CiteULike: mcphee's modularity

Spontaneous evolution of modularity and network motifs.

Nadav Kashtan — 2005-09-27T18:51:05-00:00

Proc Natl Acad Sci U S A (20 September 2005)

Biological networks have an inherent simplicity: they are modular with a design that can be separated into units that perform almost independently. Furthermore, they show reuse of recurring patterns termed network motifs. Little is known about the evolutionary origin of these properties. Current models of biological evolution typically produce networks that are highly nonmodular and lack understandable motifs. Here, we suggest a possible explanation for the origin of modularity and network motifs in biology. We use standard evolutionary algorithms to evolve networks. A key feature in this study is evolution under an environment (evolutionary goal) that changes in a modular fashion. That is, we repeatedly switch between several goals, each made of a different combination of subgoals. We find that such "modularly varying goals" lead to the spontaneous evolution of modular network structure and network motifs. The resulting networks rapidly evolve to satisfy each of the different goals. Such switching between related goals may represent biological evolution in a changing environment that requires different combinations of a set of basic biological functions. The present study may shed light on the evolutionary forces that promote structural simplicity in biological networks and offers ways to improve the evolutionary design of engineered systems.

Representation and structural difficulty in genetic programming

Nguyen Hoai — 2008-02-14T14:23:47-00:00

Evolutionary Computation, IEEE Transactions on, Vol. 10, No. 2. (2006), pp. 157-166.

Standard tree-based genetic programming suffers from a structural difficulty problem in that it is unable to search effectively for solutions requiring very full or very narrow trees. This deficiency has been variously explained as a consequence of restrictions imposed by the tree structure or as a result of the numerical distribution of tree shapes. We show that by using a different tree-based representation and local (insertion and deletion) structural modification operators, that this problem can be almost eliminated even with trivial (stochastic hill-climbing) search methods, thus eliminating the above explanations. We argue, instead, that structural difficulty is a consequence of the large step size of the operators in standard genetic programming, which is itself a consequence of the fixed-arity property embodied in its representation.

Co-evolutionary modular neural networks for automatic problem decomposition

VR Khare — 2008-02-04T14:37:13-00:00

Evolutionary Computation, 2005. The 2005 IEEE Congress on, Vol. 3 (2005), pp. 2691-2698 Vol. 3.

Decomposing a complex computational problem into sub-problems, which are computationally simpler to solve individually and which can be combined to produce a solution to the full problem, can efficiently lead to compact and general solutions. Modular neural networks represent one of the ways in which this divide-and-conquer strategy can be implemented. Here we present a co-evolutionary model which is used to design and optimize modular neural networks with task-specific modules. The model consists of two populations. The first population consists of a pool of modules and the second population synthesizes complete systems by drawing elements from the pool of modules. Modules represent a part of the solution, which co-operates with others in the module population to form a complete solution. With the help of two artificial supervised learning tasks created by mixing two sub-tasks we demonstrate that if a particular task decomposition is better in terms of performance on the overall task, it can be evolved using this co-evolutionary model.

Environments Conducive to Evolution of Modularity

Vineet Khare — 2008-02-04T14:35:08-00:00

Parallel Problem Solving from Nature - PPSN IX (2006), pp. 603-612.

Modularity has been recognised as one of the crucial aspects of natural complex systems. Since these are results of evolution, it has been argued that modular systems must have selective advantages over their monolithic counterparts. Simulation results with artificial neuro-evolutionary complex systems, however, are indecisive in this regard. It has been shown that advantages of modularity, if judged on a static task, in these systems are very much dependent on various factors involved in the training of these systems. We present a couple of dynamic environments and argue that environments like these might be partly responsible for the evolution of modular systems. These environments allow for a better, more direct use of structural information present within modular systems hence limit the influence of other factors. We support these arguments with the help of a co-evolutionary model and a fitness measure based on system performance in these dynamic environments.

Modularity in genetic programming

J Woodward — 2008-01-22T11:01:48-00:00

(2003)

Genetic Programming uses a tree based representation to express solutions to problems. Trees are constructed from a primitive set which consists of a function set and a terminal set. An extension to GP is the ability to define modules, which are in turn tree based representations defined in terms of the primitives. The most well known of these methods is Koza's Automatically Defined Functions. In this paper it is proved that for a given problem, the minimum number of nodes in the main tree plus ...