PUBLICATIONS

Conference Papers

Simon Hickinbotham, Edward Clark, Susan Stepney, Tim Clarke, Adam Nellis, Mungo Pay, Peter Young.
Molecular microprograms.
In ECAL 2009, Budapest, Hungary, September 2009. LNCS. Springer, 2009

Abstract:Bacteria offer an evolutionary model in which rich interactions between phenotype and genotype lead to compact genomes with efficient metabolic pathways. Central to this is the expression and folding of sequences of amino acids to form proteins. We seek an analogous process that supports a rich artificial heredity. These systems can be simulated by stochastic chemistry models, but there is currently no scope for open-ended evolution of the molecular species that make up the models. Instruction-set based Artifical Life has appropriate evolutionary properties, but the individual is represented as a single executing sequence with little additional physiology. We describe a novel combination of stochastic chemistries and evolvable molecule microprograms that gives a rich evolutionary framework. Key to this approach is the use of inexact sequence matching for binding between individual molecules and for branching of molecular microprograms. We illustrate the approach by implementation of two steady-state replicase RNA analogues that demonstrate "invasion when rare".

@inproceedings(SS-ECAL09c,
  author = "Simon Hickinbotham and Edward Clark and Susan Stepney and Tim Clarke
            and Adam Nellis and Mungo Pay and Peter Young",
  title = "Molecular microprograms",
  crossref = "ECAL09"

)

@proceedings(ECAL09,
  title = "ECAL 2009, Budapest, Hungary, September 2009",
  booktitle = "ECAL 2009, Budapest, Hungary, September 2009",
  series = "LNCS",
  publisher = "Springer",
  year = 2009
)

Simon Hickinbotham, Edward Clark, Susan Stepney, Tim Clarke, Peter Young.
Gene Regulation in a Particle Metabolome.
in CEC 2009, Trondheim, Norway, May 2009. IEEE Press 2009

Abstract: The bacterial genome is well understood by biologists. Although its efficiency and adaptability should make it a good model for evolutionary algorithms, the bacterial genome is tightly coupled with the components of the bacterial metabolism, referred to here as the metabolome. This paper explores an approach to modelling an artificial bacterial metabolome in an efficient and modular manner, so that analogues of bacterial genome organisation and gene regulation can be implemented in evolutionary algorithms. We propose a particulate model of bacterial metabolic pathways in which the constituents drift in a fixed, limited space and obey a limited set of biologically plausible reaction rules. The potential of this model is demonstrated by creating a network that is capable of appropriate behavioural switching that can be observed in bacteria.

full text (pdf) 
@inproceedings(SS-CEC09-p,
  author = "Simon Hickinbotham and Edward Clark and Susan Stepney and Tim Clarke and Peter Young",
  title = "Gene Regulation in a Particle Metabolome",
  crossref = "CEC09"
)

@proceedings(CEC09,
  title = "CEC 2009, Trondheim, Norway, May 2009",
  booktitle = "CEC 2009, Trondheim, Norway, May 2009",
  publisher = "IEEE Press",
  year = 2009

Susan Stepney, Tim Clarke, Peter Young.
PLAZZMID: An evolutionary agent-based architecture inspired by bacteria and bees.,
In ECAL 2007, Lisbon, Portugal, September 2007. LNAI 4648:1151-1160. Springer, 2007

Abstract: Classical evolutionary algorithms have been extremely successful at solving certain problems. But they implement a very simple model of evolutionary biology that misses out several aspects that might be exploited by more sophisticated algorithms. We have previously critiqued the traditional naïve approach to bio-inspired algorithm design, that moves straight from a simplistic description of the biology into some algorithm. Here we present a process for developing richer evolutionary algorithms abstracted from various processes of biological evolution, with a corresponding richer analogical computational structure, and indicate how that might be further abstracted.

full text (pdf) 
@inproceedings(SS-ECAL07a,
  author = "Susan Stepney and Tim Clarke and Peter Young",
  title = "PLAZZMID: An evolutionary agent-based architecture
           inspired by bacteria and bees",
  pages = "1151--1160",
  crossref = "ECAL07"
)

@proceedings(ECAL07,
  title = "ECAL 2007, Lisbon, Portugal, September 2007",
  booktitle = "ECAL 2007, Lisbon, Portugal, September 2007",
  series = "LNAI",
  volume = 4648,
  publisher = "Springer",
  year = 2007
)