Publications
2008
Dual Phase Evolution and Self-Organisation in Networks.
Greg Paperin ; David G. Green ; Tania G. Leishman (2008).
The Seventh International Conference on Simulated Evolution And Learning (SEAL'08).
Editor TBD (ed.).
07/12/2008.
Springer.
ISBN TBD.
ISSN TBD.
Keywords : Dual Phase Evolution ; networks ; phase change ; scale-free networks ; modularity .More details Abstract:
Dual Phase Evolution (DPE) is a widespread natural process in which complex systems adapt and self-organise by switching alternately between two phases: a phase of global interactions and a phase of local interactions. We show that in evolving networks of agents, DPE can give rise to a wide variety of topologies. In particular, it can lead to the spontaneous emergence of stabilising modular structure. Export: Tagged - XML - BibTex .Full details
Evolving sequence patterns for prediction of sub-cellular locations of eukaryotic proteins.
Greg Paperin (2008).
Genetic and Evolutionary Computation Conference 2008 (GECCO’08).
Pp. 1135-1136.
Association for Computing Machinery.
ISBN 978-1-60558-130-9.
Keywords : protein localisation ; classifier ; machine learning ; pattern learning .More details Abstract:
A genetic algorithm (GA) is utilised to discover known and novel PROSITE-like sequence templates that can be used to classify the sub-cellular location of eukaryotic proteins. While traditional machine learning techniques present a black-box approach to this problem, the current method explicitly represents the discovered localisation motifs. A combined multi-class location classifier is presented and compared to other techniques based on genetic programming. Without consideration of additional structural information the presented method outperforms the alternative techniques. Link : http://portal.acm.org/citation.cfm?id=1389095.1389315 Export: Tagged - XML - BibTex .Full details
Holey Fitness Landscapes and the Maintenance of Evolutionary Diversity.
Greg Paperin ; Suzanne Sadedin ; David G. Green ; Alan Dorin (2008).
11th International Conference on Artificial Life (ALife XI).
Seth Bullock; Jason Noble; Richard Watson; Mark Bedau (ed.).
MIT Press.
Keywords : Holey Fitness Landscape ; diversity ; reproductive isolation ; speciation ; hybridisation .More details Abstract:
Analytical models show that high-dimensional fitness landscapes form “holey” rather than “rugged” topographies, but the implications of this finding for biological and artificial life systems remain largely unexplored. One of the reasons for this gap can be attributed to serious difficulties in the implementation of individual-based holey fitness landscape (HFL) models. Here, we introduce a method for simulating HFLs in spatially explicit individual-based models that overcomes these difficulties. We examine how the HFL changes predictions for the maintenance of genetic diversity in the face of migration. Previous models suggest that ecologically-based reproductive isolation will rapidly collapse under migration. Our results indicate that an underlying HFL can often maintain diversity in this situation. Hybrid species emerge frequently when HFL genetics are simulated, but are usually doomed to extinction because of small population sizes. However, hybridisation can also lead to novel adaptations and potentially the exploitation of new ecological niches. More generally, the results imply that HFL genetics should not be neglected in studies of adaptation and diversity. Export: Tagged - XML - BibTex .Full details
Using Holey Fitness Landscapes to Counteract Premature Convergence in Evolutionary Algorithms.
Greg Paperin (2008).
Graduate Student Workshop at the Genetic and Evolutionary Computation Conference 2008 (GECCO’08).
Steven Gustafson (ed.).
Pp. 1815-1818.
Association for Computing Machinery.
ISBN 978-1-60558-131-6.
Keywords : evolutionary algorithm ; genetic algorithm ; Holey Fitness Landscape ; gene flow ; premature convergence ; reproductive isolation .More details Abstract:
Premature convergence is a persisting problem in evolutionary optimisation, in particular – genetic algorithms. While a number of methods exist to approach this issue, they usually require problem specific calibration or only partially resolve the issue, at best by delaying the premature convergence of an evolving population. Analytical models in biology show that resiliently diverse populations evolve on high-dimensional fitness landscapes with “holey” rather than “rugged” topographies, but the implications for artificial evolutionary systems remain largely unexplored. Here I show how holey fitness landscapes (HFLs) can be incorporated in an evolutionary algorithm and use this approach to investigate the ability of HFLs to maintain genetic diversity in an evolving population. The results indicate that an underlying HFL can counteract premature genetic convergence and sustain diversity. They also suggest that HFL may provide a flexible mechanism for dynamic creation and maintenance of subpopulations that concentrate their evolutionary search in different regions of the solution space. Finally, I discuss on-going work on using the HFL model in optimisation problems. Link : http://portal.acm.org/citation.cfm?id=1388978 Export: Tagged - XML - BibTex .Full details
2007
A Dual Phase Evolution model of adaptive radiation in landscapes.
Greg Paperin ; David G. Green ; Suzanne Sadedin ; Tania G. Leishman (2007).
3rd Australian Conference on Artificial Life (ACAL’07).
Markus Randall; Hussein A. Abbass; Janet Wiles (ed.).
Vol. 4828/2007.
Pp. 131-143.
Springer.
ISBN 978-3-540-76930-9.
ISSN 0302-9743.
DOI 10.1007/978-3-540-76931-6.
Keywords : Dual Phase Evolution ; complexity ; speciation ; adaptive radiation ; landscape connectivity ; simulation .More details Abstract:
In this study, we describe an evolutionary mechanism – Dual Phase Evolution (DPE) – and argue that it plays a key role in the emergence of internal structure in complex adaptive systems (CAS). Our DPE theory proposes that CAS exhibit two well-defined phases – selection and variation – and that shifts from one phase to the other are triggered by external perturbations. We discuss empirical data which demonstrates that DPE processes play a prominent role in species evolution within landscapes and argue that processes governing a wide range of self-organising phenomena are similar in nature. In support, we present a simulation model of adaptive radiation in landscapes. In the model, organisms normally exist within a connected landscape in which selection maintains them in a stable state. Intermittent disturbances (such as fires, commentary impacts) flip the system into a disconnected phase, in which populations become fragmented, freeing up areas of empty space in which selection pressure lessens and genetic variation predominates. The simulation results show that the DPE mechanism may indeed facilitate the appearance of complex diversity in a landscape ecosystem. Link : http://www.springerlink.com/content/0481n48135l3n517/ Export: Tagged - XML - BibTex .Full details
Complexity in Speciation: Effects of disasters on adaptive radiation in a Dual Phase Evolution model.
Greg Paperin ; David G. Green ; Suzanne Sadedin ; Tania G. Leishman (2007).
8th Asia-Pacific Complex Systems Conference (Complex’07).
Keywords : Dual Phase Evolution ; complexity ; speciation ; adaptive radiation ; landscape connectivity .More details Abstract:
Recent studies suggest that macro-evolutionary patterns such as punctuated equilibrium may be generated by a process termed Dual Phase Evolution (DPE). According to the DPE hypothesis, evolution in landscapes exhibits two phases – selection and variation. Disturbances such as mass extinctions can flip the landscape from selection to variation phases. Similar processes occur in a wide range of artificial, natural and social complex systems. Here, we show that mass extinctions induce DPE in a simulation model of adaptive radiation. The model is based on a previous model of adaptive radiation which did not incorporate Dual Phase Evolution. Results confirm that mass extinctions caused by external disturbances can trigger periods of rapid species turnover and adaptive radiation (variation phases), which are followed by long periods without innovation (selection phases). Our simulations also show that the spatial configuration of disasters leading to mass extinctions strongly influences whether and to what extent such disasters are capable of inducing evolutionary variation phases. Link : http://www.complex07.org/index/sitemember-abstracts-action#General%20Track Export: Tagged - XML - BibTex .Full details
Dual Phase Evolution – a mechanism for self-organisation and optimisation.
Tania G. Leishman ; David G. Green ; Greg Paperin (2007).
Asia-Pacific Symposium on Intelligent and Evolutionary Systems 2007 (APSIES’07).
Keywords : Dual Phase Evolution ; complexity ; networks ; criticality ; phase change ; evolution ; self-organization ; landscape ; optimization .More details Abstract:
We describe a process, Dual Phase Evolution (DPE), which is a widespread mechanism by which systems evolve. The process occurs in systems that switch between two phases: a balance phase and a variation phase. In DPE, processes drive systems to settle in a “balance” phase, but external stimuli can flip the system into a temporary “variation” phase, in which rapid change occurs on all scales. The system gradually returns to a new balance phase, often with different structure than formerly. We argue that the system occurs in many natural systems and show how it results from landscape connectivity in both evolution and long-term forest change. We describe how it underlies certain optimization algorithms, and can be implemented to improve the performance of existing optimization methods. Finally, we present simulation experiments that show how DPE may play a role in creating cliques, clusters, modules and other kinds of order within social networks. Link : http://www.nda.ac.jp/cs/IES2007/finalprog.htm Export: Tagged - XML - BibTex .Full details
Fitness Landscapes in Individual-Based Simulation Models of Adaptive Radiation.
Greg Paperin ; David G. Green ; Alan Dorin (2007).
2007 International Symposium on Computational Models for Life Sciences (CMLS’07).
Tuan D. Pham; Xiaobo Zhou (ed.).
Vol. 952.
Pp. 268-278.
American Institute of Physics.
ISBN 978-0-7354-0466-3.
ISSN 0094-243X.
DOI 10.1063/1.2816631.
Keywords : Holey Fitness Landscape ; adaptive radiation ; speciation ; individual-based modelling ; fitness landscape ; fitness .More details Abstract:
We provide a brief overview of the use of FLs in evolutionary biology and introduce an FL model suitable for individual-based models of species evolution. Our model combines different features of several analytic FL models used in evolutionary biology. Our new model overcomes several difficulties encountered with previous FL models, particularly arbitrary divergence thresholds. We discuss the difficulties encountered during the implementation of our model and how we have overcome these. We present a detailed numerical analysis of the proposed family of FLs that will inform future work based on our FL model. Link : http://link.aip.org/link/?APCPCS/952/268/1 Export: Tagged - XML - BibTex .Full details
Security of Communication and Quantum Technology.
Greg Paperin (2007).
Encyclopaedia of Information Ethics and Security.
Marian Quigley (ed.).
Idea Group Publishing.
ISBN 159140987X.
Keywords : physics ; networks ; security .More details Abstract:
In this article we aim to analyse some of the advances in security of communication since this discipline evolved and to pinpoint the main problems. We then introduce a modern attempt to solve some of these problems, in particular the key distribution problem, by using the theory of quantum mechanics to construct a communication system that automatically detects eavesdropping. We examine some of the implications of quantum mechanics relevant to this field and then introduce a selection of communication protocols based on them. Finally we examine how secure these protocols are and identify their potential weaknesses. Link : http://books.igi-online.com/content/details.asp?ID=16806 Export: Tagged - XML - BibTex .Full details
2006
Biology of Applied Digital Ecosystems.
Gerard Briscoe ; Suzanne Sadedin ; Greg Paperin (2006).
Inaugural IEEE International Conference on Digital Ecosystems and Technologies 2007 (DEST’07).
Pp. 458-463.
IEEE.
ISBN 1-4244-0470-3.
DOI 10.1109/DEST.2007.372015.
Keywords : digital ecosystem ; complexity ; ecosystem ; evolution .More details Abstract:
A primary motivation for research in digital ecosystems is the desire to exploit the self-organising properties of natural ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex, dynamic problems. However, the biological processes that contribute to these properties have not been made explicit in digital ecosystem research. Here, we discuss how biological properties contribute to the self-organising features of natural ecosystems. These properties include populations of evolving agents, a complex dynamic environment, and spatial distributions which generate local interactions. The potential for exploiting these properties in artificial systems is then considered. An example architecture, the Digital Business Ecosystem (DBE), is considered in detail. Simulation results imply that the DBE performs better at large scales than a comparable service-oriented architecture. These results suggest that incorporating ideas from theoretical ecology can contribute to useful self-organising properties in digital ecosystems. Link : http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4233749 Export: Tagged - XML - BibTex .Full details
