Model Creation and Equivalence Proofs of Cellular Automata and Artificial Neural Networks

Computational methods and mathematical models have invaded arguably every scientific discipline forming its own field of research called computational science. Mathematical models are the theoretical foundation of computational science. Since Newton's time, differential equations in mathematical models have been widely and successfully used to describe the macroscopic or global behaviour of systems. With spatially inhomogeneous, time-varying, local element-specific, and often non-linear interactions, the dynamics of complex systems is in contrast more efficiently described by local rules and thus in an algorithmic and local or microscopic manner. The theory of mathematical modelling taking into account these characteristics of complex systems has to be established still. We recently presented a so-called allagmatic method including a system metamodel to provide a framework for describing, modelling, simulating, and interpreting complex systems. Implementations of cellular automata and artificial neural networks were described and created with that method. Guidance from philosophy were helpful in these first studies focusing on programming and feasibility. A rigorous mathematical formalism, however, is still missing. This would not only more precisely describe and define the system metamodel, it would also further generalise it and with that extend its reach to formal treatment in applied mathematics and theoretical aspects of computational science as well as extend its applicability to other mathematical and computational models such as agent-based models. Here, a mathematical definition of the system metamodel is provided. Based on the presented formalism, model creation and equivalence of cellular automata and artificial neural networks are proved. It thus provides a formal approach for studying the creation of mathematical models as well as their structural and operational comparison.Comment: 13 pages, 1 tabl

Artificial Immune Systems - Models, algorithms and applications

Copyright © 2010 Academic Research Publishing Agency.This article has been made available through the Brunel Open Access Publishing Fund.Artificial Immune Systems (AIS) are computational paradigms that belong to the computational intelligence family and are inspired by the biological immune system. During the past decade, they have attracted a lot of interest from researchers aiming to develop immune-based models and techniques to solve complex computational or engineering problems. This work presents a survey of existing AIS models and algorithms with a focus on the last five years.This article is available through the Brunel Open Access Publishing Fun

Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living things. Mathematical idealisations of biochemically reacting systems must be able to capture stochastic phenomena. While robust theory exists to describe such stochastic models, the computational challenges in exploring these models can be a significant burden in practice since realistic models are analytically intractable. Determining the expected behaviour and variability of a stochastic biochemical reaction network requires many probabilistic simulations of its evolution. Using a biochemical reaction network model to assist in the interpretation of time course data from a biological experiment is an even greater challenge due to the intractability of the likelihood function for determining observation probabilities. These computational challenges have been subjects of active research for over four decades. In this review, we present an accessible discussion of the major historical developments and state-of-the-art computational techniques relevant to simulation and inference problems for stochastic biochemical reaction network models. Detailed algorithms for particularly important methods are described and complemented with MATLAB implementations. As a result, this review provides a practical and accessible introduction to computational methods for stochastic models within the life sciences community

Instantaneous modelling and reverse engineering of data-consistent prime models in seconds!

A theoretical framework that supports automated construction of dynamic prime models purely from experimental time series data has been invented and developed, which can automatically generate (construct) data-driven models of any time series data in seconds. This has resulted in the formulation and formalisation of new reverse engineering and dynamic methods for automated systems modelling of complex systems, including complex biological, financial, control, and artificial neural network systems. The systems/model theory behind the invention has been formalised as a new, effective and robust system identification strategy complementary to process-based modelling. The proposed dynamic modelling and network inference solutions often involve tackling extremely difficult parameter estimation challenges, inferring unknown underlying network structures, and unsupervised formulation and construction of smart and intelligent ODE models of complex systems. In underdetermined conditions, i.e., cases of dealing with how best to instantaneously and rapidly construct data-consistent prime models of unknown (or well-studied) complex system from small-sized time series data, inference of unknown underlying network of interaction is more challenging. This article reports a robust step-by-step mathematical and computational analysis of the entire prime model construction process that determines a model from data in less than a minute

Developmental motifs reveal complex structure in cell lineages

Many natural and technological systems are complex, with organisational structures that exhibit characteristic patterns, but defy concise description. One effective approach to analysing such systems is in terms of repeated topological motifs. Here, we extend the motif concept to characterise the dynamic behaviour of complex systems by introducing developmental motifs, which capture patterns of system growth. As a proof of concept, we use developmental motifs to analyse the developmental cell lineage of the nematode Caenorhabditis elegans, revealing a new perspective on its complex structure. We use a family of computational models to explore how biases arising from the dynamics of the developmental gene network, as well as spatial and temporal constraints acting on development, contribute to this complex organisation

Nature-Inspired Coordination Models: Current Status and Future Trends

Coordination models and languages are meant to provide abstractions and mechanisms to harness the space of interaction as one of the foremost sources of complexity in computational systems. Nature-inspired computing aims at understanding the mechanisms and patterns of complex natural systems in order to bring their most desirable features to computational systems. Thus, the promise of nature-inspired coordination models is to prove themselves fundamental in the design of complex computational systems|such as intelligent, knowledge-intensive, pervasive, adaptive, and self-organising ones. In this paper, we survey the most relevant nature-inspired coordination models in the literature, focussing in particular on tuple-based models, and foresee the most interesting research trends in the field

ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra

Background: Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, with the goal to gain a better understanding of the system. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. Although there exist sophisticated algorithms to determine the dynamics of discrete models, their implementations usually require labor-intensive formatting of the model formulation, and they are oftentimes not accessible to users without programming skills. Efficient analysis methods are needed that are accessible to modelers and easy to use. Method: By converting discrete models into algebraic models, tools from computational algebra can be used to analyze their dynamics. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Results: A method for efficiently identifying attractors, and the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness, i.e., while the number of nodes in a biological network may be quite large, each node is affected only by a small number of other nodes, and robustness, i.e., small number of attractors