Tag-based modules in genetic programming

In this paper we present a new technique for evolving mod-ular programs with genetic programming. The technique is based on the use of “tags ” that evolving programs may use to label and later to refer to code fragments. Tags may refer inexactly, permitting the labeling and use of code fragments to co-evolve in an incremental way. The technique can be implemented as a minor modification to an existing, general purpose genetic programming system, and it does not re-quire pre-specification of the module architecture of evolved programs. We demonstrate that tag-based modules readily evolve and that this allows problem solving effort to scale well with problem size. We also show that the tag-based module technique is effective even in complex, non-uniform problem environments for which previous techniques per-form poorly. We demonstrate the technique in the context of the stack-based genetic programming system PushGP, but we also briefly discuss ways in which it may be used with other kinds of genetic programming systems

Sequential Symbolic Regression with Genetic Programming

This chapter describes the Sequential Symbolic Regression (SSR) method, a new strategy for function approximation in symbolic regression. The SSR method is inspired by the sequential covering strategy from machine learning, but instead of sequentially reducing the size of the problem being solved, it sequentially transforms the original problem into potentially simpler problems. This transformation is performed according to the semantic distances between the desired and obtained outputs and a geometric semantic operator. The rationale behind SSR is that, after generating a suboptimal function f via symbolic regression, the output errors can be approximated by another function in a subsequent iteration. The method was tested in eight polynomial functions, and compared with canonical genetic programming (GP) and geometric semantic genetic programming (SGP). Results showed that SSR significantly outperforms SGP and presents no statistical difference to GP. More importantly, they show the potential of the proposed strategy: an effective way of applying geometric semantic operators to combine different (partial) solutions, avoiding the exponential growth problem arising from the use of these operators

Automated Problem Decomposition for the Boolean Domain with Genetic Programming

Researchers have been interested in exploring the regularities and modularity of the problem space in genetic programming (GP) with the aim of decomposing the original problem into several smaller subproblems. The main motivation is to allow GP to deal with more complex problems. Most previous works on modularity in GP emphasise the structure of modules used to encapsulate code and/or promote code reuse, instead of in the decomposition of the original problem. In this paper we propose a problem decomposition strategy that allows the use of a GP search to find solutions for subproblems and combine the individual solutions into the complete solution to the problem

Cis-regulatory module detection using constraint programming

We propose a method for finding CRMs in a set of co-regulated genes. Each CRM consists of a set of binding sites of transcription factors. We wish to find CRMs involving the same transcription factors in multiple sequences. Finding such a combination of transcription factors is inherently a combinatorial problem. We solve this problem by combining the principles of itemset mining and constraint programming. The constraints involve the putative binding sites of transcription factors, the number of sequences in which they co-occur and the proximity of the binding sites. Genomic background sequences are used to assess the significance of the modules. We experimentally validate our approach and compare it with state-of-the-art techniques

Network-based business process management: embedding business logic in communications networks

Advanced Business Process Management (BPM) tools enable the decomposition of previously integrated and often ill-defined processes into re-usable process modules. These process modules can subsequently be distributed on the Internet over a variety of many different actors, each with their own specialization and economies-of-scale. The economic benefits of process specialization can be huge. However, how should such actors in a business network find, select, and control, the best partner for what part of the business process, in such a way that the best result is achieved? This particular management challenge requires more advanced techniques and tools in the enabling communications networks. An approach has been developed to embed business logic into the communications networks in order to optimize the allocation of business resources from a network point of view. Initial experimental results have been encouraging while at the same time demonstrating the need for more robust techniques in a future of massively distributed business processes.active networks;business process management;business protocols;embedded business logic;genetic algorithms;internet distributed process management;payment systems;programmable networks;resource optimization

Matchmaker, Matchmaker, Make Me a Match: Geometric, Variational, and Evolutionary Implications of Criteria for Tag Affinity

Genetic programming and artificial life systems commonly employ tag-matching schemes to determine interactions between model components. However, the implications of criteria used to determine affinity between tags with respect to constraints on emergent connectivity, canalization of changes to connectivity under mutation, and evolutionary dynamics have not been considered. We highlight differences between tag-matching criteria with respect to geometric constraint and variation generated under mutation. We find that tag-matching criteria can influence the rate of adaptive evolution and the quality of evolved solutions. Better understanding of the geometric, variational, and evolutionary properties of tag-matching criteria will facilitate more effective incorporation of tag matching into genetic programming and artificial life systems. By showing that tag-matching criteria influence connectivity patterns and evolutionary dynamics, our findings also raise fundamental questions about the properties of tag-matching systems in nature

Evolving artificial cell signaling networks using molecular classifier systems

Nature is a source of inspiration for computational techniques which have been successfully applied to a wide variety of complex application domains. In keeping with this we examine Cell Signaling Networks (CSN) which are chemical networks responsible for coordinating cell activities within their environment. Through evolution they have become highly efficient for governing critical control processes such as immunological responses, cell cycle control or homeostasis. Realising (and evolving) Artificial Cell Signaling Networks (ACSNs) may provide new computational paradigms for a variety of application areas. Our abstraction of Cell Signaling Networks focuses on four characteristic properties distinguished as follows: Computation, Evolution, Crosstalk and Robustness. These properties are also desirable for potential applications in the control systems, computation and signal processing field. These characteristics are used as a guide for the development of an ACSN evolutionary simulation platform. In this paper we present a novel evolutionary approach named Molecular Classifier System (MCS) to simulate such ACSNs. The MCS that we have designed is derived from Holland's Learning Classifier System. The research we are currently involved in is part of the multi disciplinary European funded project, ESIGNET, with the central question of the study of the computational properties of CSNs by evolving them using methods from evolutionary computation, and to re-apply this understanding in developing new ways to model and predict real CSNs