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E-book: X-Machines for Agent-Based Modeling: FLAME Perspectives

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From the Foreword:

"This book exemplifies one of the most successful approaches to modeling and simulating [ the] new generation of complex systems. FLAME was designed to make the building of large scale complex systems models straightforward and the simulation code that it generates is highly efficient and can be run on any modern technology. FLAME was the first such platform that ran efficiently on high performance parallel computers and a version for GPU technology is also available. At its heart, and the reason why it is so efficient and robust, is the use of a powerful computational model Communicating X-machines which is general enough to cope with most types of modelling problems. As well as being increasingly important in academic research, FLAME is now being applied in industry in many different application areas. This book describes the basics of FLAME and is illustrated with numerous examples." Professor Mike Holcombe, University of Sheffield, UK

Agent-based models have shown applications in various fields such as biology, economics, and social science. Over the years, multiple agent-based modeling frameworks have been produced, allowing experts with non-computing background to easily write and simulate their models. However, most of these models are limited by the capability of the framework, the time it takes for a simulation to finish, or how to handle the massive amounts of data produced. FLAME (Flexible Large-scale Agent-based Modeling Environment) was produced and developed through the years to address these issues.

This book contains a comprehensive summary of the field, covers the basics of FLAME, and shows how concepts of X-machines, can be stretched across multiple fields to produce agent models. It has been written with several audiences in mind. First, it is organized as a collection of models, with detailed descriptions of how models can be designed, especially for beginners. A number of theoretical aspects of software engineering and how they relate to agent-based models are discussed for students interested in software engineering and parallel computing. Finally, it is intended as a guide to developers from biology, economics, and social science, who want to explore how to write agent-based models for their research area. By working through the model examples provided, anyone should be able to design and build agent-based models and deploy them. With FLAME, they can easily increase the agent number and run models on parallel computers, in order to save on simulation complexity and waiting time for results.

Because the field is so large and active, the book does not aim to cover all aspects of agent-based modeling and its research challenges. The models are presented to show researchers how they can build complex agent functions for their models. The book demonstrates the advantage of using agent-based models in simulation experiments, providing a case to move away from differential equations and build more reliable, close to real, models.

The Open Access version of this book, available at https://doi.org/10.1201/9781315370729, has been made available under a Creative Commons Attribution-Non Commercial-No Derivatives 4.0 license.
Foreword xiii
Preface xvii
List of Figures
xix
List of Tables
xxv
FLAME Contributors xxvii
1 Setting the Stage: Complex Systems, Emergence and Evolution
1(16)
1.1 Complex and Adaptive Systems
3(1)
1.2 What Is Chaos?
4(1)
1.3 Constructing Artificial Systems
5(1)
1.4 Importance of Emergence
6(1)
1.5 Dynamic Systems
6(1)
1.6 Is There Evolution at Work?
7(2)
1.6.1 Adaptation
8(1)
1.7 Distributing Intelligence?
9(1)
1.8 Modeling and Simulation
10(7)
1.8.1 Research Examples
12(5)
2 Artificial Agents
17(26)
2.1 Intelligent Agents
18(3)
2.1.1 "Can Machines Think?"
19(2)
2.2 Engineering Self-Organizing Systems
21(12)
2.2.1 Bring in the Agents
22(1)
2.2.2 Characteristics of Agent-Based Models
23(10)
2.3 Agent-Based Modeling Frameworks
33(4)
2.4 Adaptive Agent Design
37(1)
2.5 Mathematical Foundations
38(1)
2.6 Objects or Agents?
39(1)
2.7 Influence of Other Research Areas on ABM
40(3)
3 Designing X-Agents Using FLAME
43(18)
3.1 FLAME and Its X-Machine Methodology
44(4)
3.1.1 Transition Functions
47(1)
3.1.2 Memory and States
47(1)
3.2 Using Agile Methods to Design Agents
48(3)
3.2.1 Extension to Extreme Programming
51(1)
3.3 Overview: FLAME Version 1.0
51(3)
3.4 Libmboard (FLAME message board library)
54(4)
3.4.1 Compiling and Installing Libmboard
55(2)
3.4.2 FLAME's Synchronization Points
57(1)
3.5 FLAME's Missing Functionality
58(3)
4 Getting Started with FLAME
61(26)
4.1 Setting Up FLAME
62(2)
4.1.1 MinGW
63(1)
4.1.2 GDB GNU Debugger
63(1)
4.1.3 Dotty as an Extra Installation
64(1)
4.2 Messaging Library: Libmboard
64(1)
4.3 How to Run a Model?
65(1)
4.4 Implementation Details
65(3)
4.5 Using Grids
68(1)
4.6 Integrating with More Libraries
69(2)
4.7 Writing a Model - Fox and Rabbit Predator Model
71(13)
4.7.1 Adding Complexity to Models
72(1)
4.7.2 XML Model Description File
72(4)
4.7.3 C Function
76(5)
4.7.4 Additional Files
81(2)
4.7.5 0.xml File
83(1)
4.8 Enhancing the Environment
84(3)
4.8.1 Constant Variables
84(1)
4.8.2 Time Rules
84(3)
5 Agents in Social Science
87(34)
5.1 Sugarscape Model
92(15)
5.1.1 Evolution from Bottom-Up
93(1)
5.1.2 Distribution of Wealth
94(1)
5.1.3 Location Is Important!
95(9)
5.1.4 Find Agents around Me
104(1)
5.1.5 Handle Multiple `Eaten' Requests
105(1)
5.1.6 Change Starting Conditions
105(2)
5.2 Modeling Social Networks
107(7)
5.2.1 Set Up a Recurring Function
112(1)
5.2.2 Assigning Conditions with Functions
113(1)
5.2.3 Using Dynamic Arrays and Data Structures
113(1)
5.2.4 Creating Local Dynamic Arrays
114(1)
5.3 Modeling Pedestrians in Crowds
114(7)
5.3.1 Calculate Movement toward Other Agents
116(2)
5.3.2 Entering and Exiting Agents
118(3)
6 Agents in Economic Markets and Games
121(54)
6.1 Perfect Rationality versus Bounded Rationality
125(1)
6.2 Modeling Multiple Shopper Behaviors
126(3)
6.3 Learning Firms in a Cournot Model
129(23)
6.3.1 Genetic Programming with Agents
143(7)
6.3.2 Filtering Messages in Advance
150(1)
6.3.3 Comparing Two Data Structures
151(1)
6.4 A Virtual Mall Model: Labor and Goods Market Combined
152(7)
6.5 Programming Games
159(5)
6.5.1 Nash Equilibrium
160(1)
6.5.2 Evolutionary Game Theory
161(1)
6.5.3 Evolutionary Stable State
162(1)
6.5.4 Game Theory versus Evolutionary Game Theory
162(1)
6.5.5 Continuous Strategies
163(1)
6.5.6 Red Queen and Equilibrium
163(1)
6.6 Learning in an Iterated Prisoner's Dilemma Game
164(9)
6.7 Multi-Agent Systems and Games
173(2)
7 Agents in Biology
175(62)
7.1 Example Models
176(8)
7.1.1 Molecular Systems Models
176(3)
7.1.2 Tissue and Organ Models
179(3)
7.1.3 Ecological Models
182(1)
7.1.4 Industrial Applications of Agent-Based Modeling with FLAME
183(1)
7.2 Modeling Epithelial Tissue
184(3)
7.2.1 Merging with Other Toolkits
185(2)
7.3 Modeling Drosophila Embryo Development
187(11)
7.3.1 Stochastic Modeling
188(1)
7.3.2 Converting to an Agent-Based Model
188(8)
7.3.3 Find Optimum Model Settings
196(2)
7.4 Output Files for Analysis
198(4)
7.5 Modeling Pharaoh's Ants (Monomorium pharaonis)
202(22)
7.6 Model Drug Delivery for Cancer Treatment
224(13)
7.6.1 Using Multiple Outputs
234(3)
8 Testing Agent Behavior
237(10)
8.1 Unit and System Testing
237(2)
8.2 Statistical Testing of Data
239(4)
8.3 Statistics Testing on Code
243(1)
8.4 Testing Simulation Durations
244(3)
9 FLAME's Future
247(36)
9.1 Flame to Flame GPU
247(29)
9.1.1 Visualizing Is Easy in FLAME GPU
273(3)
9.1.2 Utilizing Vector Calculations
276(1)
9.2 Commercial Applications of FLAME
276(7)
Bibliography 283(16)
Index 299
Dr. Mariam Kiran is a well-recognized researcher in agent-based modeling, high performance simulations and cloud computing. She has published numerous papers in these fields, both, in theory and practical implementations, exploiting grid and cloud ecosystems for improving computational performance for multi-domain research. She has an extensive record of research collaborations across the world, serving as a board member for Complex Systems research in CoMSES, and several joint projects funded by European Research and UK Engineering Council. She is also active in education research of software engineering in team building and writing software for simulations.

Mariam Kiran received her PhD in Computer Science from University of Sheffield, Sheffield UK in 2010. She is currently involved in many projects at Lawrence Berkeley National Labs, California, optimizing high performance computing problems across various disciplines. Prior to this, she was working as an Associate Professor at University of Bradford, leading the Cloud Computing research in the School.