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Dual Phase Evolution in Complex Adaptive Systems

 

Publication Type:

Journal Article

Source:

Roy Soc J Interface. The Royal Society, Volume 8, Issue 58, pp. 609-629.

ISSN:

1742-5662

DOI:

10.1098/​rsif.2010.0719

URL:

http://rsif.royalsocietypublishing.org/content/8/58/609.short

Keywords:

Dual Phase Evolution; network; connectivity; phase change; complex system; phase transition

Abstract:

Understanding the origins of complexity is a key challenge in many sciences. Although networks are known to underlie most systems, showing how they contribute to well-known phenomena remains an issue. Here, we show that recurrent phase transitions in network connectivity underlie emergent phenomena in many systems. We identify properties that are typical of systems in different connectivity phases, as well as characteristics commonly associated with the phase transitions. We synthesize these common features into a common framework, which we term dual-phase evolution (DPE). Using this framework, we review the literature from several disciplines to show that recurrent connectivity phase transitions underlie the complex properties of many biological, physical and human systems. We argue that the DPE framework helps to explain many complex phenomena, including perpetual novelty, modularity, scale-free networks and criticality. Our review concludes with a discussion of the way DPE relates to other frameworks, in particular, self-organized criticality and the adaptive cycle.

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Dual Phase Evolution as a Framework for Understanding Complex Adaptive Systems

 

Publication Type:

Book Chapter

Authors:

Greg Paperin; Suzanne Sadedin (2011)

Source:

Kurosh Madani; António Dourado Correia; Agostinho Rosa; Joaquim Filipe (eds.), Computational Intelligence. Springer, Volume 343, pp. 151-164.

ISBN:

978-3-642-20205-6

DOI:

10.1007/978-3-642-20206-3

URL:

http://www.springerlink.com/content/l2288475htw53562/

Keywords:

Dual Phase Evolution; network; connectivity; phase change; self-organised criticality; adaptive cycle

Abstract:

This is a republication of this 2009 paper.

Evidence from several fields suggests that dual phase evolution (DPE) may account for distinctive features associated with complex adaptive systems. Here, we review empirical and theoretical evidence for DPE in natural systems and examine the relationship of DPE to self-organized criticality and adaptive cycles. A general model for DPE in networks is outlined, with preliminary data illustrating the emergence of phase changes.

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Implications of the Social Brain Hypothesis for Evolving Human-Like Cognition in Digital Organisms

 

Publication Type:

Book Chapter

Authors:

Suzanne Sadedin; Greg Paperin (2011)

Source:

George Kampis; István Karsai; Eörs Szathmáry (eds.), Advances in Artificial Life. Darwin Meets von Neumann. ECAL'09. Revised Selected Papers II. Springer, Volume 5778, pp. 61-68.

ISBN:

978-3-642-21313-7

DOI:

10.1007/978-3-642-21314-4

URL:

http://www.springerlink.com/content/xv4v38q78w2066n4/

Keywords:

artificial intelligence; sociality; evolution; social selection; Machiavellian intelligence; ALife

Abstract:

This is a republication of this 2009 paper.

Data show that human-like cognitive traits do not evolve in animals through natural selection. Rather, human-like cognition evolves through runaway selection for social skills. Here, we discuss why social selection may be uniquely effective for promoting human-like cognition, and the conditions that facilitate it. These observations suggest future directions for artificial life research aimed at generating human-like cognition in digital organisms.

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The Dual Phase Evolution Framework for Understanding Evolutionary Dynamics in Complex Adaptive Systems

 

Publication Type:

Conference Proceedings

Authors:

Greg Paperin; Suzanne Sadedin (2009)

Source:

Proceedings of 2009 International Conference on Evolutionary Computation (ICEC'09), Madeira, Portugal.

Keywords:

Dual Phase Evolution; network; connectivity; phase change; self-organised criticality; adaptive cycle

Abstract:

Evidence from several fields suggests that dual phase evolution (DPE) may account for distinctive features associated with complex adaptive systems. Here, we review empirical and theoretical evidence for DPE in natural systems and examine the relationship of DPE to self-organized criticality and adaptive cycles. A general model for DPE in networks is outlined, with preliminary data illustrating the emergence of phase changes.

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Implications of the social brain hypothesis for evolving human-like cognition in digital organisms

 

Publication Type:

Conference Proceedings

Authors:

Suzanne Sadedin; Greg Paperin (2009)

Source:

Proceedings of 10th European Conference on Artificial Life (ECAL’09), Budapest. Springer.

Keywords:

artificial intelligence; sociality; evolution; social selection; Machiavellian intelligence; ALife

Abstract:

Data show that human-like cognitive traits do not evolve in animals through natural selection. Rather, human-like cognition evolves through runaway selection for social skills. Here, we discuss why social selection may be uniquely effective for promoting human-like cognition, and the conditions that facilitate it. These observations suggest future directions for artificial life research aimed at generating human-like cognition in digital organisms.

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Towards formalising the theory of Dual Phase Evolution

 

Publication Type:

Conference Paper

Authors:

Greg Paperin; Suzanne Sadedin (2009)

Source:

Presented at 10th European Conference on Artificial Life (ECAL’09), Budapest. Springer.

Keywords:

Dual Phase Evolution; complexity; network; criticality; phase change; connectivity

Abstract:

Evidence from several fields suggests that Dual Phase Evolution (DPE) may account for distinctive features associated with complex adaptive systems. We review empirical and theoretical evidence for DPE in natural systems and examine the relationship of DPE to other complexity theories such self-organised criticality and adaptive cycles.

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FIT1004 / FIT2010 - Databases

This page contains additional learning material, tips and examples for unit FIT1004/FIT2010 (Databases) at Monash.

FIT1004/2010 is an introductory unit on databases at Monash University directed primarily towards Bachelor of Business Information Systems students. The FIT1004 and FIT2010 units are largely the same, with FIT1004 being offered for first year students, and FIT2010 for second year students.

                                                                                                                                                                                                                                                                                       

Library for animated bar-graphs in HTML pages based on coloured tables and JavaScript

This project aims to provide a convenient, easy and fast way to include bar-graphs and bar-charts of various kinds into web pages.

The approach taken utilises only coloured tables and JavaScript to achieve the goal, i.e. no images are used. An object-oriented JavaScript library handles the insertion of bar-charts into any HTML page. The graphs can be static or animated, and the animation can be controlled by the user in an interactive fashion.

                                                                                                                                                                                                                                                                                       

Dual Phase Evolution and Self-Organisation in Networks

 

Publication Type:

Conference Proceedings

Source:

Xiaodong Li; Michael Kirley; Mengjie Zhang; David G. Green; Vic Ciesielski; Hussein Abbass; Zbigniew Michalewicz; Tim Hendtlass; Kalyanmoy Deb; K.C. Tan; Jürgen Branke; Yuhui Shi (eds.), Proceedings of The Seventh International Conference on Simulated Evolution And Learning (SEAL'08), Melbourne, Australia. Springer, Volume 5361/2008, pp. 575-584.

ISBN:

978-3-540-89693-7

ISSN:

0302-9743

URL:

http://www.springerlink.com/content/l71001w15707t867/

Keywords:

Dual Phase Evolution; complexity; network; criticality; phase change; evolution; self-organisation; scale-free network; modularity

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.

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CSE2305 - Object-Oriented Software Engineering

I was teaching the computer lab and tutorial clases for
CSE2305 - Object-Oriented Software Engineering (Spring semester 2006).
The unit mainly concentrated on object oriented programming using C++.

                                                                                                                                                                                                                                                                                       

Intersection Testing

Corresponding unit: 
Advanced Computer Graphics
Mark: 
Binary passed
Info: 

The aim of the course was specifically to create an applied tutorial into one of the topics treated in the unit. My topic was intersection testing.
Thus, the attached paper specifically represents an introduction into collision detection and intersection testing for students interested in the topic. Some basic algebra skills are required.
Note that the general part of the paper makes extensive use of Wikipedia and other open online sources. Interested readers will wind a wealth of supplementary information there.

                                                                                                                                                                                                                                                                                       

Advanced Computer Graphics

Unit code: 
WiSe0506-18.362
Year: 
Advanced level (University of Hamburg, 2006)
Final mark: 
Course completed
Description: 

Understanding and practical application (using OpenGL) of current state-of-art graphics rendering techniques and pipeline.
Really nice unit. Based on seminars rather than lectures.
Everyone presented a topic in-depth. My topic was intersection testing.

Unit courseworks: 
1
                                                                                                                                                                                                                                                                                       

Protein localisation

Mark: 
A
Info: 

This is about evolving sequence patterns for prediction of sub-cellular locations of eukaryotic proteins. See question sheet for more details.
A few years after it was completed as a Master's coursework assignment, this work has been published in peer-reviewed conference proceedings. Instead of providing the original solution I thus refer to the shortened version that has been published as Paperin (2008): Evolving Sequence Patterns For Prediction Of Sub-Cellular Locations Of Eukaryotic Proteins.

                                                                                                                                                                                                                                                                                       

Ant Colony Optimisation Coursework

Corresponding unit: 
Evolutionary Computation
Mark: 
Don't remember, I think, A.
Info: 

Well, I was very stressed and short on time, so I am not sure whether the tone was appropriate, but I think, it is still nice work. I do not have the question sheet any more, but basically this is a simulation model to solve Travelling Salesman Problem instances using Ant Colony Optimisation.

                                                                                                                                                                                                                                                                                       

Genetic Programming Coursework

Corresponding unit: 
Evolutionary Computation
Mark: 
A+
Info: 

This is how JAGA was born. Enjoy.

                                                                                                                                                                                                                                                                                       

Genetic Algorithms Coursework

Corresponding unit: 
Evolutionary Computation
Mark: 
No idea
Info: 

This coursework is about Genetic Algorithms. See question sheet for details. Note, what did not get done here, was well ready for the second coursework.

                                                                                                                                                                                                                                                                                       

Coursework 5

Corresponding unit: 
Supervised Machine Learning
Mark: 
No idea
Info: 

Something about estimators. I can't find the question sheet.

                                                                                                                                                                                                                                                                                       

Coursework 4

Corresponding unit: 
Supervised Machine Learning
Mark: 
No idea
Info: 

Decision trees.
Questions are repeated on the answer sheet. See there.

                                                                                                                                                                                                                                                                                       

Coursework 3

Corresponding unit: 
Supervised Machine Learning
Mark: 
No idea
Info: 

I really don't know any more...
Page 3 seems to be lost too..

                                                                                                                                                                                                                                                                                       

Coursework 2

Corresponding unit: 
Supervised Machine Learning
Mark: 
Do not remember
Info: 

I am not quite sure any more, but I think this was about an implementation of a Perceptron and evaluating it on some datasets. Unfortunately, the question sheet is lost.

                                                                                                                                                                                                                                                                                       

Coursework 1

Corresponding unit: 
Distributed Systems and Security
Mark: 
Don't remember
Info: 

I really do not remember any more.
From the looks of it - some sort of Java RMI based system. Solution includes Java sources, docs and binaries.

                                                                                                                                                                                                                                                                                       

FIT1002 - Computer programming

This page contains additional learning materials for unit FIT1002 (Computer Programming) at Monash University.

This is an introductory unit on computer programming in Java for first year students. I was teaching the problem class seminars for FIT1002 - Computer programming in spring semester 2007.

                                                                                                                                                                                                                                                                                       

Holey Fitness Landscapes and the Maintenance of Evolutionary Diversity

 

Publication Type:

Conference Proceedings

Source:

Seth Bullock; Jason Noble; Richard Watson; Mark Bedau (eds.), Proceedings of 11th International Conference on Artificial Life (ALife XI), Winchester, UK. MIT Press, pp. 450-457.

ISBN:

978-0-262-75017-2

Keywords:

Holey Fitness Landscape; diversity; reproductive isolation; speciation; hybridisation

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.

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Using Holey Fitness Landscapes to Counteract Premature Convergence in Evolutionary Algorithms

 

Publication Type:

Conference Proceedings

Authors:

Greg Paperin (2008)

Source:

Steven Gustafson (ed.), Proceedings of Graduate Student Workshop at the Genetic and Evolutionary Computation Conference 2008 (GECCO’08), Atlanta, USA. Association for Computing Machinery, pp. 1815-1818.

ISBN:

978-1-60558-131-6

URL:

http://portal.acm.org/citation.cfm?id=1388978

Keywords:

evolutionary algorithm; genetic algorithm; Holey Fitness Landscape; gene flow; premature convergence; reproductive isolation

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.

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Evolving sequence patterns for prediction of sub-cellular locations of eukaryotic proteins

 

Publication Type:

Conference Poster

Authors:

Greg Paperin (2008)

Source:

Genetic and Evolutionary Computation Conference 2008 (GECCO’08), Atlanta, USA. Association for Computing Machinery, pp. 1135-1136.

ISBN:

978-1-60558-130-9

URL:

http://portal.acm.org/citation.cfm?id=1389095.1389315

Keywords:

protein localisation; classifier; machine learning; pattern learning

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.

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Fitness Landscapes in Individual-Based Simulation Models of Adaptive Radiation

 

Publication Type:

Conference Proceedings

Source:

Tuan D. Pham; Xiaobo Zhou (eds.), Proceedings of 2007 International Symposium on Computational Models for Life Sciences (CMLS’07), Gold Coast, Australia. American Institute of Physics, Volume 952, pp. 268-278.

ISBN:

978-0-7354-0466-3

ISSN:

0094-243X

DOI:

10.1063/1.2816631

URL:

http://link.aip.org/link/?APCPCS/952/268/1

Keywords:

Holey Fitness Landscape; adaptive radiation; speciation; individual-based modelling; fitness landscape; fitness

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.

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Dual Phase Evolution – a mechanism for self-organisation and optimisation

 

Publication Type:

Conference Paper

Source:

Presented at Asia-Pacific Symposium on Intelligent and Evolutionary Systems 2007 (APSIES’07).

URL:

http://www.nda.ac.jp/cs/IES2007/finalprog.htm

Keywords:

Dual Phase Evolution; complexity; networks; criticality; phase change; evolution; self-organisation; landscape; optimisation

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.

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A Dual Phase Evolution model of adaptive radiation in landscapes

 

Publication Type:

Conference Proceedings

Source:

Markus Randall; Hussein A. Abbass; Janet Wiles (eds.), Proceedings of 3rd Australian Conference on Artificial Life (ACAL’07), Gold Coast, Australia. Springer, Volume 4828/2007, pp. 131-143.

ISBN:

978-3-540-76930-9

ISSN:

0302-9743

DOI:

10.1007/978-3-540-76931-6

URL:

http://www.springerlink.com/content/0481n48135l3n517/

Keywords:

Dual Phase Evolution; complexity; speciation; adaptive radiation; landscape connectivity; simulation

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.

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Complexity in Speciation: Effects of disasters on adaptive radiation in a Dual Phase Evolution model

 

Publication Type:

Conference Paper

Source:

Presented at 8th Asia-Pacific Complex Systems Conference (Complex’07), Gold Coast, Australia.

URL:

http://www.complex07.org/index/sitemember-abstracts-action#General%20Track

Keywords:

Dual Phase Evolution; complexity; speciation; adaptive radiation; landscape connectivity

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.

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Security of Communication and Quantum Technology

 

Publication Type:

Book Chapter

Authors:

Greg Paperin (2007)

Source:

Marian Quigley (ed.), Encyclopaedia of Information Ethics and Security. Idea Group Publishing.

ISBN:

159140987X

URL:

http://books.igi-online.com/content/details.asp?ID=16806

Keywords:

physics; data network; security

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.

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