochastic biochemical reaction network requires many probabilistic simulations of its evolution. Using a biochemical reaction network model to assist in the interpretation of time course data from a biological experiment is an even greater challenge due to the intractability of the likelihood function for determining observation probabilities. These computational challenges have been subjects of active research for over four decades. In this review, we present an accessible discussion of the major historical developments and state-of-the-art computational techniques relevant to simulation and inference problems for stochastic biochemical reaction network models. Detailed algorithms for particularly important methods are described and complemented with MATLAB implementations. As a result, this review provides a practical and accessible introduction to computational methods for stochastic models within the life sciences community

Path Integral Ground State with a Fourth-Order Propagator: Application to Condensed Helium

Ground state properties of condensed Helium are calculated using the Path Integral Ground State (PIGS) method. A fourth-order approximation is used as short (imaginary) time propagator. We compare our results with those obtained with other Quantum Monte Carlo techniques and different propagators. For this particular application, we find that the fourth-order propagator performs comparably to the pair product approximation, and is far superior to the primitive approximation. Results obtained for the equation of state of condensed Helium show that PIGS compares favorably to other QMC methods traditionally utilized for this type of calculation

Stochastic simulation algorithm for the quantum linear Boltzmann equation

We develop a Monte Carlo wave function algorithm for the quantum linear Boltzmann equation, a Markovian master equation describing the quantum motion of a test particle interacting with the particles of an environmental background gas. The algorithm leads to a numerically efficient stochastic simulation procedure for the most general form of this integro-differential equation, which involves a five-dimensional integral over microscopically defined scattering amplitudes that account for the gas interactions in a non-perturbative fashion. The simulation technique is used to assess various limiting forms of the quantum linear Boltzmann equation, such as the limits of pure collisional decoherence and quantum Brownian motion, the Born approximation and the classical limit. Moreover, we extend the method to allow for the simulation of the dissipative and decohering dynamics of superpositions of spatially localized wave packets, which enables the study of many physically relevant quantum phenomena, occurring e.g. in the interferometry of massive particles.Comment: 21 pages, 9 figures; v2: corresponds to published versio