Simulating complex social behaviour with the genetic action tree kernel

The concept of genetic action trees combines action trees with genetic algorithms. In this paper, we create a multi-agent simulation on the base of this concept and provide the interested reader with a software package to apply genetic action trees in a multi-agent simulation to simulate complex social behaviour. An example model is introduced to conduct a feasibility study with the described method. We find that our library can be used to simulate the behaviour of agents in a complex setting and observe a convergence to a global optimum in spite of the absence of stable states

Evolutionary-based sparse regression for the experimental identification of duffing oscillator

In this paper, an evolutionary-based sparse regression algorithm is proposed and applied onto experimental data collected from a Duffing oscillator setup and numerical simulation data. Our purpose is to identify the Coulomb friction terms as part of the ordinary differential equation of the system. Correct identification of this nonlinear system using sparse identification is hugely dependent on selecting the correct form of nonlinearity included in the function library. Consequently, in this work, the evolutionary-based sparse identification is replacing the need for user knowledge when constructing the library in sparse identification. Constructing the library based on the data-driven evolutionary approach is an effective way to extend the space of nonlinear functions, allowing for the sparse regression to be applied on an extensive space of functions. The results show that the method provides an effective algorithm for the purpose of unveiling the physical nature of the Duffing oscillator. In addition, the robustness of the identification algorithm is investigated for various levels of noise in simulation. The proposed method has possible applications to other nonlinear dynamic systems in mechatronics, robotics, and electronics

Evolutionary Networks for Multi-Behavioural Robot Control : A thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Computer Science Massey University, Albany, New Zealand

Artificial Intelligence can be applied to a wide variety of real world problems, with varying levels of complexity; nonetheless, real world problems often demand for capabilities that are difficult, if not impossible to achieve using a single Artificial Intelligence algorithm. This challenge gave rise to the development of hybrid systems that put together a combination of complementary algorithms. Hybrid approaches come at a cost however, as they introduce additional complications for the developer, such as how the algorithms should interact and when the independent algorithms should be executed. This research introduces a new algorithm called Cascading Genetic Network Programming (CGNP), which contains significant changes to the original Genetic Network Programming. This new algorithm has the facility to include any Artificial Intelligence algorithm into its directed graph network, as either a judgement or processing node. CGNP introduces a novel ability for a scalable multiple layer network, of independent instances of the CGNP algorithm itself. This facilitates problem subdivision, independent optimisation of these underlying layers and the ability to develop varying levels of complexity, from individual motor control to high level dynamic role allocation systems. Mechanisms are incorporated to prevent the child networks from executing beyond their requirement, allowing the parent to maintain control. The ability to optimise any data within each node is added, allowing for general purpose node development and therefore allowing node reuse in a wide variety of applications without modification. The abilities of the Cascaded Genetic Network Programming algorithm are demonstrated and proved through the development of a multi-behavioural robot soccer goal keeper, as a testbed where an individual Artificial Intelligence system may not be sufficient. The overall role is subdivided into three components and individually optimised which allow the robot to pursue a target object or location, rotate towards a target and provide basic functionality for defending a goal. These three components are then used in a higher level network as independent nodes, to solve the overall multi- behavioural goal keeper. Experiments show that the resulting controller defends the goal with a success rate of 91%, after 12 hours training using a population of 400 and 60 generations

An Artificial Life Simulation Library Based on Genetic Algorithm, 3-Character Genetic Code and Biological Hierarchy

Genetic algorithm (GA) is inspired by biological evolution of genetic organisms by optimizing the genotypic combinations encoded within each individual with the help of evolutionary operators, suggesting that GA may be a suitable model for studying real-life evolutionary processes. This paper describes the design of a Python library for artificial life simulation, Digital Organism Simulation Environment (DOSE), based on GA and biological hierarchy starting from genetic sequence to population. A 3-character instruction set that does not take any operand is introduced as genetic code for digital organism. This mimics the 3-nucleotide codon structure in naturally occurring DNA. In addition, the context of a 3-dimensional world composing of ecological cells is introduced to simulate a physical ecosystem. Using DOSE, an experiment to examine the changes in genetic sequences with respect to mutation rates is presented

Combining polynomial chaos expansions and genetic algorithm for the coupling of electrophysiological models

The number of computational models in cardiac research has grown over the last decades. Every year new models with di erent assumptions appear in the literature dealing with di erences in interspecies cardiac properties. Generally, these new models update the physiological knowledge using new equations which reect better the molecular basis of process. New equations require the fi tting of parameters to previously known experimental data or even, in some cases, simulated data. This work studies and proposes a new method of parameter adjustment based on Polynomial Chaos and Genetic Algorithm to nd the best values for the parameters upon changes in the formulation of ionic channels. It minimizes the search space and the computational cost combining it with a Sensitivity Analysis. We use the analysis of di ferent models of L-type calcium channels to see that by reducing the number of parameters, the quality of the Genetic Algorithm dramatically improves. In addition, we test whether the use of the Polynomial Chaos Expansions improves the process of the Genetic Algorithm search. We conclude that it reduces the Genetic Algorithm execution in an order of 103 times in the case studied here, maintaining the quality of the results. We conclude that polynomial chaos expansions can improve and reduce the cost of parameter adjustment in the development of new models.Peer ReviewedPostprint (author's final draft

Effective simulation techniques for biological systems

In this paper we give an overview of some very recent work on the stochastic simulation of systems involving chemical reactions. In many biological systems (such as genetic regulation and cellular dynamics) there is a mix between small numbers of key regulatory proteins, and medium and large numbers of molecules. In addition, it is important to be able to follow the trajectories of individual molecules by taking proper account of the randomness inherent in such a system. We describe different types of simulation techniques (including the stochastic simulation algorithm, Poisson Runge-Kutta methods and the Balanced Euler method) for treating simulations in the three different reaction regimes: slow, medium and fast. We then review some recent techniques on the treatment of coupled slow and fast reactions for stochastic chemical kinetics and discuss how novel computing implementations can enhance the performance of these simulations

TinkerCell: Modular CAD Tool for Synthetic Biology

Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application named TinkerCell has been created in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various C and Python programs that are hosted by TinkerCell via an extensive C and Python API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. Because TinkerCell associates parameters and equations in a model with their respective part, parts can be loaded from databases along with their parameters and rate equations. The modular network design can be used to exchange modules as well as test the concept of modularity in biological systems. The flexible modeling framework along with the C and Python API allows TinkerCell to serve as a host to numerous third-party algorithms. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at www.tinkercell.com.Comment: 23 pages, 20 figure