Computational Model Library

Peer reviewed B3GET

Kristin Crouse | Published Thu Nov 14 20:07:16 2019 | Last modified Tue Sep 20 19:43:54 2022

B3GET simulates populations of virtual organisms evolving over generations, whose evolutionary outcomes reflect the selection pressures of their environment. The model simulates several factors considered important in biology, including life history trade-offs, investment in fighting ability and aggression, sperm competition, infanticide, and competition over access to food and mates. Downloaded materials include starting genotype and population files. Edit the these files and see what changes occur in the behavior of virtual populations!

View the B3GET user manual here.

We consider scientific communities where each scientist employs one of two characteristic methods: an “adequate” method (A) and a “superior” method (S). The quality of methodology is relevant to the epistemic products of these scientists, and generate credit for their users. Higher-credit methods tend to be imitated, allowing to explore whether communities will adopt one method or the other. We use the model to examine the effects of (1) bias for existing methods, (2) competence to assess relative value of competing methods, and (3) two forms of interdisciplinarity: (a) the tendency for members of a scientific community to receive meaningful credit assignment from those outside their community, and (b) the tendency to consider new methods used outside their community. The model can be used to show how interdisciplinarity can overcome the effects of bias and incompetence for the spread of superior methods.

If you have any questions about the model run, please send me an email and I will respond as soon as possible.
Under complex system perspectives, we build the multi-agent system to back-calculate this unification process of the Warring State period, from 32 states in 475 BC to 1 state (Qin) in 221 BC.

This project was developed during the Santa Fe course Introduction to Agent-Based Modeling 2022. The origin is a Cellular Automata (CA) model to simulate human interactions that happen in the real world, from Rubens and Oliveira (2009). These authors used a market research with real people in two different times: one at time zero and the second at time zero plus 4 months (longitudinal market research). They developed an agent-based model whose initial condition was inherited from the results of the first market research response values and evolve it to simulate human interactions with Agent-Based Modeling that led to the values of the second market research, without explicitly imposing rules. Then, compared results of the model with the second market research. The model reached 73.80% accuracy.
In the same way, this project is an Exploratory ABM project that models individuals in a closed society whose behavior depends upon the result of interaction with two neighbors within a radius of interaction, one on the relative “right” and other one on the relative “left”. According to the states (colors) of neighbors, a given cellular automata rule is applied, according to the value set in Chooser. Five states were used here and are defined as levels of quality perception, where red (states 0 and 1) means unhappy, state 3 is neutral and green (states 3 and 4) means happy.
There is also a message passing algorithm in the social network, to analyze the flow and spread of information among nodes. Both the cellular automaton and the message passing algorithms were developed using the Python extension. The model also uses extensions csv and arduino.

Peer reviewed HyperMu’NmGA - Effect of Hypermutation Cycles in a NetLogo Minimal Genetic Algorithm

Cosimo Leuci | Published Tue Oct 27 21:15:40 2020 | Last modified Sun Jul 31 09:08:14 2022

A minimal genetic algorithm was preliminarily developed to search for the solution of an elementary arithmetic problem. It has been modified to explore the effect of a mutator gene and the consequent entrance into a hypermutation state. The phenomenon is particularly important in some types of tumorigenesis and in a more general way, in cells and tissues submitted to chronic sublethal environmental or genomic stress.
Since a long time, some scholars suppose that organisms speed up their own evolution by varying mutation rate, but evolutionary biologists are not convinced that evolution can select a mechanism promoting more (often harmful) mutations looking forward an environmental challenge.
The model aims to shed light on these controversial points of view and it provides also the features required to check the role of sex and genetic recombination in the mutator genes diffusion.

The model is based on the influence function of the Leviathan model (Deffuant, Carletti, Huet 2013 and Huet and Deffuant 2017) with the addition of group idenetity. We aim at better explaining some patterns generated by this model, using a derived mathematical approximation of the evolution of the opinions averaged.

We consider agents having an opinion/esteem about each other and about themselves. During dyadic meetings, agents change their respective opinion about each other, and possibly about other agents they gossip about, with a noisy perception of the opinions of their interlocutor. Highly valued agents are more influential in such encounters. Moreover, each agent belongs to a single group and the opinions within the group are attracted to their average.

We show that a group hierarchy can emerges from this model, and that the inequality of reputations among groups have a negative effect on the opinions about the groups of low status. The mathematical analysis of the opinion dynamic shows that the lower the status of the group, the more detrimental the interactions with the agents of other groups are for the opinions about this group, especially when gossip is activated. However, the interactions between agents of the same group tend to have a positive effect on the opinions about this group.

Leviathan model and its approximation

Thibaut Roubin Guillaume Deffuant | Published Thu Sep 17 15:21:40 2020 | Last modified Mon Sep 6 14:45:35 2021

The model is based on the influence function of the Leviathan model (Deffuant, Carletti, Huet 2013 and Huet and Deffuant 2017). We aim at better explaining some patterns generated by this model, using a derived mathematical approximation of the evolution of the opinions averaged.

We consider agents having an opinion/esteem about each other and about themselves. During dyadic meetings, agents change their respective opinion about each other, and possibly about other agents they gossip about, with a noisy perception of the opinions of their interlocutor. Highly valued agents are more influential in such encounters.

We show that the inequality of reputations among agents have a negative effect on the opinions about the agents of low status.The mathematical analysis of the opinion dynamic shows that the lower the status of the agent, the more detrimental the interactions are for the opinions about this agent, especially when gossip is activated, while the interactions always tend to increase the opinions about agents of high status.

This study simulates the evolution of artificial economies in order to understand the tax relevance of administrative boundaries in the quality of life of its citizens. The modeling involves the construction of a computational algorithm, which includes citizens, bounded into families; firms and governments; all of them interacting in markets for goods, labor and real estate. The real estate market allows families to move to dwellings with higher quality or lower price when the families capitalize property values. The goods market allows consumers to search on a flexible number of firms choosing by price and proximity. The labor market entails a matching process between firms (given its location) and candidates, according to their qualification. The government may be configured into one, four or seven distinct sub-national governments, which are all economically conurbated. The role of government is to collect taxes on the value added of firms in its territory and invest the taxes into higher levels of quality of life for residents. The results suggest that the configuration of administrative boundaries is relevant to the levels of quality of life arising from the reversal of taxes. The model with seven regions is more dynamic, but more unequal and heterogeneous across regions. The simulation with only one region is more homogeneously poor. The study seeks to contribute to a theoretical and methodological framework as well as to describe, operationalize and test computer models of public finance analysis, with explicitly spatial and dynamic emphasis. Several alternatives of expansion of the model for future research are described. Moreover, this study adds to the existing literature in the realm of simple microeconomic computational models, specifying structural relationships between local governments and firms, consumers and dwellings mediated by distance.

Cooperation is essential for all domains of life. Ironically, it is intrinsically vulnerable to exploitation by cheats. Hence, there is an explanatory necessity that triggers a lot of evolutionary biologists to search for mechanisms that could support cooperation. In general, cooperation can emerge and be maintained when cooperators are sufficiently interacting with themself to provide a kind of assortment and reciprocity. One of the most crucial and common mechanisms to achieve that task are kin selection, spatial structure, and enforcement (punishment). Here I used agent-based simulation models to investigate these pivotal mechanisms against conditional defector strategies and concluded it could easily violate all of them and take over the population. This surprising outcome may cue us to rethink the evolution of cooperation as it illustrates that maintaining cooperation may be more difficult than previously thought. Moreover, besides the theoretical findings, there are empirical applications such as invading the cooperator population of pathogens by genetically engineered conditional defectors, which could be a potential therapy for many incurable diseases.

Evolution of Conditional Cooperation

Marco Janssen Miles Manning Oyita Udiani | Published Thu Aug 1 04:03:07 2013 | Last modified Fri May 13 22:07:23 2022

Cultural group selection model used to evaluate the conditions for agents to evolve who have other-regarding preferences in making decisions in public good games.

This website uses cookies and Google Analytics to help us track user engagement and improve our site. If you'd like to know more information about what data we collect and why, please see our data privacy policy. If you continue to use this site, you consent to our use of cookies.