A Low Dimensional Approximation For Competence In Bacillus Subtilis

The behaviour of a high dimensional stochastic system described by a Chemical Master Equation (CME) depends on many parameters, rendering explicit simulation an inefficient method for exploring the properties of such models. Capturing their behaviour by low-dimensional models makes analysis of system behaviour tractable. In this paper, we present low dimensional models for the noise-induced excitable dynamics in Bacillus subtilis, whereby a key protein ComK, which drives a complex chain of reactions leading to bacterial competence, gets expressed rapidly in large quantities (competent state) before subsiding to low levels of expression (vegetative state). These rapid reactions suggest the application of an adiabatic approximation of the dynamics of the regulatory model that, however, lead to competence durations that are incorrect by a factor of 2. We apply a modified version of an iterative functional procedure that faithfully approximates the time-course of the trajectories in terms of a 2-dimensional model involving proteins ComK and ComS. Furthermore, in order to describe the bimodal bivariate marginal probability distribution obtained from the Gillespie simulations of the CME, we introduce a tunable multiplicative noise term in a 2-dimensional Langevin model whose stationary state is described by the time-independent solution of the corresponding Fokker-Planck equation.Comment: 12 pages, to be published in IEEE/ACM Transactions on Computational Biology and Bioinformatic

Scalable Population Synthesis with Deep Generative Modeling

Population synthesis is concerned with the generation of synthetic yet realistic representations of populations. It is a fundamental problem in the modeling of transport where the synthetic populations of micro-agents represent a key input to most agent-based models. In this paper, a new methodological framework for how to 'grow' pools of micro-agents is presented. The model framework adopts a deep generative modeling approach from machine learning based on a Variational Autoencoder (VAE). Compared to the previous population synthesis approaches, including Iterative Proportional Fitting (IPF), Gibbs sampling and traditional generative models such as Bayesian Networks or Hidden Markov Models, the proposed method allows fitting the full joint distribution for high dimensions. The proposed methodology is compared with a conventional Gibbs sampler and a Bayesian Network by using a large-scale Danish trip diary. It is shown that, while these two methods outperform the VAE in the low-dimensional case, they both suffer from scalability issues when the number of modeled attributes increases. It is also shown that the Gibbs sampler essentially replicates the agents from the original sample when the required conditional distributions are estimated as frequency tables. In contrast, the VAE allows addressing the problem of sampling zeros by generating agents that are virtually different from those in the original data but have similar statistical properties. The presented approach can support agent-based modeling at all levels by enabling richer synthetic populations with smaller zones and more detailed individual characteristics.Comment: 27 pages, 15 figures, 4 table

Methodological Issues in Spatial Microsimulation Modelling for Small Area Estimation

In this paper, some vital methodological issues of spatial microsimulation modelling for small area estimation have been addressed, with a particular emphasis given to the reweighting techniques. Most of the review articles in small area estimation have highlighted methodologies based on various statistical models and theories. However, spatial microsimulation modelling is emerging as a very useful alternative means of small area estimation. Our findings demonstrate that spatial microsimulation models are robust and have advantages over other type of models used for small area estimation. The technique uses different methodologies typically based on geographic models and various economic theories. In contrast to statistical model-based approaches, the spatial microsimulation model-based approaches can operate through reweighting techniques such as GREGWT and combinatorial optimization. A comparison between reweighting techniques reveals that they are using quite different iterative algorithms and that their properties also vary. The study also points out a new method for spatial microsimulation modellingBayesian prediction approach; combinatorial optimisation; GREGWT; microdata; small area estimation; spatial microsimulation

Compressed sensing imaging techniques for radio interferometry

Radio interferometry probes astrophysical signals through incomplete and noisy Fourier measurements. The theory of compressed sensing demonstrates that such measurements may actually suffice for accurate reconstruction of sparse or compressible signals. We propose new generic imaging techniques based on convex optimization for global minimization problems defined in this context. The versatility of the framework notably allows introduction of specific prior information on the signals, which offers the possibility of significant improvements of reconstruction relative to the standard local matching pursuit algorithm CLEAN used in radio astronomy. We illustrate the potential of the approach by studying reconstruction performances on simulations of two different kinds of signals observed with very generic interferometric configurations. The first kind is an intensity field of compact astrophysical objects. The second kind is the imprint of cosmic strings in the temperature field of the cosmic microwave background radiation, of particular interest for cosmology.Comment: 10 pages, 1 figure. Version 2 matches version accepted for publication in MNRAS. Changes includes: writing corrections, clarifications of arguments, figure update, and a new subsection 4.1 commenting on the exact compliance of radio interferometric measurements with compressed sensin

A Critical Review on Population Synthesis for Activity- and Agent-Based Transportation Models

Traditional four-step transportation planning models fail to capture novel transportation modes such as car/ridesharing. Hence, agent-based models are replacing those traditional models for their scalability, robustness, and capability of simulating nontraditional transportation modes. A crucial step in developing agent-based models is the definition of agents, e.g., household and persons. While model developers wish to capture typical workday travel patterns of the entire study population of travelers, such detailed data are unavailable due to privacy concerns and technical and financial feasibility issues. Hence, modelers opt for population syntheses based on travel diary surveys, land use data, and census data. The most prominent techniques are iterative proportional fitting (IPF), iterative proportional updating (IPU), combinatorial optimization, Markov-based and fitness-based syntheses, and other emerging approaches. Yet, at present, there is no clear guideline on using any of the available techniques. To bridge this gap, this chapter presents a comprehensive synthesis of practice and documents available successful studies

Transonic flow studies

Major emphasis was on the design of shock free airfoils with applications to general aviation. Unsteady flow, transonic flow, and shock wave formation were examined