From Models to Simulations

This book analyses the impact computerization has had on contemporary science and explains the origins, technical nature and epistemological consequences of the current decisive interplay between technology and science: an intertwining of formalism, computation, data acquisition, data and visualization and how these factors have led to the spread of simulation models since the 1950s. Using historical, comparative and interpretative case studies from a range of disciplines, with a particular emphasis on the case of plant studies, the author shows how and why computers, data treatment devices and programming languages have occasioned a gradual but irresistible and massive shift from mathematical models to computer simulations

"Rotterdam econometrics": publications of the econometric institute 1956-2005

This paper contains a list of all publications over the period 1956-2005, as reported in the Rotterdam Econometric Institute Reprint series during 1957-2005.

Microsimulation as an Instrument to Evaluate Economic and Social Programmes

In recent years microsimulation models (MSMs) have been increasingly applied in quantitative analyses of the individual impacts of economic and social programme policies. The suitability of using microsimulation as an instrument to analyze main and side policy impacts at the individual level will be discussed in this paper by characterizing: the general approach and principles of the two general microsimulation approaches: static and dynamic (cross-section and lifecycle) microsimulation, the structure of MSMs with institutional regulations and behavioural response, panel data and behavioural change, deterministic and stochastic microsimulation, the 4M-strategy to combine microtheory, microdata, microestimation and microsimulation, and pinpointing applications and recent developments. To demonstrate the evaluation of economic and social programmes by microsimulation, two examples concerning a dynamic (cross-section and life-cycle) microsimulation of the German retirement pension reform and a combined static/dynamic microsimulation of the recent German tax reform with its behavioural impacts on formal and informal economic activities of private households are briefly described. Evaluating the evaluation of economic and social programmes with microsimulation models finally is followed by concluding remarks about some future developments.microsimulation, evaluation of economic and social-political programms

Microsimulation as an Instrument to Evaluate Economic and Social Programmes

In recent years microsimulation models (MSMs) have been increasingly applied in quantitative analyses of the individual impacts of economic and social programme policies. The suitability of using microsimulation as an instrument to analyze main and side policy impacts at the individual level will be discussed in this paper by characterizing: the general approach and principles of the two general microsimulation approaches: static and dynamic (cross-section and lifecycle) microsimulation, the structure of MSMs with institutional regulations and behavioural response, panel data and behavioural change, deterministic and stochastic microsimulation, the 4M-strategy to combine microtheory, microdata, microestimation and microsimulation, and pinpointing applications and recent developments. To demonstrate the evaluation of economic and social programmes by microsimulation, two examples concerning a dynamic (cross-section and life-cycle) microsimulation of the German retirement pension reform and a combined static/dynamic microsimulation of the recent German tax reform with its behavioural impacts on formal and informal economic activities of private households are briefly described. Evaluating the evaluation of economic and social programmes with microsimulation models finally is followed by concluding remarks about some future developments.microsimulation, evaluation of economic and social-political programms

Quantitative magnetic resonance image analysis via the EM algorithm with stochastic variation

Quantitative Magnetic Resonance Imaging (qMRI) provides researchers insight into pathological and physiological alterations of living tissue, with the help of which researchers hope to predict (local) therapeutic efficacy early and determine optimal treatment schedule. However, the analysis of qMRI has been limited to ad-hoc heuristic methods. Our research provides a powerful statistical framework for image analysis and sheds light on future localized adaptive treatment regimes tailored to the individual's response. We assume in an imperfect world we only observe a blurred and noisy version of the underlying pathological/physiological changes via qMRI, due to measurement errors or unpredictable influences. We use a hidden Markov random field to model the spatial dependence in the data and develop a maximum likelihood approach via the Expectation--Maximization algorithm with stochastic variation. An important improvement over previous work is the assessment of variability in parameter estimation, which is the valid basis for statistical inference. More importantly, we focus on the expected changes rather than image segmentation. Our research has shown that the approach is powerful in both simulation studies and on a real dataset, while quite robust in the presence of some model assumption violations.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS157 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Microsimulation - A Survey of Methods and Applications for Analyzing Economic and Social Policy

This essential dimensions of microsimulation as an instrument to analyze and forecast the individual impacts of alternative economic and social policy measures are surveyed in this study. The basic principles of microsimulation, which is a tool for practical policy advising as well as for research and teaching, are pointed out and the static and dynamic (cross-section and life-cycle) approaches are compared to one another. Present and past developments of microsimulation models and their areas of application are reviewed, focusing on the US, Europe and Australia. Based on general requirements and components of microsimulation models a microsimulation model's actual working mechanism are discussed by a concrete example: the concept and realization of MICSIM, a PC microsimulation model based on a relational database system, an offspring of the Sfb 3 Statitic Microsimulation Model. Common issues of microsimulation modeling are regarded: micro/macro link, behavioural response and the important question of evaluating microsimulation results. The concluding remarks accentuate the increasing use of microcomputers for microsimulation models also for teaching purposes.Microsimulation, Microanalytic Simulation Models, Microanalysis, Economic and Social Policy Analysis

Phenotypic evolution studied by layered stochastic differential equations

Time series of cell size evolution in unicellular marine algae (division Haptophyta; Coccolithus lineage), covering 57 million years, are studied by a system of linear stochastic differential equations of hierarchical structure. The data consists of size measurements of fossilized calcite platelets (coccoliths) that cover the living cell, found in deep-sea sediment cores from six sites in the world oceans and dated to irregular points in time. To accommodate biological theory of populations tracking their fitness optima, and to allow potentially interpretable correlations in time and space, the model framework allows for an upper layer of partially observed site-specific population means, a layer of site-specific theoretical fitness optima and a bottom layer representing environmental and ecological processes. While the modeled process has many components, it is Gaussian and analytically tractable. A total of 710 model specifications within this framework are compared and inference is drawn with respect to model structure, evolutionary speed and the effect of global temperature.Comment: Published in at http://dx.doi.org/10.1214/12-AOAS559 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Nonparametric inference of doubly stochastic Poisson process data via the kernel method

Doubly stochastic Poisson processes, also known as the Cox processes, frequently occur in various scientific fields. In this article, motivated primarily by analyzing Cox process data in biophysics, we propose a nonparametric kernel-based inference method. We conduct a detailed study, including an asymptotic analysis, of the proposed method, and provide guidelines for its practical use, introducing a fast and stable regression method for bandwidth selection. We apply our method to real photon arrival data from recent single-molecule biophysical experiments, investigating proteins' conformational dynamics. Our result shows that conformational fluctuation is widely present in protein systems, and that the fluctuation covers a broad range of time scales, highlighting the dynamic and complex nature of proteins' structure.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS352 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Bayesian inference and model choice in a hidden stochastic two-compartment model of hematopoietic stem cell fate decisions

Despite rapid advances in experimental cell biology, the in vivo behavior of hematopoietic stem cells (HSC) cannot be directly observed and measured. Previously we modeled feline hematopoiesis using a two-compartment hidden Markov process that had birth and emigration events in the first compartment. Here we perform Bayesian statistical inference on models which contain two additional events in the first compartment in order to determine if HSC fate decisions are linked to cell division or occur independently. Pareto Optimal Model Assessment approach is used to cross check the estimates from Bayesian inference. Our results show that HSC must divide symmetrically (i.e., produce two HSC daughter cells) in order to maintain hematopoiesis. We then demonstrate that the augmented model that adds asymmetric division events provides a better fit to the competitive transplantation data, and we thus provide evidence that HSC fate determination in vivo occurs both in association with cell division and at a separate point in time. Last we show that assuming each cat has a unique set of parameters leads to either a significant decrease or a nonsignificant increase in model fit, suggesting that the kinetic parameters for HSC are not unique attributes of individual animals, but shared within a species.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS269 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org