24,479 research outputs found
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
Experiment selection for the discrimination of semi-quantitative models of dynamical systems
AbstractModeling an experimental system often results in a number of alternative models that are all justified by the available experimental data. To discriminate among these models, additional experiments are needed. Existing methods for the selection of discriminatory experiments in statistics and in artificial intelligence are often based on an entropy criterion, the so-called information increment. A limitation of these methods is that they are not well-adapted to discriminating models of dynamical systems under conditions of limited measurability. Moreover, there are no generic procedures for computing the information increment of an experiment when the models are qualitative or semi-quantitative. This has motivated the development of a method for the selection of experiments to discriminate among semi-quantitative models of dynamical systems. The method has been implemented on top of existing implementations of the qualitative and semi-quantitative simulation techniques QSIM, Q2, and Q3. The applicability of the method to real-world problems is illustrated by means of an example in population biology: the discrimination of four competing models of the growth of phytoplankton in a bioreactor. The models have traditionally been considered equivalent for all practical purposes. Using our model discrimination approach and experimental data we show, however, that two of them are superior for describing phytoplankton growth under a wide range of experimental conditions
Data-driven modelling of biological multi-scale processes
Biological processes involve a variety of spatial and temporal scales. A
holistic understanding of many biological processes therefore requires
multi-scale models which capture the relevant properties on all these scales.
In this manuscript we review mathematical modelling approaches used to describe
the individual spatial scales and how they are integrated into holistic models.
We discuss the relation between spatial and temporal scales and the implication
of that on multi-scale modelling. Based upon this overview over
state-of-the-art modelling approaches, we formulate key challenges in
mathematical and computational modelling of biological multi-scale and
multi-physics processes. In particular, we considered the availability of
analysis tools for multi-scale models and model-based multi-scale data
integration. We provide a compact review of methods for model-based data
integration and model-based hypothesis testing. Furthermore, novel approaches
and recent trends are discussed, including computation time reduction using
reduced order and surrogate models, which contribute to the solution of
inference problems. We conclude the manuscript by providing a few ideas for the
development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and
Multiscale Dynamics (American Scientific Publishers
Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems
Approximate Bayesian computation methods can be used to evaluate posterior
distributions without having to calculate likelihoods. In this paper we discuss
and apply an approximate Bayesian computation (ABC) method based on sequential
Monte Carlo (SMC) to estimate parameters of dynamical models. We show that ABC
SMC gives information about the inferability of parameters and model
sensitivity to changes in parameters, and tends to perform better than other
ABC approaches. The algorithm is applied to several well known biological
systems, for which parameters and their credible intervals are inferred.
Moreover, we develop ABC SMC as a tool for model selection; given a range of
different mathematical descriptions, ABC SMC is able to choose the best model
using the standard Bayesian model selection apparatus.Comment: 26 pages, 9 figure
Cooperation, Norms, and Revolutions: A Unified Game-Theoretical Approach
Cooperation is of utmost importance to society as a whole, but is often
challenged by individual self-interests. While game theory has studied this
problem extensively, there is little work on interactions within and across
groups with different preferences or beliefs. Yet, people from different social
or cultural backgrounds often meet and interact. This can yield conflict, since
behavior that is considered cooperative by one population might be perceived as
non-cooperative from the viewpoint of another.
To understand the dynamics and outcome of the competitive interactions within
and between groups, we study game-dynamical replicator equations for multiple
populations with incompatible interests and different power (be this due to
different population sizes, material resources, social capital, or other
factors). These equations allow us to address various important questions: For
example, can cooperation in the prisoner's dilemma be promoted, when two
interacting groups have different preferences? Under what conditions can costly
punishment, or other mechanisms, foster the evolution of norms? When does
cooperation fail, leading to antagonistic behavior, conflict, or even
revolutions? And what incentives are needed to reach peaceful agreements
between groups with conflicting interests?
Our detailed quantitative analysis reveals a large variety of interesting
results, which are relevant for society, law and economics, and have
implications for the evolution of language and culture as well
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