Recent journal
articles
Lohaus, R., Geard, N.L.,
Wiles, J., and Azevedo, R.B.R. (2007). A generative bias towards average complexity in artificial cell
lineages, Proc. Royal Society B,
274(1619):1741-1750.
http://www.journals.royalsoc.ac.uk/content/k730117854602728/
J. P. Connor, M. Symons, G. F. X. Feeney, R. M. Young, and J. Wiles, "The Application of Machine Learning Techniques as an Adjunct to Clinical Decision Making in Alcohol Dependence Treatment: A Preliminary Study," Substance Use and Misuse. In press.
Geard, N. L. and Wiles, J. (accepted). LinMap: Visualising Complexity Gradients in Evolutionary Landscapes. Artificial Life, Special Issue on Complexity.
Willadsen, K. and Wiles, J. (in press). Robustness and state-space structure of Boolean gene regulatory models, J. Theoretical Biology.
Milford, M., Schulz, R., Prasser, D., Wyeth, G. and Wiles, J. (in press). Learning spatial concepts from RatSLAM representations, Robotics and Autonomous Systems www.elsevier.com/locate/robot
Geard, N. L. and Wiles, J. (in press). Directed evolution of artificial cell lineages. In Eds. M.Randall, H. Abbass, and J. Wiles, Progress in Artificial Life, Lecture Notes in Artificial Intelligence (LNAI 4828, Series Editor J.G. Carbonell) (Proceedings of the Third Australian Conference on Artificial Life, Gold Cost, Dec 4-6, 2007.)
J.B. Aimone, J. Wiles and F.H. Gage, (2006)
“Potential role for adult neurogenesis in the encoding of time in new
memories,” Nature Neuroscience
9(6):723-7.
http://www.nature.com/neuro/journal/v9/n6/abs/nn1707.html
J. Wiles and B. Tonkes, "Hyperspace geography: Visualizing fitness landscapes beyond 4D," Artificial Life 12(2). 2006.
P. Sweetser and J. Wiles, Using Cellular Automata to Facilitate Emergence in Game Environments, Journal of Game Development. In Press.
P. Sweetser and J. Wiles, Scripting versus Emergence: Issues for Game Developers and Players in Game Environment Design. International Journal of Intelligent Games and Simulations, 4 (1): 1-9.
D. Johnson, J. Gardner, and J. Wiles, (2004) "Experience as a Moderator of the Media Equation: The Impact of Flattery and Praise," International Journal of Human-Computer Studies, 61(3):237-258. [IF 1.34]
N. Geard and J. Wiles, "A Gene Network Model for Developing Cell Lineages," Artificial Life, 11(1-2):249-268, 2005.
J. Wiles, J. Watson, B. Tonkes, and T. W. Deacon, "Transient Phenomena in Learning and Evolution: Genetic Assimilation and Genetic Redistribution," Artificial Life, vol. 11(1-2):177-188, 2005.
J. Wiles and B. Tonkes (2003). Mapping the Royal Road and other Hierarchical Functions, Evolutionary Computation, 11:2, 129-150.
Recent Conference
papers
Schulz, R., Prasser, D., Stockwell, P., Wyeth, G., and Wiles, J. (accepted). The formation, generative power, and evolution of toponyms: grounding a vocabulary in a cognitive map. Evolang, Italy, April 2008.
J. Watson, S. Maetschke and J. Wiles (2007). An introduction to Dsweep, a lightweight tool for distributed parameter sweeps. In Seventh International Workshop on Information Processing in Cells and Tissues (IPCAT), Oxford 29-31 August 2007.
J. Watson and J. Wiles (2007). Modeling the fitness of plant morphologies across three levels of complexity. In Seventh International Workshop on Information Processing in Cells and Tissues (IPCAT), Oxford 29-31 August 2007.
J. S. Hallinan, DR. Bradley and J. Wiles, (2006). Effects of Constitutive Gene Expression on the Dynamics of Random Boolean Networks, IEEE Congress on Evolutionary Computation, Vol. 1 Vancouver July. pp. 2305-2362
J. S. Hallinan, DR. Bradley, JS. Mattick and J. Wiles, (2006). Effects of an RNA control layer on the state space of Boolean models of genetic regulatory networks, IEEE Congress on Evolutionary Computation, Vol.1 Vancouver July. pp. 2551-2555.
N. Geard, and Wiles, J., (2006). Investigating ontogenetic space with developmental cell lineages. In Rocha, L. M., Yaeger, L. S., Bedau, M. A., Floreano, D., Goldstone, R. L., and Vespignani, A., editors, Artificial Life X: Proceedings of the Tenth International Conference on the Synthesis and Simulation of Living Systems, pp. 56-62, Cambridge, MA. The MIT Press.
R. Schulz, P. Stockwell,
M. Wakabayashi and J. Wiles. (2006). Generalization in Languages Evolved for
Mobile Robots, In Rocha, L. M., Yaeger, L. S., Bedau, M. A., Floreano, D.,
Goldstone, R. L., and Vespignani, A., editors, Artificial
Life X: Proceedings of the Tenth International Conference on the Synthesis and
Simulation of Living Systems, pp. xxxx,
Cambridge, MA. The MIT Press.
Schulz, R. Stockwell, P. Wakabayashi, M. and Wiles, J. (2006). Towards a spatial language for mobile robots, The evolution of language: Proceedings of the 6th International Conference (EVOLANG6), Vol. 1, pp. 291 – 298. World Scientific.
Watson, J., Hawkins, J., Bradley, D., Dassanayake, D., Wiles, J. & Hanan, J. (2005). Towards a network pattern language for complex systems. In Abbass, H.A., Bossamaier, T., & Wiles, J. (Eds), Recent Advances in Artificial Life, Vol. 3 of Advances in Natural Computation, pp. 309-317, 349-358. World Scientific.
Geard, N., Willadsen, K. & Wiles, J., (2005). Perturbation Analysis: A Complex Systems Pattern. In Abbass, H., Bossamaier, T., and Wiles, J. (editors), Recent Advances in Artificial Life, pp. 69-84, Singapore, World Scientific Publishing.
Wiles, J., Watson, J. (2005). Patterns in complex systems modeling. Intelligent Data Engineering and Automated Learning Ideal 2005, Proceedings: Lecture Notes in Computer Science, M. Gallagher, et al., Ed.: Springer Verlag, Vol. 3578, pp. 532-539. [IF 0.45]
P. Sweetser and J. Wiles, (2005). Combining influence maps and cellular automata for reactive game agents, Intelligent Data Engineering and Automated Learning Ideal 2005, Proceedings: Lecture Notes in Computer Science, Vol. 3578, pp. xxxx. [IF 0.45]
B. Skellett, B.
Cairns, N. Geard, B. Tonkes,
and J. Wiles, "Rugged NK landscapes contain the highest peaks," in
Proceedings of the Genetic and Evolutionary Computation Conference (GECCO*2005).
http://www.cse.unsw.edu.au/~btonkes/papers/rugged_nk.pdf
J. Watson, N. Geard, and J. Wiles,
"Towards more biological mutation operators in gene regulation
studies," BioSystems,
vol. 76(1-3), pp. 239--248, 2004. (Updated version of a paper in the
Proceedings of the Fifth International Workshop in Information Processing in
Cells and Tissues: Sept 8-11, Lausanne, 2003, pp. 355-370)
http://linkinghub.elsevier.com/retrieve/pii/S030326470400084X
J. S. Hallinan and J. Wiles, "Evolving genetic regulatory networks using an artificial genome," in 2nd Asia-Pacific Bioinformatics Conference (APBC2004), Conferences in Research and Practice in Information Technology, Vol. 29., Y.-P. Chen, Ed. Dunedin, NZ: Australian Computer Society, Inc., 2004.
J. S. Hallinan and J. Wiles, "Asynchronous Dynamics of an Artificial Genetic Regulatory Network," in ALife IX The 9th International Conference on Artificial Life. Boston, Ma: MIT Press, 2004.
K. Willadsen and J. Wiles, "Dynamics of
gene expression in an artificial genome," in Proceedings of the 2003
Congress on Evolutionary Computation (CEC2003), R. Sarker,
R. Reynolds, H. Abbass, K.-C. Tan, R. McKay, D. Essam, and T. Gedeon, Eds.
Piscataway, NJ: IEEE,
2003, pp. 1245-1251.
J. Watson, J. Wiles and J. Hanan (2003).
Towards more relevant evolutionary models: Integrating an artificial genome
with a developmental phenotype, Proceedings
of the First Australian Conference on Artificial Life. pp 288-298.
J. Watson, N. Geard and J.Wiles, (2003). Towards more biological mutation operators in gene regulation studies. Proceedings of the Fifth International Workshop in Information Processing in Cells and Tissues, Sept 8-11, Lausanne, pp 355-370.
N. Geard and J. Wiles, (2003). Structure and dynamics of a gene network model incorporating small RNAs, Proceedings of the 2003 Congress on Evolutionary Computation, Dec 8-12, Canberra. pp. 1493-1500.
N. Geard and J. Wiles, (2003). A Gene Regulatory Network for Cell Differentiation in Caenorhabditis elegans, Proceedings of the First Australian Conference on Artificial Life. pp 86-100.
Watson, J., Geard, N. & Wiles, J.,
(2002).
Stability and Task Complexity: A Neural Network Model of Evolution and
Learning. To appear in Proceedings of the 8th
International Conference on the Simulation and Synthesis of Living Systems
(Alife VIII)
Edited
volumes
M.Randall, H. Abbass, and J. Wiles, Eds. Progress in Artificial Life, Lecture Notes in Artificial Intelligence (LNAI 4828, Series Editor J.G. Carbonell) (Proceedings of the Third Australian Conference on Artificial Life, Gold Cost, Dec 4-6, 2007.)
H. Abbass, T. Bossamaier and J. Wiles, Eds. Recent Advances in Artificial Life, World Scientific Advances in Natural Computation Series (Series Editor X. Yao). (Proceedings of the Second Australian Conference on Artificial Life, Sydney 4-7 Dec, 2005.)
H. Abbass, Bossamaier, T., and Wiles, J. Eds, Recent Advances in Artificial Life, Singapore, World Scientific Advances in Natural Computation Series (Series Editor X. Yao). (Proceedings of the Australian Conference on Artificial Life, Canberra 6-7 Dec, 2003.)
J. Wiles and J. S. Hallinan, Eds. Special Issue on Evolutionary Computation and Cognitive Science, in IEEE Trans. on Evolutionary Computation, vol. 5, 2001.
Book Chapters
J. Wiles, and J. Hallinan. J. (2003). Evolutionary Computation and Cognitive Science. In D.B. Fogel & C.J. Robinson (Eds). Computational Intelligence, IEEE Press, Wiley. pp. 179-189.
J. Hallinan, & J.Wiles. (2002). Evolutionary Computation. In L. Nadel (editor) The Encyclopedia of Cognitive Sciences. Macmillan.
B. Tonkes, A. Blair, and J. Wiles. (2002). Methodological issues in simulating the emergence of language. In A. Wray (Ed) The Transition to Language. UK: Oxford University Press.
J. Wiles, A. Blair, and M. Boden, (2001). Representation beyond finite states: alternatives to push down automata, in S. Kremer and J. Kolen, (Eds.) Field Guide to Dynamic Recurrent Networks, IEEE Press, Wiley, 129-142.
Recurrent Neural Networks and Dynamical Language Processing
- Bodén, M. and Wiles, J. (2002), On learning context free and context sensitive languages, IEEE Transactions on Neural Networks. 13(2), pp. 491-493. [.pdf]
- Wiles, J., Blair, A. and Bodén, M. (2001), Representation Beyond Finite States: Alternatives to Push-Down Automata, in A Field Guide to Dynamical Recurrent Networks, Kolen, J. F. and Kremer, S. C. (eds.), pp. 129-142, IEEE Press. [.ps]
- Bodén, M. and Wiles, J. (2000), Context-free and context-sensitive dynamics in recurrent neural networks, Connection Science, 12 (3/4), pp. 197-210. [.pdf]
- Bodén,
M., Wiles, J., Tonkes, B. & Blair, A.
(1999). Learning to predict a context-free language: Analysis of dynamics
in recurrent hidden units. In D. Willshaw &
A. Murray (Eds) Proceedings
of the Ninth International Conference on Artificial Neural Networks
(ICANN99), 359 - 364.
compressed PostScript - Bodén,
M., Wiles, J., Tonkes, B. & Blair, A. (1999),
On the ability of recurrent nets to learn deeply
embedded structures. Presented at the IJCAI 99 workshop on sequence
learning,
compressed PostScript - Tonkes,
B., Blair, A. & Wiles, J. (1998). Inductive bias in context-free
language learning. In Proceedings of the Ninth
Australian Conference on Neural Networks (ACNN98), 52 - 56.
Abstract gzipped PostScript - Tonkes,
B. & Wiles, J. (1999). Learning a context-free task with a recurrent
neural network: An analysis of stability. In R. Heath, B. Hayes, A.
Heathcote & C. Hooker (Eds) Dynamical Cognitive Science: Proceedings of the Fourth
Biennial Conference of the Australasian Cognitive Science Society
(OzCogSci97).
Abstract gzipped PostScript - Rodriguez P., Wiles, J., & Elman, J.L. (1999). A recurrent neural network that learns to count. Connection Science, 11, 5-40. Adobe PDF version.
- Wiles, J., & Elman, J.
L. (1995). Learning to count without a counter: A case study of dynamics
and activation landscapes in recurrent networks. Proceedings of the
Seventeenth Annual Conference of the Cognitive Science Society.
Complexity and evolutionary computation
- Wiles, J., & Tonkes, B. (2002). Hyperspace graph paper: Visualizing interactions between search algorithms and landscapes. To appear: Proceedings of Alife VIII Visualisation Workshop.
- Wiles, J. & Tonkes, B. (2002). Visualisation of hierarchical cost
surfaces for evolutionary computation. In Proceedings
of the 2002 Congress on Evolutionary Computation, 157 - 162. The
visualisation tool discussed in this paper has its own web page.
Abstract gzipped PostScript PDF - Geard,
N., Wiles, J., Hallinan, J., Tonkes, B., & Skellett, B. (2002). A comparison of neutral
landscapes - NK, NKp and NKq.
In Proceedings of the 2002 Congress on Evolutionary
Computation, 205 - 210.
zipped PostScript
Evolution of Language
- Tonkes,
B. & Wiles, J. (2002). Methodological issues in simulating the
emergence of language. In A. Wray (Ed) The Transition
to Language, chapter 11.
Abstract gzipped PostScript PDF - Tonkes,
B., Blair, A., & Wiles, J. (2000). Evolving learnable languages. In S.
A. Solla, T. K. Leen
& K.-R.Muller (Eds)
Advances in Neural Information Processing Systems 12,
(NIPS*99) MIT Press, 66 - 72.
Abstract gzipped PostScript PDF - Tonkes,
B., Blair, A. & Wiles, J. (1998). A paradox of neural encoders and
decoders, or, why don't we talk backwards? In B. McKay, X. Yao, C. S.
Newton, J.-H. Kim & T. Furuhashi (Eds) Lecture Notes in Artificial
Intelligence vol 1585: Proceedings of the Second Asia-Pacific Conference
on Simulated Evolution and Learning (SEAL98), Springer, 357 - 364.
Abstract gzipped PostScript PDF at Springer (subscription required)
Learning and Evolution (Baldwin Effect)
- Wiles, J., Watson, J., Tonkes, B., & Deacon, T. W. (2002). Strange loops
in learning and evolution. Submitted, InterJournal Complex Systems, 572. Presented
at the International Conference on Complex Systems (ICCS 2002), New
England Complex Systems Institute.
Abstract online @ InterJournal - Wiles, J., Tonkes, B. & Watson, J. (2001). How learning can
guide evolution in hierarchical modular tasks. In J. D. Moore & K. Stenning (Eds), Proceedings of the 23rd Annual Conference of the Cognitive
Science Society (CogSci 2001).
Abstract gzipped PostScript PDF - Wiles, J., Shulz, R., Bolland, S., Tonkes, B., & Hallinan, J. (2001). Selection
procedures for module discovery: Exploring evolutionary algorithms for
cognitive science. In J. D. Moore & K. Stenning
(Eds), Proceedings of the
23rd Annual Conference of the Cognitive Science Society (CogSci 2001).
PDF - Wiles, J., Schulz, R.,
Hallinan, J., Bolland, S. & Tonkes, B. (2001). Probing the persistent question
marks. In L. Spector, E. Goodman, A. Wu, W. B.
Langdon, H.-M. Voigt, M. Gen, S. Sen, M. Dorigo,
gzipped PostScript
Recreational and Affective Computing
- Johnson, D.,
- Johnson, D., & Wiles, J. (2001). Computer Games With Intelligence. Australian Journal of Intelligent Information Processing Systems, 7, 61-68. [pdf] [doc] (long paper)
- Johnson, D., & Wiles, J. (2001, December 2 - 5). Computer Games With Intelligence. Paper presented at the 2001 IEEE International Fuzzy Systems Conference, Melbourne. [pdf] [doc] (short paper)
- Johnson, D., & Wiles,
J. (2001, June 27-29). Effective affective user interface design in games.
Paper presented at the International Conference on Affective Human Factors
Design,
List of
Papers by Year (not complete)
2002
Watson, J., Geard, N. & Wiles, J., (2002). Stability and Task Complexity: A Neural Network Model
of Evolution and Learning. To appear in Proceedings of the
8th International Conference on the Simulation and Synthesis of Living Systems
(Alife VIII). [PDF]
Wiles, J., Watson, J., Tonkes, B.
& Deacon, T. (2002). Strange loops in learning and
evolution. Presented at ICCS02, submitted to InterJournal
(May 2002). [PDF]
[InterJournal]
Geard, N.,
Wiles, J., Hallinan, J. Tonkes, B. & Skellett, B., (2002). A Comparison
of Neutral Landscapes - NK, NKp and NKq. In (ED) X. Yao Proceedings
of the 2002 Congress on Evolutionary Computation. 205-210
[PDF]
Geard, N. & Wiles, J., (2002). Diversity
Maintenance on Neutral Landscapes: An Argument for Recombination. In Proceedings of the 2002 Congress on Evolutionary Computation.
211-213 [PDF]
Wiles, J. & Tonkes, B., (2002). Visualisation of Hierarchical Cost Surfaces for Evolutionary
Computing. In Proceedings of the 2002 Congress on
Evolutionary Computation. 157-162 [PDF]
Willadsen, K. & Wiles, J., (2002). All binary representations are
equal: But some are more equal than others. In Proceedings
of the 2002 Congress on Evolutionary Computation. 570-575
[PDF]
Watson, J. & Wiles, J., (2002). The rise and fall of learning: A
neural network model of the genetic assimilation of acquired traits. In Proceedings of the 2002 Congress on Evolutionary Computation
(CEC 2002), pp. 600-605. 600-605 [PDF]
Tonkes, B. & Wiles, J. (2002).
Methodological issues in simulating the emergence of language. In A. Wray (Ed) The Transition to Language, chapter 11.
2001
Wiles, J., Tonkes, B. & Watson, J. (2001). How learning can guide evolution in hierarchical
modular tasks. In J. D. Moore & K. Stenning
(Eds), Proceedings of the 23rd Annual Conference
of the Cognitive Science Society (CogSci 2001).
Wiles, J., Shulz, R., Bolland, S., Tonkes, B., &
Hallinan, J. (2001). Selection procedures for module discovery:
Exploring evolutionary algorithms for cognitive science. In
J. D. Moore & K. Stenning (Eds),
Proceedings of the 23rd Annual Conference of the Cognitive Science Society
(CogSci 2001).
Wiles, J., Schulz, R., Hallinan, J., Bolland,
S. & Tonkes, B. (2001). Probing
the persistent question marks. In L. Spector,
E. Goodman, A. Wu, W. B. Langdon, H.-M. Voigt, M. Gen, S.
Sen, M. Dorigo, S. Pezeshk,
M. Garzon & E. Burke (Eds),
Proceedings of the Genetic and Evolutionary Computation Conference
(GECCO-2001).
2000
Tonkes, B., Blair, A., & Wiles, J. (2000).
Evolving learnable languages. In S. A. Solla, T. K. Leen & K.-R.Muller (Eds) Advances in
Neural Information Processing Systems 12, (NIPS*99) MIT Press, 66 - 72. [PDF]
1998
Tonkes, B., Blair, A. & Wiles, J. (1998). Inductive bias in context-free language learning. In Proceedings of the Ninth Australian Conference on Neural
Networks (ACNN98), 52 - 56. [PDF]
Tonkes,
B., Blair, A. & Wiles, J. (1998). A paradox of neural encoders and
decoders, or, why don't we talk backwards? In B. McKay, X. Yao, C. S. Newton,
J.-H. Kim & T. Furuhashi (Eds)
Lecture Notes in Artificial Intelligence vol 1585: Proceedings of the Second
Asia-Pacific Conference on Simulated Evolution and Learning (SEAL98),
Springer, 357 - 364. [PDF]
1994
Bakker, P., Phillips, S., & Wiles, J. (1994). The 1000-2-1000
encoder: A matter of Representation. Neural Network World, 4(5),
527-534. Abstract. HTML
1993
Phillips, S. & Wiles, J., (1993). Exponential Generalizations from a Polynomial Number of Examples in
a Combinatorial Domain. In Proceedings of the International Joint Conference
on Neural Networks, pp. 505-508
Phillips, S., Wiles, J. & Schwartz, S., (1991). A Comparison
of Three Classification Algorithms on the Diagnosis of Abdominal Pains. In M. Jabri (Ed.), Proceedings of the
Second Australian Conference on Neural Networks, pp. 283-287.
Schwartz,
S., Wiles, J., & Phillips, S., (1995). Connectionist,
rule-based and Bayesian decision aids: an empirical comparison. In P. Slezak, T. Caelli & R. Clark
(Eds.), Perspectives on Cognitive Science: Theories, Experiments and
Foundations, pp. 167-180.
Schwartz,
S., Wiles, J., Gough,
Bakker, P., Phillips, S., &
Wiles, J., (1993). The N-2-N encoder: A matter of Representation. In S. Gielen & B. Kappen (Eds.), Proceedings
of the International Joint Conference on Neural Networks, pp. 554-557.