Publications by Dr Colin Johnson
Publication period (11/1996 onwards) - ordered by publication type and date
Books
-
Studying
programming.
Sally Fincher and the Computing Education Research Group.
Palgrave Study Guides. Palgrave Macmillan, January 2006.
Journal Papers
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A
hierarchical multi-label classification ant colony algorithm for protein
function prediction.
F.E.B. Otero, A.A. Freitas, and C.G. Johnson.
Memetic Computing, 2(3):165-181, September 2010.
-
A
hierarchical multi-label classification ant colony algorithm for protein
function prediction.
F.E.B. Otero, A.A. Freitas, and C.G. Johnson.
Memetic Computing, 2(3):165-181, January 2010.
-
Semantic
analysis of program initialisation in genetic programming.
Lawrence Beadle and Colin G Johnson.
Genetic Programming and Evolvable Machines, 10(3):307-337, September
2009.
-
Message-passing algorithms for the prediction of protein domain interactions from
protein–protein interaction data.
Mudassar Iqbal, Alex A. Freitas, Colin G. Johnson, and Massimo Vergassola.
Bioinformatics, 24(18):2064-2070, September 2008.
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Particle
swarm for attribute selection in bayesian classification: an application to
protein function prediction.
Elon S Correa, Alex A Freitas, and Colin G Johnson.
Journal of Artificial Evolution and Applications, 2008:12 pages, May
2008.
-
A design
framework for metaheuristics.
Colin G. Johnson.
Artificial Intelliigence Review, 29(2):163-178, April 2008.
-
Developing
a computer science-specific learning taxonomy.
U. Fuller, C.G. Johnson, T. Ahoniemi, D. Cukierman, I. Hernán-Losada, J.
Jackova, E. Lahtinen, T.L. Lewis, D. McGee Thompson, C. Riesdel, and E.
Thompson.
ACM SIGCSE Bulletin, 39(4):152-170, December 2007.
-
Journeys in
non-classical computation II: Initial journeys and waypoints.
S Stepney, SL Braunstein, JA Clark, A Tyrrell, A Adamatzky, RE Smith, T Addis,
C Johnson, J Timmis, P Welch, R Milner, and D Partridge.
International Journal of Parallel, Emergent and Distributed Systems,
21(2):97-125, April 2006.
-
Journeys in
non-classical computation I: A grand challenge for computing research.
S. Stepney, S.L. Braunstein, J.A. Clark, A. Tyrrell, A. Adamatzky, R.E. Smith,
T. Addis, C. Johnson, J. Timmis, P. Welch, R. Milner, and D. Partridge.
International Journal of Parallel, Emergent and Distributed Systems,
20(1):5-19, March 2005.
-
Simulating
complex intracellular processes using object-oriented computational
modelling.
Colin G. Johnson, Jacki P. Goldman, and William J. Gullick.
Progress in Biophysics and Molecular Biology, 86(3):379-406, November
2004.
-
Individual-based simulation of the clustering behaviour of epidermal growth factor
receptors.
Jacki P. Goldman, William J. Gullick, and Colin G. Johnson.
Scientific Programming, 12(1):25-43, January 2004.
-
Exploring
sound-space with interactive genetic algorithms.
Colin G. Johnson.
Leonardo, 36(1):51-54, January 2003.
-
Evolutionary computing in visual art and music.
Colin G. Johnson and Juan Jesus Romero Cardalda.
Leonardo, 35(2):175-184, April 2002.
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Understanding complex systems through examples: A framework for qualitative example
finding.
Colin G. Johnson.
Systems Research and Information Systems, 10(3-4):239-267, January
2001.
-
Modelling
robot manipulators with multivariate B-splines.
Colin G. Johnson and Duncan Marsh.
Robotica, 17(3):239-247, May 1999.
Book Chapters
-
A hybrid
rule-induction/likelihood-ratio based approach for predicting protein-protein
interactions.
M. Iqbal, A.A. Freitas, and C.G. Johnson.
In Christine L. Mumford and Lakhmi C. Jain, editors, Computational
Intelligence: Collaboration, Fusion and Emergence, Intelligent Systems
Reference Library, pages 623-637. Springer, July 2009.
-
An
empirical evaluation of the effectiveness of different types of predictor
attributes in protein function prediction..
F. Otero, M. Segond, A.A. Freitas, C.G. Johnson, D. Robilliard, and C. Fonlupt,
volume Foundations of Computational Intelligence Vol. 5 of Studies in
Computational Intelligence 205, pages 339-357.
Springer, June 2009.
-
The
non-classical mind: Cognitive science and non-classical computing.
Colin G. Johnson.
In Alfons Schuster, editor, Intelligent Computing Everywhere, pages
45-59. Springer, October 2007.
-
Does a
functioning mind need a functioning body?.
Colin G Johnson.
In Darryl N Davis, editor, Visions of Mind, pages 307-321. Idea Group
Publishing, January 2005.
-
What kinds
of natural processes can be regarded as computations?.
Colin G Johnson.
In Ray Paton, editor, Computation in Cells and Tissues: Perspectives and
Tools of Thought. Springer, January 2004.
Conference Papers
-
Evolving
high-level imperative program trees with strongly formed genetic
programming.
Tom Castle and Colin G. Johnson.
In Alberto Moraglio, Sara Silva, Krzysztof Krawiec, Penousal Machado, and
Carlos Cotta, editors, Proceedings of the 15th European Conference on
Genetic Programming, EuroGP 2012, volume 7244 of LNCS, pages
1-12, Malaga, April 2012. Springer.
-
The aco
encoding.
A. Moraglio, F.E.B. Otero, and C.G. Johnson.
In M. Dorigo et al., editor, Swarm Intelligence - 7th International
Conference (ANTS 2010), Lecture Notes in Computer Science 6234, pages
528-535, September 2010.
-
ME-CGP:
Multi expression Cartesian genetic programming..
Phil T. Cattani and Colin G. Johnson.
In Proceedings of the 2010 IEEE World Congress on Computational
Intelligence, July 2010.
-
The
Effect of Level of Rationality on Macro-Activities of the
Lucas-Island Model.
Ahmed Okasha and Colin G. Johnson.
In 2010 IEEE Congress on Evolutionary Computation. IEEE Press, July
2010.
-
Positional
effect of crossover and mutation in Grammatical Evolution.
Tom Castle and C. G. Johnson.
In Anna I. Esparcia-Alcazar, Aniko Ekart, Sara Silva, Stephen Dignum, and Sima
Uyar, editors, Proceedings of the 13th European Conference on Genetic
Programming, EuroGP 2010, volume 6021 of LNCS, Istanbul, April
2010. EvoStar, Springer.
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Typed
cartesian genetic programming for image classification.
Phil T. Cattani and Colin G. Johnson.
In Proceedings of the 2009 UK Workshop on Computational Intelligence,
pages 106-111, University of Nottingham, September 2009.
-
Semantically driven mutation in genetic programming.
Lawrence Beadle and Colin G. Johnson.
In Proceedings of the 2009 IEEE Congress on Evolutionary Computation,
pages 1336-1342. IEEE Press, May 2009.
-
Handling
continuous attributes in ant colony classification algorithms.
F.E.B. Otero, A.A. Freitas, and C.G. Johnson.
In Proc. of the 2009 IEEE Symposium on Computational Intelligence in Data
Mining (CIDM 2009), pages 225-231. IEEE Press, March 2009.
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A
hierarchical classification ant colony algorithm for predicting gene ontology
terms.
F.E.B. Otero, A.A. Freitas, and C.G. Johnson.
In C. Pizzuti, M.D. Ritchie, and M. Giacobini, editors, Proc. 7th European
Conference on Evolutionary Computation, Machine Learning and Data Mining in
Bioinformatics (EvoBio-2009), volume Lecture Notes in Computer Science
5483, pages 68-79. Springer, March 2009.
-
cAnt-Miner: an ant colony classification algorithm to cope with continuous
attributes.
F.E.B. Otero, A.A. Freitas, and C.G. Johnson.
In M. Dorigo et al., editor, Ant Colony Optimization and Swarm
Intelligence (Proc. ANTS 2008), LNCS 5217, pages 48-59. Springer,
September 2008.
-
Multi-level
neutrality in optimization.
Colin G. Johnson.
In Proceedings of the 2008 IEEE World Congress on Computational
Intelligence, pages 2604-2609. IEEE Press, June 2008.
-
Protein
interaction inference using particle swarm optimization algorithm..
M. Iqbal, A.A. Freitas, and C.G. Johnson.
In E. Marchiori and J.H. Moore, editors, Proc. Sixth European Conf. on
Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
(EvoBio-2008), Lecture Notes in Computer Science 4973, pages 61-70.
Springer, March 2008.
-
Semantically driven crossover in genetic programming.
Lawrence Beadle and Colin G Johnson.
In IEEE World Congress on Computational Intelligence, pages 111-116.
IEEE, January 2008.
-
Particle
swarm and bayesian networks applied to attribute selection for protein
functional classification..
E.S. Correa, A.A. Freitas, and C.G. Johnson.
In T. Yu, editor, Proc. of the GECCO-2007 Workshop on Particle Swarms: The
Second Decade, pages 2651-2658. ACM, July 2007.
-
A genetic
algorithm for coverage problems.
Colin G. Johnson.
In Dirk Thierens et al., editor, Proceedings of the 2007 Genetic and
Evolutionary Computation Conference, volume II, page 1521. ACM Press,
July 2007.
-
Genetic
programming with fitness based on model checking.
Colin G. Johnson.
In Marc Ebner and et al., editors, Genetic Programming, volume 4445
of Lecture Notes in Computer Science, pages 114-124.
Springer-Verlag, April 2007.
-
Is
Bloom's taxonomy appropriate for computer science?.
Colin G. Johnson and Ursula Fuller.
In Anders Berglund and Mattias Wiggberg, editors, Proceedings of the Sixth
Baltic Sea Conference on Computing Education Research, volume 2007-006
of Uppsala University Department of Information Technology Technical
Reports, pages 120-123. Uppsala University, February 2007.
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A new
discrete particle swarm algorithm applied to attribute selection in a
bioinformatics data set..
E.S. Correa, A.A. Freitas, and C.G. Johnson.
In M. Keijzer and et. al., editors, Proc. Genetic and Evolutionary
Computation Conference (GECCO-2006), pages 35-42. ACM Press, July 2006.
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A design
framework for metaheuristics: Problem types and avoiding bottlenecking.
Colin G. Johnson.
In Konstantinos Sirlantzis, editor, Proceedings of the Sixth International
Conference on Recent Advances in Soft Computing. University of Kent,
July 2006.
-
Timbre
interfaces using adjectives and adverbs.
Colin G. Johnson and Alex Gounaropoulos.
In Norbert Schnell and et al, editors, New Interfaces for Musical
Expression, pages 101-102, Paris, June 2006. IRCAM.
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Abstract
interpretation of student programs as a strategy for courseware
development.
Colin G. Johnson.
In Methods, Materials and Tools for Programming Education, volume 5
of Tampere Polytechnic Series A. Research Reports, pages 14-19,
Tampere, Finland, May 2006. Tampere Polytechnic University of Applied
Sciences.
-
Synthesising timbres and timbre-changes from adjectives/adverbs.
Alex Gounaropoulos and Colin Johnson.
In F. Rothlauf and et al, editors, Applications of Evolutionary
Computing, volume 3907 of Lecture Notes in Computer Science,
pages 664-675. Springer-Verlag, April 2006.
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Roles of
variables and program analysis.
Craig Bishop and Colin G. Johnson.
In Tapio Salakoski, editor, Proceedings of the 5th Finnish/Baltic
Conference on Computer Science Education. University of Turku, November
2005.
-
Varying the
topology and probability of re-initialization in particle swarm
optimization.
Mudassar Iqbal, Alex A. Freitas, and Colin G. Johnson.
In E.-G. Talbi, editor, Evolution Artificielle 2005. University of
Lille, October 2005.
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Advances in
artificial life - proc. 8th european conf. (ecal-2005).
MS Capcarrere, AA Freitas, PJ Bentley, CG Johnson, and J Timmis, editors,
volume Lecture Notes in Artificial Intelligence 3630. Springer Verlag,
September 2005.
-
Search and
notions of creativity.
Colin G. Johnson.
In Tony Veale, Alison Pease, and Geraint Wiggins, editors, Proceedings of
the IJCAI-2005 Workshop on Computational Creativity. IJCAI, July 2005.
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What can
post-classical computation do for post-cognitivist psychology?.
Colin G. Johnson.
In Proceedings of the 2005 Post-Cognitivist Psychology Conference.
University of Strathclyde, July 2005.
-
Non-classical computation and the computationalist stance towards the natural and
cognitive sciences.
Colin G. Johnson.
In Susan Stepney, editor, The Grand Challenge in Non-Classical
Computation. University of York, April 2005.
-
Varieties
of openness in evolutionary computation.
Colin G. Johnson.
In Robert Zimmer, editor, Proceedings of the Workshop on Creative
Evolutionary Computation. Goldsmiths College, February 2005.
-
Using tabu
search and genetic algorithms in mathematics research.
Colin G. Johnson.
In Ahmed Lotfi, editor, Proceedings of the Fifth International Conference
on Recent Advances in Soft Computing, pages 243-248. Nottingham Trent
University, December 2004.
-
Automatic
programming with ant colony optimization.
Jennifer Green, Jacqueline L. Whalley, and Colin G. Johnson.
In Mark Withall and Chris Hinde, editors, Proceedings of the 2004 UK
Workshop on Computational Intelligence, pages 70-77. Loughborough
University, September 2004.
-
Post-industrial-revolution HCI.
Colin G. Johnson.
In Anne Bruseberg, Peter Johnson, and Peter J. Wild, editors, Coping with
Complexity: Sharing New Approaches for the Design of Human-Computer Systems
in Complex Settings, pages 7-8. University of Bath, September 2004.
-
Do somatic
markers need to be somatic? Analogies from evolution and from hardware
interlocks.
Colin G. Johnson.
In Proceedings of the AISB 2004 Convention, pages 33-35. Sociaty for
the Study of Artificial Intelligence and Simulation of Behaviour, April 2004.
-
Artificial
immune systems and the grand challenge for non-classical computation.
Susan Stepney, John A. Clark, Colin G. Johnson, Derek Partridge, and Robert E.
Smith.
In Jon Timmis, Peter Bentley, and Emma Hart, editors, Proceedings of the
2003 International Conference on Artificial Immune Systems, LNCS 2787,
pages 204-216. Springer, September 2003.
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Colour
merging for the visualization of biomolecular sequence data.
Mark Alston, Gary Robinson, and Colin G. Johnson.
In E. Banissi, K. Borner, C. Chen, G. Clapworthy, C. Maple, A. Lobben, C.
Moore, J. Roberts, A. Ursyn, and J. Zhang, editors, Proceedings of the
Seventh International Conference on Information Visualization, pages
169-175. IEEE Computer Society, July 2003.
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Artificial
immune systems programming for symbolic regression.
Colin G. Johnson.
In C. Ryan, T. Soule, M. Keijzer, E. Tsang, R. Poli, and E. Costa, editors,
Genetic Programming: 6th European Conference, LNCS 2610, pages
345-353. Springer, April 2003.
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Towards a
prehistory of evolutionary and adaptive computation in music.
Colin G. Johnson.
In G. Raidl, D. Corne, E. Marchiori, J. Gottlieb, S. Cagnoni, J. Romero, C.
Johnson, E. Hart, M. Middendorf, A. Guillot, and J.-A. Meyer, editors,
Applications of Evolutionary Computing, LNCS 2611, pages 502-509.
Springer, April 2003.
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An ant
colony algorithm for multiple sequence alignment in bioinformatics.
Jonathan D. Moss and Colin G. Johnson.
In David W. Pearson, Nigel C. Steele, and Rudolf F. Albrecht, editors,
Artificial Neural Networks and Genetic Algorithms, pages 182-186.
Springer, April 2003.
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Applications
of evolutionary computing.
G. Raidl, D. Corne, E. Marchiori, J. Gottlieb, S. Cagnoni, J. Romero, C.
Johnson, E. Hart, M. Middendorf, A. Guillot, and J.-A. Meyer, editors, LNCS
2611. Springer, April 2003.
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Genetic
programming with guaranteed constraints.
Colin G. Johnson.
In Ahmad Lofti, Bob John, and Jon Garibaldi, editors, Recent Advances in
Soft Computing. Physica/Springer-Verlag, December 2002.
-
What can
automatic programming learn from theoretical computer science?.
Colin G. Johnson.
In Xin Yao, editor, Proceedings of the 2002 UK Workshop on Computational
Intelligence. University of Birmingham, September 2002.
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A virtual
lab for exploring the [PSI]+ yeast prion.
Jacqueline L. Whalley, Mick F. Tuite, and Colin G. Johnson.
In Faramarz Valafar, editor, Proceedings of the International Conference
on Mathematics and Engineering Techniques in Medicine and Biological
Sciences, volume II, pages 583-589. CSERA Press, June 2002.
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Deriving
genetic programming fitness properties by static analysis.
Colin G. Johnson.
In Evelyne Lutton, James A. Foster, Julian Miller, Conor Ryan, and Andrea G. B.
Tettamanzi, editors, Proceedings of the 4th European Conference on
Genetic Programming, EuroGP 2002, volume 2278 of Lecture Notes in
Computer Science, pages 299-308, Berlin, April 2002. Springer-Verlag.
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Individual-based simulation of the clustering behaviour of epidermal growth factor
receptors.
Jacki P. Goldman, William J. Gullick, Dennis Bray, and Colin G. Johnson.
In Gary Lamont, editor, Proceedings of the 2002 ACM Symposium on Applied
Computing, pages 127-131. ACM Press, March 2002.
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Finding
diverse examples with genetic algorithms.
Colin G. Johnson.
In Robert John and Ralph Birkenhead, editors, Developments in Soft
Computing, Advances in Soft Computing, pages 92-99.
Physica/Springer-Verlag, July 2001.
-
Phase
transitions in multi-robot interactions.
Colin G. Johnson and Steven J. Brodie.
In U. Nehmzow and C. Melhuish, editors, Towards Intelligent Mobile Robots
- Proceedings of the 3rd British Conference on Autonomous Mobile Robotics and
Autonomous Systems, University of Manchester Technical Reports volume
UMCS-01-4-1, page 7. University of Manchester, April 2001.
-
Proceedings
of the AISB'01 symposium on emotion, cognition and affective
computing.
Colin G. Johnson, editor. Society for the Study of Artificial Intelligence and
the Simulation of Behaviour, AISB Press, March 2001.
-
Effective
affective communication in virtual environments.
C.G. Johnson and Gareth J.F. Jones.
In Daniel Ballin, editor, Proceedings of the Second Workshop on
Intelligent Virtual Agents, pages 135-138. University of Salford,
September 1999.
-
Exploring
the sound-space of synthesis algorithms using interactive genetic
algorithms.
Colin G. Johnson.
In A. Patrizio, G.A. Wiggins, and H. Pain, editors, Proceedings of the
AISB'99 Symposium on Musical Creativity, pages 20-27, Brighton, April
1999. Society for the Study of Artificial Intelligence and Simulation of
Behaviour.
-
Modelling
robot manipulators in a CAD environment using B-splines.
Colin G. Johnson.
In Nikolaos G. Bourbakis, editor, IEEE International Joint Symposia on
Intelligence and Systems, pages 194-201. Institute of Electrical and
Electronic Engineers, IEEE Press, November 1996.
Miscellaneous
-
A
Design Framework for Evolutionary Algorithms.
Colin Johnson.
PhD thesis, Computing Laboratory, University of Kent, Canterbury, Kent, UK,
July 2003.
-
Journeys in
non-classical computation: A grand challenge for computing research.
S. Stepney, J.A. Clark, A. Tyrrell, C.G. Johnson, J. Timmis, D. Partridge, A.
Adamatsky, and R.E. Smith.
Grand Challenge Report 7, National E-Science Centre, University of Edinburgh,
May 2003.
-
Detecting
collisions in sets of moving particles: a survey and some experiments.
Colin G. Johnson and Jacqueline Whalley.
Technical Report 8-02, University of Kent, Computing Laboratory, June 2002.
-
Portrait
of 2000/01 Part I Assessments, Part 1: Statistical Analysis.
Janet Carter, Jill Tardivel, Sally Fincher, Ursula Fuller, Colin Johnson, Janet
Linington, and Ian Utting.
Technical Report 10-01, University of Kent, Computing Laboratory, University of
Kent at Canterbury, August 2001.