The Mind Agents in Netlogo 3.1

In [Houk, 2005], the “Agents of the mind” idea is proposed as a suitable framework for studying the dynamics and complexities of mind. “Agents of the mind” is inspired by the society of mind idea of Marvin Minsky [Minsky, 1988]. According to the society of mind, the mind is a complex system. The mind agents are elusive to identify. The mind is proposed as a hierarchy of agents. The higher hierarchy agents compose of lower hierarchy agents. Higher level agents do not command lower level agents but they basically trigger or invoke lower level agents. Agents are functional entities and they interact with each other. One important part of the society of mind idea is that agents at the lowest level are the real workers. Higher level functionalities emerge as a result of the functioning of the lower level agents and the interactions between them. In agents of the mind project, computational distributed processing modules (DPM) are posited for corresponding anatomically defined assemblies and they are referred to as the agents of the mind. M1 is an anatomical area in the cerebral cortex which produces voluntary commands via its loops through basal ganglia and cerebellum. M1-DPM is a computational distributed processing module which simulates M1 area and its loops for voluntary commands production. We use Netlogo 3.1 agent-based programming environment to illuminate the properties of mind. In this work, the attractor network in cerebellar loop and the effects of Purkinje cell on production of motor commands have been studied. The results are reported in this paper

NL4Py: Agent-Based Modeling in Python with Parallelizable NetLogo Workspaces

NL4Py is a NetLogo controller software for Python, for the rapid, parallel execution of NetLogo models. NL4Py provides both headless (no graphical user interface) and GUI NetLogo workspace control through Python. Spurred on by the increasing availability of open-source computation and machine learning libraries on the Python package index, there is an increasing demand for such rapid, parallel execution of agent-based models through Python. NetLogo, being the language of choice for a majority of agent-based modeling driven research projects, requires an integration to Python for researchers looking to perform statistical analyses of agent-based model output using these libraries. Unfortunately, until the recent introduction of PyNetLogo, and now NL4Py, such a controller was unavailable. This article provides a detailed introduction into the usage of NL4Py and explains its client-server software architecture, highlighting architectural differences to PyNetLogo. A step-by-step demonstration of global sensitivity analysis and parameter calibration of the Wolf Sheep Predation model is then performed through NL4Py. Finally, NL4Py's performance is benchmarked against PyNetLogo and its combination with IPyParallel, and shown to provide significant savings in execution time over both configurations

Tools of the Trade: A Survey of Various Agent Based Modeling Platforms

Agent Based Modeling (ABM) toolkits are as diverse as the community of people who use them. With so many toolkits available, the choice of which one is best suited for a project is left to word of mouth, past experiences in using particular toolkits and toolkit publicity. This is especially troublesome for projects that require specialization. Rather than using toolkits that are the most publicized but are designed for general projects, using this paper, one will be able to choose a toolkit that already exists and that may be built especially for one's particular domain and specialized needs. In this paper, we examine the entire continuum of agent based toolkits. We characterize each based on 5 important characteristics users consider when choosing a toolkit, and then we categorize the characteristics into user-friendly taxonomies that aid in rapid indexing and easy reference.Agent Based Modeling, Individual Based Model, Multi Agent Systems

My Way or the Highway: a More Naturalistic Model of Altruism Tested in an Iterative Prisoners' Dilemma

There are three prominent solutions to the Darwinian problem of altruism, kin selection, reciprocal altruism, and trait group selection. Only one, reciprocal altruism, most commonly implemented in game theory as a TIT FOR TAT strategy, is not based on the principle of conditional association. On the contrary, TIT FOR TAT implements conditional altruism in the context of unconditionally determined associates. Simulations based on Axelrod\'s famous tournament have led many to conclude that conditional altruism among unconditional partners lies at the core of much human and animal social behavior. But the results that have been used to support this conclusion are largely artifacts of the structure of the Axelrod tournament, which explicitly disallowed conditional association as a strategy. In this study, we modify the rules of the tournament to permit competition between conditional associates and conditional altruists. We provide evidence that when unconditional altruism is paired with conditional association, a strategy we called MOTH, it can out compete TIT FOR TAT under a wide range of conditions.Game Theory; Altruism; Prisoners' Dilemma; TIT FOR TAT; MOTH; Docking; Netlogo

What Makes Complex Systems Complex?

This paper explores some of the factors that make complex systems complex. We first examine the history of complex systems. It was Aristotle’s insight that how elements are joined together helps determine the properties of the resulting whole. We find (a) that scientific reductionism does not provide a sufficient explanation; (b) that to understand complex systems, one must identify and trace energy flows; and (c) that disproportionate causality, including global tipping points, are all around us. Disproportionate causality results from the wide availability of energy stores. We discuss three categories of emergent phenomena—static, dynamic, and adaptive—and recommend retiring the term emergent, except perhaps as a synonym for creative. Finally, we find that virtually all communication is stigmergic

Making Models Match: Replicating an Agent-Based Model

Scientists have increasingly employed computer models in their work. Recent years have seen a proliferation of agent-based models in the natural and social sciences. But with the exception of a few "classic" models, most of these models have never been replicated by anyone but the original developer. As replication is a critical component of the scientific method and a core practice of scientists, we argue herein for an increased practice of replication in the agent-based modeling community, and for widespread discussion of the issues surrounding replication. We begin by clarifying the concept of replication as it applies to ABM. Furthermore we argue that replication may have even greater benefits when applied to computational models than when applied to physical experiments. Replication of computational models affects model verification and validation and fosters shared understanding about modeling decisions. To facilitate replication, we must create standards for both how to replicate models and how to evaluate the replication. In this paper, we present a case study of our own attempt to replicate a classic agent-based model. We begin by describing an agent-based model from political science that was developed by Axelrod and Hammond. We then detail our effort to replicate that model and the challenges that arose in recreating the model and in determining if the replication was successful. We conclude this paper by discussing issues for (1) researchers attempting to replicate models and (2) researchers developing models in order to facilitate the replication of their results.Replication, Agent-Based Modeling, Verification, Validation, Scientific Method, Ethnocentrism