/publications
This is a list of my academic publications to date. PDF
copies and bibtex should be available for them all. If you
require a copy of a paper and I have forgotten to include it
here, or you notice an error on this page, please don't
hesitate to email me.
Ph.D. Thesis
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An Exploration of Tree-Adjoining Grammars for Grammatical Evolution
By Eoin Murphy
University College Dublin, 2014.
[pdf↓]@PhdThesis{murphy:PhDThesis:2014, author = "Eoin Murphy", title = "An Exploration of Tree-Adjoining Grammars for Grammatical Evolution", school = "University College Dublin", year = "2014", address = "Ireland", month = "6 " # dec, keywords = "genetic algorithms, genetic programming, Grammatical Evolution, TAG, TAGE", URL = "http://ncra.ucd.ie/papers/EoinMurphy_thesis.pdf", size = "302 pages", abstract = "Grammars are an important tool for Evolutionary Computation (EC). Grammars offer a flexible means of search space restriction, and provide a mechanism for imposing language and search biases. This thesis explores the use of a particular grammar type, Tree-Adjoining Grammars (TAGs) for use with Grammatical Evolution (GE), a grammar-based EC algorithm. To date, much of the work on GE has used Context-Free Grammars (CFGs). TAGs have been shown to be more powerful than CFGs and can generate some context-sensitive languages. TAGs also exhibit interesting properties, such as, each intermediate stage of TAG derivation being a fully structured feasible sentence from the language. The focus of this thesis is to explore the use of TAGs for representation in GE. A definition of TAGs is given and a comprehensive survey of TAGs in EC is presented. Following this, a novel representation and mapping process is developed which combines the linear chromosome used by GE with TAGs. This extension of GE, called Tree-Adjoining Grammatical Evolution (TAGE), is compared with canonical GE on a number of benchmark problems. TAGE demonstrates a performance benefit over GE. Further study of the two representations is presented, which identifies core representational differences, such as, invalid individuals and neutral crossover operations, both of which do not occur in TAGE. These differences are shown to account for some of improved performance of TAGE. Subsequent to this, a novel method of rendering search landscapes is presented. Single mutation event landscapes are generated for GE and TAGE for a number of common grammars. It is shown that TAGE search spaces are much more densely connected than those of GE, affording TAGE greater opportunities to move about the search space. Further representational differences in the form of preferential language biases are discovered when developing methods of generating similar initial populations for both TAGE and GE. Two main biases are identified, adjunction constraints and grammar transformation biases. These biases affect the distributions of tree structures generated by TAGE. Methods of mitigating these biases are presented and it is shown that these biases can provide problem dependent performance benefits. The developmental nature of the feasibility property of TAGs is exploited by integrating an on line artificial gene regulatory network (GRN) model with TAGE in the form of Developmental TAGE (DTAGE). DTAGE is shown to improve the usability of this GRN model by facilitating it with the use of the TAGE mapping process. DTAGE is demonstrated to be capable of evolving GRNs whose output, when provided with feedback in the form of state information from dynamic problem environments, maps to phenotypes that can survive in those environments. In summary, this thesis explores the utility and capability of TAGs for representation in GE. Differences in representation between TAGs and CFGs for use with GE are identified and studied in terms of performance. TAGs are then exploited in the development of a novel evolutionary developmental system combining TAGs, GE and a GRN model.", notes = "Supervisor: Michael O'Neill", }
Conference Papers
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Differential Gene Expression with Tree-Adjunct Grammars
By Eoin Murphy, Miguel Nicolau, Erik Hemberg, Michael O'Neill and Anthony Brabazon
In Proceedings of the 12th international conference on Parallel Problem Solving from Nature: PPSN XII, Taormina, Sicily, Italy, 2012. Springer Verlag.
[pdf↓]@InProceedings{murphy:2012:ppsn, author = {Eoin Murphy and Miguel Nicolau and Erik Hemberg and Michael O'Neill and Anthony Brabazon}, title = {Differential Gene Expression with Tree-Adjunct Grammars}, booktitle = {Proceedings of the 12th international conference on Parallel Problem Solving from Nature: PPSN XII}, year = {2012}, location = {Taormina, Sicily, Italy}, publisher = {Springer-Verlag}, address = {Berlin, Heidelberg}, } -
Grammar Bias and Initialisation in Grammar Based Genetic Programming
By Eoin Murphy, Erik Hemberg, Miguel Nicolau, Michael O'Neill and Anthony Brabazon
In Proceedings of the 15th European Conference on Genetic Programming, EuroGP 2012, volume 7244, pages 85-96, Malaga, Spain, 2012. Springer Verlag.
[pdf↓]@InProceedings{murphy:2012:EuroGP, author = "Eoin Murphy and Erik Hemberg and Miguel Nicolau and Michael O'Neill and Anthony Brabazon", title = "Grammar Bias and Initialisation in Grammar Based Genetic Programming", booktitle = "Proceedings of the 15th European Conference on Genetic Programming, EuroGP 2012", year = "2012", month = "11-13 " # apr, editor = "Alberto Moraglio and Sara Silva and Krzysztof Krawiec and Penousal Machado and Carlos Cotta", series = "LNCS", volume = "7244", publisher = "Springer Verlag", address = "Malaga, Spain", pages = "85--96", organisation = "EvoStar", isbn13 = "978-3-642-29138-8", doi = "doi:10.1007/978-3-642-29139-5_8", size = "12 pages", keywords = "genetic algorithms, genetic programming, grammatical evolution, TAG, TAGE, Grammar bias, Initialisation", abstract = "Preferential language biases which are introduced when using Tree-Adjoining Grammars in Grammatical Evolution affect the distribution of generated derivation structures, and as such, present difficulties when designing initialisation methods. Similar initial populations allow for a fairer comparison between different GP methods. This work proposes methods for dealing with these biases and examines their effect on performance over four well known benchmark problems. In addition, a comparison is performed with a previous study that did not employ similar phenotype distributions in their initial populations. It is found that the use of this form of initialisation has a positive effect on performance.", notes = "TAG grammar uses up whole of chromosome. Part of \cite{Moraglio:2012:GP} EuroGP'2012 held in conjunction with EvoCOP2012 EvoBIO2012, EvoMusArt2012 and EvoApplications2012", } -
Semantic-based Subtree Crossover Applied to Dynamic Problems
By Quang Uy Nguyen, Eoin Murphy, Michael O'Neill and Xuan Hoai Nguyen
In The Third International Conference on Knowledge and Systems Engineering, KSE'2011, Hanoi University, 2011.
[pdf↓]@InProceedings{Quang:2011:KSE, author = "Quang Uy Nguyen and Eoin Murphy and Michael O'Neill and Xuan Hoai Nguyen", title = "Semantic-based Subtree Crossover Applied to Dynamic Problems", booktitle = "The Third International Conference on Knowledge and Systems Engineering, KSE'2011", year = "2011", editor = "Tu Bao Ho and R. I. McKay and Xuan Hoai Nguyen and The Duy Bui", address = "Hanoi University", month = "14--16 " # oct, keywords = "genetic algorithms, genetic programming", notes = "http://fit.hanu.edu.vn/kse2011/programme.html", } -
A Comparison of GE and TAGE in Dynamic
Environments
By Eoin Murphy, Michael O'Neill and Anthony Brabazon
In GECCO '11: Proceedings of the 13th annual conference on Genetic and evolutionary computation, Dublin, Ireland, 2011. ACM.
[pdf↓]@InProceedings{Murphy:2011:GECCO, author = "Eoin Murphy and Michael O'Neill and Anthony Brabazon", title = "A comparison of {GE} and {TAGE} in dynamic environments", booktitle = "GECCO '11: Proceedings of the 13th annual conference on Genetic and evolutionary computation", year = "2011", editor = "Natalio Krasnogor and Pier Luca Lanzi and Andries Engelbrecht and David Pelta and Carlos Gershenson and Giovanni Squillero and Alex Freitas and Marylyn Ritchie and Mike Preuss and Christian Gagne and Yew Soon Ong and Guenther Raidl and Marcus Gallager and Jose Lozano and Carlos Coello-Coello and Dario Landa Silva and Nikolaus Hansen and Silja Meyer-Nieberg and Jim Smith and Gus Eiben and Ester Bernado-Mansilla and Will Browne and Lee Spector and Tina Yu and Jeff Clune and Greg Hornby and Man-Leung Wong and Pierre Collet and Steve Gustafson and Jean-Paul Watson and Moshe Sipper and Simon Poulding and Gabriela Ochoa and Marc Schoenauer and Carsten Witt and Anne Auger", isbn13 = "978-1-4503-0557-0", pages = "1387--1394", keywords = "genetic algorithms, genetic programming, grammatical evolution", month = "12-16 " # jul, organisation = "SIGEVO", address = "Dublin, Ireland", doi = "doi:10.1145/2001576.2001763", publisher = "ACM", publisher_address = "New York, NY, USA", abstract = "The lack of study of genetic programming in dynamic environments is recognised as a known issue in the field of genetic programming. This study compares the performance of two forms of genetic programming, grammatical evolution and a variation of grammatical evolution which uses tree-adjunct grammars, on a series of dynamic problems. Mean best fitness plots for the two representations are analysed and compared.", notes = "Also known as \cite{2001763} GECCO-2011 A joint meeting of the twentieth international conference on genetic algorithms (ICGA-2011) and the sixteenth annual genetic programming conference (GP-2011)", } -
Examining Mutation Landscapes In Grammar Based Genetic Programming
Award
This work was awarded Best Paper at EuroGP 2011
By Eoin Murphy, Michael O'Neill and Anthony Brabazon
In Proceedings of the 14th European Conference on Genetic Programming, EuroGP 2011, volume 6621, pages 131-142, Turin, Italy, 2011. Springer Verlag.
[pdf↓]@inproceedings{LNCS66210130, editor = "Sara Silva and James A. Foster and Miguel Nicolau and Penousal Machado and Mario Giacobini", booktitle = "Genetic Programming", publisher = "Springer", location = "Heidelberg", series = "Lecture Notes in Computer Science", volume = "6621", year = "2011", isbn = "978-3-642-20406-7", author = "Eoin Murphy and Michael O'Neill and Anthony Brabazon", title = "Examining Mutation Landscapes in Grammar Based Genetic Programming", pages = "130--141" } -
Tree-Adjunct Grammatical Evolution
By Eoin Murphy, Michael O'Neill, Edgar Galvan-Lopez and Anthony Brabazon
In 2010 IEEE World Congress on Computational Intelligence, pages 4449-4456, Barcelona, Spain, 2010. IEEE Press.
[pdf↓]@InProceedings{murphy_etal:cec2010, author = "Eoin Murphy and Michael O'Neill and Edgar Galvan-Lopez and Anthony Brabazon", title = "Tree-Adjunct Grammatical Evolution", booktitle = "2010 IEEE World Congress on Computational Intelligence", pages = "4449--4456", year = "2010", address = "Barcelona, Spain", month = "18-23 " # jul, organization = "IEEE Computational Intelligence Society", publisher = "IEEE Press", keywords = "genetic algorithms, genetic programming, grammatical evolution, TAG", isbn13 = "978-1-4244-6910-9", doi = "doi:10.1109/CEC.2010.5586497", abstract = "In this paper we investigate the application of tree-adjunct grammars to grammatical evolution. The standard type of grammar used by grammatical evolution, context-free grammars, produce a subset of the languages that tree-adjunct grammars can produce, making tree-adjunct grammars, expressively, more powerful. In this study we shed some light on the effects of tree-adjunct grammars on grammatical evolution, or tree-adjunct grammatical evolution. We perform an analytic comparison of the performance of both setups, i.e., grammatical evolution and tree-adjunct grammatical evolution, across a number of classic genetic programming benchmarking problems. The results firmly indicate that tree-adjunct grammatical evolution has a better overall performance (measured in terms of finding the global optima).", } -
Comparing the Performance of the Evolvable
PiGrammatical Evolution Genotype-Phenotype Map to
Grammatical Evolution in the Dynamic Ms. Pac-Man
Environment
By Edgar Galvan-Lopez, David Fagan, Eoin Murphy, John Mark Swafford, Alexandros Agapitos, Michael O'Neill and Anthony Brabazon
In 2010 IEEE World Congress on Computational Intelligence, pages 1587-1594, Barcelona, Spain, 2010. IEEE Press.
[pdf↓]@InProceedings{galvan-lopez_etal:cec2010, author = "Edgar Galvan-Lopez and David Fagan and Eoin Murphy and John Mark Swafford and Alexandros Agapitos and Michael O'Neill and Anthony Brabazon", title = "Comparing the Performance of the Evolvable PiGrammatical Evolution Genotype-Phenotype Map to Grammatical Evolution in the Dynamic Ms. Pac-Man Environment", booktitle = "2010 IEEE World Congress on Computational Intelligence", pages = "1587--1594", year = "2010", address = "Barcelona, Spain", month = "18-23 " # jul, organization = "IEEE Computational Intelligence Society", publisher = "IEEE Press", keywords = "genetic algorithms, genetic programming, grammatical evolution", isbn13 = "978-1-4244-6910-9", doi = "doi:10.1109/CEC.2010.5586508", abstract = "In this work, we examine the capabilities of two forms of mappings by means of Grammatical Evolution (GE) to successfully generate controllers by combining high-level functions in a dynamic environment. In this work we adopted the Ms. Pac-Man game as a benchmark test bed. We show that the standard GE mapping and Position Independent GE (piGE) mapping achieve similar performance in terms of maximising the score. We also show that the controllers produced by both approaches have an overall better performance in terms of maximising the score compared to a hand-coded agent. There are, however, significant differences in the controllers produced by these two approaches: standard GE produces more controllers with invalid code, whereas the opposite is seen with piGE.", }
Workshops
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Examining Grammars and Grammatical Evolution in Dynamic Environments
Award
The presentation of this work was voted Best Presentation at the GSW, GECOO 2011
By Eoin Murphy
In Genetic and Evolutionary Computation Graduate Student Workshop, GECCO 2011, Dublin, Ireland, 2011. ACM.
[pdf↓]@InProceedings{Murphy:2011:GECCOcomp, author = "Eoin Murphy", title = "Examining grammars and grammatical evolution in dynamic environments", booktitle = "GECCO 2011 Graduate students workshop", year = "2011", editor = "Miguel Nicolau", isbn13 = "978-1-4503-0690-4", keywords = "genetic algorithms, genetic programming, grammatical evolution", pages = "779--782", month = "12-16 " # jul, organisation = "SIGEVO", address = "Dublin, Ireland", doi = "doi:10.1145/2001858.2002090", publisher = "ACM", publisher_address = "New York, NY, USA", abstract = "This paper is concerned with the effect of the grammar type on grammatical evolution when evolving in dynamic environments. Both representation and dynamic environments have been recognised as important open issues in the field of genetic programming. This paper outlines the need for further study on both topics in the context of grammatical evolution, suggesting further inspiration be taken from nature in an attempt to improve the representations available to grammatical evolution. The research undertaken to date is listed, along with the future work to be completed.", notes = "Also known as \cite{2002090} Distributed on CD-ROM at GECCO-2011. ACM Order Number 910112.", } -
Acceleration of Grammatical Evolution Using
Graphics Processing Units
By Petr Pospichal, Eoin Murphy, Michael O'Neill, Jiri Jaros and Josef Schwarz
In Genetic and Evolutionary Computation CIGPU Workshop, GECCO 2011, Dublin, Ireland, 2011. ACM.
[pdf↓]@InProceedings{Pospichal:2011:GECCOcomp, author = "Petr Pospichal and Eoin Murphy and Michael O'Neill and Josef Schwarz and Jiri Jaros", title = "Acceleration of grammatical evolution using graphics processing units: computational intelligence on consumer games and graphics hardware", booktitle = "GECCO 2011 Computational intelligence on consumer games and graphics hardware (CIGPU)", year = "2011", editor = "Simon Harding and W. B. Langdon and Man Leung Wong and Garnett Wilson and Tony Lewis", isbn13 = "978-1-4503-0690-4", keywords = "genetic algorithms, genetic programming, grammatical evolution, GPU", pages = "431--438", month = "12-16 " # jul, organisation = "SIGEVO", address = "Dublin, Ireland", doi = "doi:10.1145/2001858.2002030", publisher = "ACM", publisher_address = "New York, NY, USA", abstract = "Several papers show that symbolic regression is suitable for data analysis and prediction in financial markets. Grammatical Evolution (GE), a grammar-based form of Genetic Programming (GP), has been successfully applied in solving various tasks including symbolic regression. However, often the computational effort to calculate the fitness of a solution in GP can limit the area of possible application and/or the extent of experimentation undertaken. This paper deals with using mainstream graphics processing units (GPU) for acceleration of GE solving symbolic regression. GPU optimisation details are discussed and the NVCC compiler is analysed. We design an effective mapping of the algorithm to the CUDA framework, and in so doing must tackle constraints of the GPU approach, such as the PCI-express bottleneck and main memory transactions. This is the first occasion GE has been adapted for running on a GPU. We measure our implementation running on one core of CPU Core i7 and GPU GTX 480 together with a GE library written in JAVA, GEVA. Results indicate that our algorithm offers the same convergence, and it is suitable for a larger number of regression points where GPU is able to reach speedups of up to 39 times faster when compared to GEVA on a serial CPU code written in C. In conclusion, properly used, GPU can offer an interesting performance boost for GE tackling symbolic regression.", notes = "Also known as \cite{2002030} Distributed on CD-ROM at GECCO-2011. ACM Order Number 910112.", } -
Interpolants Induced by Marching Cases
By Hamish Carr and Eoin Murphy
In Scientific Visualization: Interactions, Features, Metaphors, Dagstuhl Follow-Ups 2011, Dagstuhl, Germany. 2011. Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik.
[pdf↓]@InCollection{carr_et_al:DFU:2011:3283, author = {Hamish Carr and Eoin Murphy}, title = {{Interpolants Induced by Marching Cases}}, booktitle = {Scientific Visualization: Interactions, Features, Metaphors}, pages = {48--58}, series = {Dagstuhl Follow-Ups}, ISBN = {978-3-939897-26-2}, ISSN = {1868-8977}, year = {2011}, volume = {2}, editor = {Hans Hagen}, publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik}, address = {Dagstuhl, Germany}, URL = {http://drops.dagstuhl.de/opus/volltexte/2011/3283}, URN = {urn:nbn:de:0030-drops-32837}, doi = {http://dx.doi.org/10.4230/DFU.Vol2.SciViz.2011.48}, annote = {Keywords: Interpolation, Marching Cubes, Isosurfaces} }
Other
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Glow Tags: The Choice of the Old Generation
By Eoin Murphy
ODCSSS, UCD, Dublin. 2008.
[pdf↓]@InCollection{murphy:odcsss:2007, author = {Eoin Murphy}, title = {Glow Tags: The Choice of the Old Generation}, year = {2007}, keywords = {Way-finding, Embedded Computing, Low-Level Hardware, Gumstix, Location sensing} }