scholarly journals Hybrid approach for parameter estimation in agent-based models

2017 ◽  
Author(s):  
Jill A. Gallaher ◽  
Andrea Hawkins-Daarud ◽  
Susan C. Massey ◽  
Kristin R. Swanson ◽  
Alexander R.A. Anderson
Keyword(s):  
Cancer Research ◽  
Parameter Estimation ◽  
Hybrid Approach ◽  
New Method ◽  
Agent Based Model ◽  
Agent Based Models ◽  
Agent Based

AbstractAgent-based models are valuable in cancer research to show how different behaviors emerge from individual interactions between cells and their environment. However, calibrating such models can be difficult, especially if the parameters that govern the underlying interactions are hard to measure experimentally. Herein, we detail a new method to converge on parameter sets that fit an agent-based model to multiscale data using a model of glioblastoma as an example.

Agent-Based Macroeconomic Modeling and Policy Analysis

2018 ◽  
Author(s):  
Herbert Dawid ◽  
Simon Gemkow ◽  
Philipp Harting ◽  
Sander van der Hoog ◽  
Michael Neugart
Keyword(s):  
Policy Analysis ◽  
Simulation Models ◽  
Proof Of Concept ◽  
Agent Based Model ◽  
Agent Based Models ◽  
Agent Based Simulation ◽  
Agent Based ◽  
Modeling Approaches ◽  
Macroeconomic Modeling ◽  
Spatial Policy

This chapter introduces the Eurace@Unibi model, one of the agent-based simulation models that are relatively new additions to the toolbox of macroeconomists, and the research that has been done within this framework. It shows how an agent-based model can be used to identify economic mechanisms and how it can be applied to spatial policy analysis. The assessment is that agent-based models in economics have passed the proof-of-concept phase and it is now time to move beyond that stage. It has been shown that new kinds of insights can be obtained that complement established modeling approaches. The chapter concludes by pointing toward some potentially fruitful areas of agent-based macroeconomic research.

scholarly journals Accurate and efficient discretizations for stochastic models providing near agent-based spatial resolution at low computational cost

2019 ◽  
Vol 16 (159) ◽  
pp. 20190421 ◽  
Author(s):  
Nabil T. Fadai ◽  
Ruth E. Baker ◽  
Matthew J. Simpson
Keyword(s):  
Single Cell ◽  
Cell Biology ◽  
Computational Cost ◽  
Kolmogorov Equation ◽  
Single Cell Level ◽  
Agent Based Model ◽  
Computationally Efficient ◽  
Agent Based Models ◽  
Cell Level ◽  
Agent Based

Understanding how cells proliferate, migrate and die in various environments is essential in determining how organisms develop and repair themselves. Continuum mathematical models, such as the logistic equation and the Fisher–Kolmogorov equation, can describe the global characteristics observed in commonly used cell biology assays, such as proliferation and scratch assays. However, these continuum models do not account for single-cell-level mechanics observed in high-throughput experiments. Mathematical modelling frameworks that represent individual cells, often called agent-based models, can successfully describe key single-cell-level features of these assays but are computationally infeasible when dealing with large populations. In this work, we propose an agent-based model with crowding effects that is computationally efficient and matches the logistic and Fisher–Kolmogorov equations in parameter regimes relevant to proliferation and scratch assays, respectively. This stochastic agent-based model allows multiple agents to be contained within compartments on an underlying lattice, thereby reducing the computational storage compared to existing agent-based models that allow one agent per site only. We propose a systematic method to determine a suitable compartment size. Implementing this compartment-based model with this compartment size provides a balance between computational storage, local resolution of agent behaviour and agreement with classical continuum descriptions.

scholarly journals The Use of Artificial Neural Networks to Forecast the Behavior of Agent-Based Models of Pathophysiology: An Example Utilizing an Agent-Based Model of Sepsis

2021 ◽  
Vol 12 ◽  
Author(s):  
Dale Larie ◽  
Gary An ◽  
R. Chase Cockrell
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Artificial Neural Networks ◽  
Multi Layer Perceptron ◽  
State Of Health ◽  
Agent Based Model ◽  
Agent Based Models ◽  
Clinical Sepsis ◽  
Agent Based ◽  
Artificial Neural

Introduction: Disease states are being characterized at finer and finer levels of resolution via biomarker or gene expression profiles, while at the same time. Machine learning (ML) is increasingly used to analyze and potentially classify or predict the behavior of biological systems based on such characterization. As ML applications are extremely data-intensive, given the relative sparsity of biomedical data sets ML training of artificial neural networks (ANNs) often require the use of synthetic training data. Agent-based models (ABMs) that incorporate known biological mechanisms and their associated stochastic properties are a potential means of generating synthetic data. Herein we present an example of ML used to train an artificial neural network (ANN) as a surrogate system used to predict the time evolution of an ABM focusing on the clinical condition of sepsis.Methods: The disease trajectories for clinical sepsis, in terms of temporal cytokine and phenotypic dynamics, can be interpreted as a random dynamical system. The Innate Immune Response Agent-based Model (IIRABM) is a well-established model that utilizes known cellular and molecular rules to simulate disease trajectories corresponding to clinical sepsis. We have utilized two distinct neural network architectures, Long Short-Term Memory and Multi-Layer Perceptron, to take a time sequence of five measurements of eleven IIRABM simulated serum cytokine concentrations as input and to return both the future cytokine trajectories as well as an aggregate metric representing the patient’s state of health.Results: The ANNs predicted model trajectories with the expected amount of error, due to stochasticity in the simulation, and recognizing that the mapping from a specific cytokine profile to a state-of-health is not unique. The Multi-Layer Perceptron neural network, generated predictions with a more accurate forecasted trajectory cone.Discussion: This work serves as a proof-of-concept for the use of ANNs to predict disease progression in sepsis as represented by an ABM. The findings demonstrate that multicellular systems with intrinsic stochasticity can be approximated with an ANN, but that forecasting a specific trajectory of the system requires sequential updating of the system state to provide a rolling forecast horizon.

scholarly journals Novel participatory methods for co-building an agent-based model of physical activity with youth

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241108
Author(s):  
Leah Frerichs ◽  
Natalie Smith ◽  
Jill A. Kuhlberg ◽  
Gretchen Mason ◽  
Damie Jackson-Diop ◽  
...  
Keyword(s):  
Physical Activity ◽  
Basic Structure ◽  
Quantitative Model ◽  
Agent Based Model ◽  
Dynamics Modeling ◽  
Agent Based Models ◽  
Technical Aspects ◽  
System Science ◽  
Agent Based ◽  
Engagement Strategies

Public health scholarship has increasingly called for the use of system science approaches to understand complex problems, including the use of participatory engagement to inform the modeling process. Some system science traditions, specifically system dynamics modeling, have an established participatory practice tradition. Yet, there remains limited guidance on engagement strategies using other modeling approaches like agent-based models. Our objective is to describe how we engaged adolescent youth in co-building an agent-based model about physical activity. Specifically, we aim to describe how we communicated technical aspects of agent-based models, the participatory activities we developed, and the resulting visual diagrams that were produced. We implemented six sessions with nine adolescent participants. To make technical aspects more accessible, we used an analogy that linked core components of agent-based models to elements of storytelling. We also implemented novel, facilitated activities that engaged youth in the development, annotation, and review of graphs over time, geographical maps, and state charts. The process was well-received by the participants and helped inform the basic structure of an agent-based model. The resulting visual diagrams created space for deeper discussion among participants about patterns of daily activity, important places for physical activity, and interactions between social and built environments. This work lays a foundation to develop and refine engagement strategies, especially for translating qualitative insights into quantitative model specifications such as ‘decision rules’.

scholarly journals Learning differential equation models from stochastic agent-based model simulations

2021 ◽  
Vol 18 (176) ◽  
Author(s):  
John T. Nardini ◽  
Ruth E. Baker ◽  
Matthew J. Simpson ◽  
Kevin B. Flores
Keyword(s):  
Differential Equation ◽  
Cell Biology ◽  
Coarse Grained ◽  
Disease Spread ◽  
Agent Based Model ◽  
Agent Based Models ◽  
Agent Based ◽  
Model Simulations ◽  
Differential Equation Models ◽  
Model Dynamics

Agent-based models provide a flexible framework that is frequently used for modelling many biological systems, including cell migration, molecular dynamics, ecology and epidemiology. Analysis of the model dynamics can be challenging due to their inherent stochasticity and heavy computational requirements. Common approaches to the analysis of agent-based models include extensive Monte Carlo simulation of the model or the derivation of coarse-grained differential equation models to predict the expected or averaged output from the agent-based model. Both of these approaches have limitations, however, as extensive computation of complex agent-based models may be infeasible, and coarse-grained differential equation models can fail to accurately describe model dynamics in certain parameter regimes. We propose that methods from the equation learning field provide a promising, novel and unifying approach for agent-based model analysis. Equation learning is a recent field of research from data science that aims to infer differential equation models directly from data. We use this tutorial to review how methods from equation learning can be used to learn differential equation models from agent-based model simulations. We demonstrate that this framework is easy to use, requires few model simulations, and accurately predicts model dynamics in parameter regions where coarse-grained differential equation models fail to do so. We highlight these advantages through several case studies involving two agent-based models that are broadly applicable to biological phenomena: a birth–death–migration model commonly used to explore cell biology experiments and a susceptible–infected–recovered model of infectious disease spread.

scholarly journals Accurate and efficient discretisations for stochastic models providing near agent-based spatial resolution at low computational cost

2019 ◽  
Author(s):  
Nabil T. Fadai ◽  
Ruth E. Baker ◽  
Matthew J. Simpson
Keyword(s):  
Single Cell ◽  
Cell Biology ◽  
Computational Cost ◽  
Kolmogorov Equation ◽  
Single Cell Level ◽  
Agent Based Model ◽  
Computationally Efficient ◽  
Agent Based Models ◽  
Cell Level ◽  
Agent Based

AbstractUnderstanding how cells proliferate, migrate, and die in various environments is essential in determining how organisms develop and repair themselves. Continuum mathematical models, such as the logistic equation and the Fisher-Kolmogorov equation, can describe the global characteristics observed in commonly-used cell biology assays, such as proliferation and scratch assays. However, these continuum models do not account for single-cell-level mechanics observed in high-throughput experiments. Mathematical modelling frameworks that represent individual cells, often called agent-based models, can successfully describe key single-cell-level features of these assays, but are computationally infeasible when dealing with large populations. In this work, we propose an agent-based model with crowding effects that is computationally efficient and matches the logistic and Fisher-Kolmogorov equations in parameter regimes relevant to proliferation and scratch assays, respectively. This stochastic agent-based model allows multiple agents to be contained within compartments on an underlying lattice, thereby reducing the computational storage compared to existing agent-based models that allow one agent per site only. We propose a systematic method to determine a suitable compartment size. Implementing this compartment-based model with this compartment size provides a balance between computational storage, local resolution of agent behaviour, and agreement with classical continuum descriptions.

scholarly journals PROBLEMS AND PROSPECTS FOR APPLICATION OF AGENT-BASED MODELLING IN THE PSYCHOLOGY OF INFLUENCE

2021 ◽  
pp. 116-139
Author(s):  
В. В. Латынов
Keyword(s):  
Optimal Level ◽  
Psychological Research ◽  
Agent Based Modeling ◽  
Model Complexity ◽  
Agent Based Model ◽  
Agent Based Models ◽  
Social Phenomena ◽  
Agent Based ◽  
Complex Models ◽  
The Impact

В статье обсуждаются вопросы применения агент-ориентированного моделирования в психологических исследованиях. Данный вид моделирования используется для изучения систем, состоящих из большого количества взаимодействующих друг с другом агентов. Рассматривается текущее состояние и перспективы использования агентных моделей. Выделяются основные направления применения агент-ориентированного моделирования в психологии: генерирование новых и совершенствование уже существующих теорий; проверка исследовательских гипотез; построение сложных моделей социальных явлений и процессов, включающих психологические закономерности разного типа. Формулируются задачи, требующие решения при создании агентной модели: задание оптимального уровня сложности модели; достижение ее психологического реализма; выбор качеств, которыми будут обладать агенты; определение правил их взаимодействия с другими агентами и средой взаимодействия. Обсуждается проблема калибрования агентной модели, т. е. основанного на данных экспериментальных исследований обоснования необходимости введения конкретных качеств и правил взаимодействия агентов. Рассматриваются возможности агент-ориентированного моделирования при изучении процессов психологического воздействия. Выделяются теории и эмпирические закономерности, требующие учета при создании агентных моделей в области психологии воздействия. Эти теории и закономерности относятся главным образом к двум областям психологического исследования, ориентированным, соответственно, на анализ закономерностей восприятия, изменения и выражения мнений и аттитюдов на уровне отдельного индивида («двухпроцессный» подход, модель знаний о воздействии М. Фристэда и П. Райта); изучение закономерностей, связанных с влиянием на мнения, аттитюды и поведение человека его членства в группе и позиции его окружения (теория «лидеров мнения», теории групповой идентичности). The article discusses the application of agent-based modeling in psychological research. This type of modeling is used to study systems consisting of a large number of agents interacting with each other. The current state and prospects of using agent-based models are considered. The main directions of application of agent-based modeling in psychology are highlighted: generating new and improving existing theories; testing research hypotheses; construction of complex models of social phenomena and processes, including psychological patterns of various types. The tasks that need to be solved when creating an agent-based model are formulated: setting the optimal level of model complexity; achieving her psychological realism; choice of qualities that agents will possess; defining the rules for their interaction with other agents and the interaction environment. The problem of calibrating the agent-based model is discussed, that is, substantiating the need to introduce specific qualities and rules for the interaction of agents based on experimental research data. The possibilities of agent-based modeling in the study of the processes of psychological influence are considered. Theories and empirical patterns are highlighted that require consideration when creating agent-based models in the field psychology of influence. These theories and patterns relate mainly to two areas of psychological research, focused, respectively, on the analysis of patterns of perception, change and expression of opinions and attitudes at the level of an individual ("two-process" approach, the model of knowledge about the impact of M. Freestad and P. Wright); study of the patterns associated with the influence on the opinions, attitudes and behavior of a person by his membership in a group and the position of his environment (theory of "opinion leaders", theories of group identity).

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