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2017

  • Morar, T. M., J. Knowles, and S. Sampaio Initialization of Bayesian Optimization Viewed as Part of a Larger Algorithm Portfolio, Data Science meets Optimization (DSO) Workshop, San Sebastian, Spain, June 2017. PDF
  • Greco, S., K. Klamroth, J. Knowles, and G. Rudolph (guest editors) (2017) Special Issue on Understanding Complexity in Multiobjective Optimization, Journal of Multi-Criteria Decision Analysis (in press). Original Call for Papers PDF (Editorial coming soon)
  • Brockhoff, D., J. Knowles, B. Naujoks, and K. Sindhya (guest editors) (2017) Special Issue on Evolutionary Multiobjective Optimization, Computers and Operations Research 79 (in press). Editorial Intro PDF
  • Miller, S. (2017) Network Fluctuation as an Explanatory Factor in the Evolution of Cooperation, Phd Thesis (supervised by J. Knowles). Corrected version in press. Uncorrected version PDF
  • Webb, A. (2017) On Selection for Evolvability, Phd Thesis (supervised by J. Knowles and co-supervised by
    J. Handl). Corrected version in press. Uncorrected version PDF
  • Garza-Fabre, M., J. Handl and J. Knowles (2017) A New Reduced-Length Genetic Representation for Evolutionary Multiobjective Clustering, Proceedings of Evolutionary Multi-criterion Optimization (in press). PDF Preprint
  • Hakanen, J. and J. Knowles (2017) On using decision maker preferences with ParEGO, Proceedings of Evolutionary Multi-criterion Optimization (in press). PDF Preprint
  • Aghamohammadi, N. R., S. Salomon and R. C. Purshouse (2017) On the effect of scalarising norm choice in a ParEGO implementation, Proceedings of Evolutionary Multi-criterion Optimization (in press). (Acknowledgment only). PDF Preprint

2016

  • S. Miller and J. Knowles (2016) Population Fluctuation Promotes Cooperation in Networks, Accepted for Oral Presentation at Learning and Intelligent Optimization (LION 10), Ischia Island (Napoli), Italy, 29 May - 1 June, 2016. This will be a presentation of our 2015 journal article of the same name published in Nature Scientific Reports.
  • R. J. Lyon, B. W. Stappers, S. Cooper, J. M. Brooke, J. D. Knowles (2016) Fifty Years of Pulsar Candidate Selection: From simple filters to a new principled real-time classification approach, Monthly Notices of the Royal Astronomical Society vol.459, issue 1, pp.1104-1123, June. Published PDF (Free)
  • Mario Garza-Fabre, Shaun M. Kandathil, Julia Handl, Joshua Knowles, Simon C. Lovell (2016) Generating, Maintaining and Exploiting Diversity in a Memetic Algorithm for Protein Structure Prediction, Evolutionary Computation. (In press).
  • Krzysztof Michalak, Joshua D. Knowles (2016) Simheuristics for the Multiobjective Nondeterministic Firefighter Problem in a Time-Constrained Setting, EVOSTOC, EvoWorkshops, March 30-April 1. (To appear in Springer LNCS) PDF (Accepted Pre-pub Version)
  • Steve Miller, Joshua Knowles (2016) The Emergence of Cooperation in Public Goods Games on Randomly Growing Dynamic Networks, EVOCOMPLEX, EvoWorkshops, March 30-April 1. (To appear in Springer LNCS) PDF (Accepted Pre-pub Version)

2015

  • D. Buckley, K. Chen, J. Knowles (2015) Rapid Skill Capture in a First-Person Shooter, IEEE Transactions on Computational Intelligence and AI in Games, ISSN 1943-068X. Open Access.
  • B.-C. Cristescu and J. Knowles (2015) Surrogate-Based Multiobjective Optimization: ParEGO Update and Test, Workshop on Computational Intelligence (UKCI). PDF
  • D. Brockhoff, A. Buzdalova, K. A. De Jong, C. M. Fonseca, T. Friedrich, H-K. Hwang, J. D. Knowles, W. B. Langdon, F. Neumann, J. L. Shapiro. (2015) Practice to Theory in Evolutionary Computation, in Dagstuhl Reports, Volume 5, Issue 2 (in press). Draft (PDF)
  • S. Greco, K. Klamroth, J. D. Knowles, and G. Rudolph (eds.) (2015) Understanding Complexity in Multiobjective Optimization (Dagstuhl Seminar 15031), in Dagstuhl Reports, Volume 5, Issue 1, pp 96-163. PDF
  • G. Brown (2015) On Unifiers, Diversifiers, and the Nature of Pattern Recognition, Pattern Recognition Letters (Special Issue on Philosophical Aspects of Pattern Recognition) doi:10.1016/j.patrec.2015.04.014. (Acknowledgment only). PDF
  • R. Allmendinger, J. Handl and J. Knowles (2015) Multiobjective Optimization: When Objectives Exhibit Non-Uniform Latencies, European Journal of Operational Research, 243 (2), 497-513. Preprint version (PDF)
  • G. Eichfelder, X. Gandibleux, M. J. Geiger, J. Jahn, A. Jaszkiewicz, J. D. Knowles, P. K. Shukla, H. Trautmann, and S. Wessing (2015) Heterogeneous Functions, in Dagstuhl Reports, Volume 5, Issue 1, pp 121-129. PDF
  • Garza-Fabre, M., Kandathil, S., Handl, J., Knowles, J. and Lovell, S.C. (2015) Using Machine Learning to Explore the Relevance of Local and Global Features During Conformational Search in Rosetta. In Proceedings of the Companion Publication of GECCO 2015 ACM Press, pp. 935-938.
  • A. Almakhlafi and J. Knowles (2015) Iterated Local Search for the Generator Maintenance Scheduling Problem, In Proceedings of the Multi-disciplinary International Conference on Scheduling: Theory and Applications (MISTA 2015), ISSN 2305-249X. PDF
  • S. Miller and J. Knowles (2015) Population Fluctuation Promotes Cooperation in Networks, Nature Scientific Reports 5, 11054. Open Access at nature.com
  • Webb, A., Handl, J. and Knowles, J. (2015) How Much Should You Select for Evolvability? In Proceedings of the European Conference on Artificial Life 2015, MIT Press, pp. 487-494. PDF
  • Miller, S. and Knowles, J. (2015) A Minimal Model for the Emergence of Cooperation in Networks. In Proceedings of the European Conference on Artificial Life 2015, MIT Press, pp. 114-121. PDF
  • M. López-Ibáñez, J. Knowles (2015) Machine Decision Makers as a Laboratory for Interactive EMO, Proceedings of Evolutionary Multicriterion Optimization (EMO'2015), LNCS 9019, Springer, pp. 295-309. PDF
  • J. Bradbury, G. Genta-Jouve, J. William Allwood, W.B. Dunn, R. Goodacre, J.D. Knowles, S. He, M.R. Viant (2015) MUSCLE: Automated Multi-objective Evolutionary Optimisation of Targeted LC-MS/MS Analysis, Bioinformatics 31 (6):975-977. Open Access

2014

  • S. Miller and J. Knowles (2014) Population Fluctuation Promotes Cooperation in Networks, arXiv:1407.8032 [cs.GT], July.
  • W.B. Dunn ... J.Knowles et al. (2014) Molecular phenotyping of a UK population: defining the human serum metabolome, Metabolomics, doi:10.1007/s11306-014-0707-1.
  • J. Handl and J. Knowles (2014) Nature-inspired clustering, In C. Hennig, M. Meila, F. Murtagh, R. Rocci (eds.) Handbook of Cluster Analysis, Chapman and Hall (CRC Press). (To appear).
  • A.M. Webb and J. Knowles (2014) Studying the Evolvability of Self-Encoding Genotype-Phenotype Maps, In Lipson, Hod et al. (eds.) ALIFE 14: The Fourteenth International Conference on the Synthesis and Simulation of Living Systems. Fourteenth International Conference on Artificial Life, pp. 79-86 MIT Press. PDF
  • R. Lyon, J. Brooke, J. Knowles, B. Stappers (2014) Hellinger Distance Trees for Imbalanced Streams, In 22nd International Conference on Pattern Recognition (ICPR 2014), IEEE, pp. 1969-1974. PDF
  • R. Allmendinger and J. Knowles (2014) Ephemeral Resource Constraints in Optimization, in R. Datta and K. Deb (eds.) Evolutionary Constrained Optimization, Springer, pp. 95-134.
  • N. Swainston, A. Currin, P.J. Day, and D.B. Kell (2014) GeneGenie: optimized oligomer design for directed evolution, Nucleic Acids Research, first published online April 29. doi:10.1093/nar/gku336 . (Acknowledgment only).

2013

  • R.J. Lyon, J.M. Brooke, J.D. Knowles and B.W. Stappers (2013) A Study on Classification in Imbalanced and Partially-Labelled Data Streams, arXiv:1307.8012 [astro-ph.IM] and presented at IEEE Conference on Systems, Man and Cybernetics, Manchester, UK.
  • D. Buckley, K. Chen and J. Knowles (2013) Predicting Skill from Gameplay Input to a First-Person Shooter, Proceedings of the IEEE Conference on Computational Intelligence and Games (CIG2013), pp. 105-112. PDF
  • S. M. Kandathil, T. L. Fletcher, Y. Yuan, J. Knowles and P. L. A. Popelier. (2013) Accuracy and tractability of a kriging model of intramolecular polarisable multipolar electrostatics and its application to histidine. Journal of Computational Chemistry 34: 1850-1861. Published version: Wiley
  • R. Aler, J. Handl and J. Knowles (2013) Comparing Multi-objective and Threshold-moving ROC Curve Generation for a Prototype-based Classifier. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO'13), pp. 1029-1036. Published version at ACM
  • A. Almakhlafi and J. Knowles. (2013) Systematic Construction of Algorithm Portfolios for a Maintenance Scheduling Problem. Proceedings of IEEE Congress on Evolutionary Computation, pp. 245-252 doi:10.1109/CEC.2013.6557577 Published version at IEEE Xplore
  • J. Handl and J. Knowles (2013) Evidence accumulation in multiobjective data clustering. 7th International Conference on Evolutionary Multi-Criterion Optimization (EMO 2013), Springer LNCS 7811, pp. 543-557. Download PDF (pre-pub); Published version at SpringerLink
  • R. Allmendinger and J. Knowles (2013) 'Hang On a Minute': Investigations on the Effects of Delayed Objective Functions in Multiobjective Optimization. 7th International Conference on Evolutionary Multi-Criterion Optimization (EMO 2013), Springer LNCS 7811, pp. 6-22. Download PDF (pre-pub). Published version at SpringerLink; Slides
  • R. Allmendinger and J. Knowles (2013) On Handling Ephemeral Resource Constraints in Evolutionary Search. Evolutionary Computation, 21(3): 497-531. Download PDF (Pre-publication); Published version at MIT Press

2012

  • O'Hagan, S., Knowles, J. and Kell, D. B. (2012) Exploiting Genomic Knowledge in Optimising Molecular Breeding Programmes: Algorithms from Evolutionary Computing. PLoS ONE 11 (7): e48862. Online 10.1371/journal.pone.0048862
  • J. Handl and J. Knowles (2012) Clustering criteria in multiobjective data clustering. Proceedings of Parallel Problem Solving from Nature (PPSN 2012), LNCS 7492/2012 pp. 32-41, Springer. SpringerLink
  • A. Almakhlafi and J. Knowles (2012) Benchmarks for Maintenance Scheduling Problems in Power Generation Proceedings of the IEEE Congress on Evolutionary Computation (CEC2012), pp. 1-8, IEEE Press. IEEE Xplore
  • Greco, S., Knowles, J.D., Miettinen, K., Zitzler, E. (Eds.) Learning in Multiobjective Optimization (Dagstuhl Seminar 12041), Dagstuhl Reports, Volume 2, Issue 1 pp. 39-49, doi:10.4230/DagRep.2.1.39
  • J. Handl, J. Knowles, R. Vernon, D. Baker, S. Lovell (2012) The dual role of fragments in fragment-assembly methods for de novo protein structure prediction. Proteins: Structure, Function and Bioinformatics, 80 (2): 490-504. doi: 10.1002/prot.23215 Wiley Online

2011

  • Small, B.G., McColl, B.W., Allmendinger, R., Pahle, J., Lopez-Castejon, G., Rothwell, N.J., Knowles, J., Mendes, P., Brough, D., Kell, D.B. (2011) Efficient discovery of anti-inflammatory small molecule combinations using evolutionary computing. Nature Chemical Biology, 7: 902-908 Nature published version; Pubmed version (free)
  • R. Allmendinger and J. Knowles (2011) Evolutionary Search in Lethal Environments In Proceedings of the International Conference on Evolutionary Computation Theory and Applications (ECTA'11), Paris, France, October 24-26.
  • Dunn W.B., Broadhurst D., Begley P., Zelena E., Francis-McIntyre S., Anderson N., Brown M., Knowles J.D., Halsall A., Haselden J.N., Nicholls A.W., Wilson I.D., Kell D.B., Goodacre R.; The Human Serum Metabolome (HUSERMET) Consortium (2011) Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nature Protocols 6(7): 1060-1083. doi: 10.1038/nprot.2011.335. Online version
  • R. Allmendinger and J. Knowles (2011): Policy Learning in Resource-Constrained Optimization. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2011), pp 1971-1978. doi: 10.1145/2001576.2001841 Download pdf
  • Manuel López-Ibáñez, Joshua D. Knowles, and Marco Laumanns (2011) On Sequential Online Archiving of Objective Vectors. In Evolutionary Multi-criterion Optimization (EMO 2011), Lecture Notes in Computer Science. Springer, Heidelberg, Germany.
    Bibtex ][ Software ][ Revised Technical Report version ]

2010

  • Rowe, W., Wedge, D., Platt, M., Kell, D.B., and Knowles, J. (2010) Convergent evolution to an aptamer observed in small populations on DNA microarrays, Physical Biology 7, 036007. Online edition.
  • Rowe, W., Wedge, D., Platt, M., Kell, D.B., and Knowles, J. (2010) Predictive Models for Population Performance on Real Biological Fitness Landscapes, Bioinformatics, 26 (17): 2145-2152. doi: 10.1093/bioinformatics/btq353
  • Allmendinger, R. and Knowles, J. (2010) Ephemeral Resource Constraints in Optimization and Their Effects on Evolutionary Search. Technical Report MLO-20042010, University of Manchester. PDF
  • Jarvis, R.M., Rowe, W., Yaffe, N.R., O'Connor, R., Knowles, J.D., Blanch, E.W. and Goodacre, R. (2010) Multiobjective evolutionary optimisation for surface-enhanced Raman scattering, Analytical and Bioanalytical Chemistry, 397:1893-1901.
  • Allmendinger, R. and Knowles, J. (2010) On-Line Purchasing Strategies for an Evolutionary Algorithm Performing Resource-Constrained Optimization Proceedings of PPSN XI, volume II, LNCS 6239, pp 161-170.
  • Allmendinger, R. and Knowles, J. (2010) Evolutionary Optimization on Problems Subject to Changes of Variables Proceedings of PPSN XI, volume II, LNCS 6239, pp 151-160.
  • Bonabeau, E., Corne, D., Knowles, J. Poli, R. (eds.) (2010)  Theoretical Computer Science C: Special Issue on Swarm Intelligence: State of the Art.
  • Corne, D., Deb, K., Knowles, J., Yao, X. (2010) Selected Applications of Natural Computing, in Handbook of Natural Computing (Rozenberg, Back, Kok (eds), Volume VI: Broader Perspective. PDF (to appear)
  • Humston, E.M., Knowles, J.D., McShea, A., Synovec, R.E. (2010) Quantitative Assessment of Moisture Damage for Cacao Bean Quality using Two-Dimensional Gas Chromatography Combined with Time-of-Flight Mass Spectrometry and Chemometrics. Journal of Chromatography A, 1217 (12): 1963-1970. doi: 10.1016/j.chroma.2010.01.069
  • Rowe, W., Platt, M., Wedge, D.C., Day, P.J., Kell D.B. and Knowles, J. (2010) Analysis of a complete DNA-protein affinity landscape. Journal of the Royal Society Interface, 7(44): 397-408. Online version doi:10.1098/rsif.2009.0193. PDF

2009

  • Knowles, J. (2009) Closed-loop evolutionary multiobjective optimization. IEEE Computational Intelligence Magazine, 4(3): 77-91. IEEE Xplore PDF
  • Knowles, J., Corne, D. and Reynolds, A. (2009) Noisy Multiobjective Optimization on a Budget of 250 Evaluations. EMO 2009, LNCS 5467, pp 36-50. Springer Link
  • Handl, J., Lovell, S. and Knowles, J. (2009) Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction Bioinformatics 25(10): 1271-1279. Advance Access.
  • Platt, M., Rowe, W., Knowles, J., Day, P.J., Kell, D.B. (2009) Analysis of aptamer sequence-activity relationships. Integrative Biology, 1: 116-122. DOI:10.1039/b814892a. Online version

2008

  • Wedge, D.C., Rowe, W., Kell, D.B. and Knowles, J. (2008) In silico Modelling of Directed Evolution: Implications for Experimental Design and Stepwise Evolution. Journal of Theoretical Biology 257 (1): 131-141. doi: 10.1016/j.jtbi.2008.11.005 Online
  • Farrelly, C.M., Kell, D.B., Knowles, J. (2008) Molecular Structure Elucidation Using Ant Colony Optimization. ANTS 2008, Springer LNCS 5217, pp. 120-131. SpringerLink
  • Knight, C. G., Platt, M., Rowe, W., Wedge, D., Khan, F., McShea, A., Day, P.J., Knowles, J. and Kell, D.B. (2008) Array-based evolution of DNA aptamers allows modeling of an explicit sequence-fitness landscape. Nucleic Acids Research 37 (1): e6. doi: 10.1093/nar/gkn899. Nucleic Acids Advance Acess
  • Handl, J., Lovell, S., Knowles, J. (2008) Multiobjectivization by decomposition of scalar cost functions. In Parallel Problem Solving from Nature - PPSN X. Springer LNCS 5199, pp. 31-40. SpringerLink
  • Handl, J., Lovell, S., Knowles, J. (2008) Investigations into the effect of multiobjectivization in protein structure prediction. In Parallel Problem Solving from Nature - PPSN X. Springer LNCS 5199, pp. 702-711. SpringerLink
  • Zitzler, E., Knowles, J. and Thiele, L. (2008) Quality Assessment of Pareto Set Approximations. In Multi-objective Optimization - Interactive and Evolutionary Approaches. Springer LNCS 5252, pp.373-404. SpringerLink
  • Knowles, J. and Nakayama, H. (2008) Meta-modeling in multi-objective optimization. In Multi-objective Optimization - Interactive and Evolutionary Approaches. Springer LNCS 5252, pp. 245-284. SpringerLink
  • Knowles, J., Corne, D. and Deb, K. (eds.) (2008) Multiobjective Problem Solving from Nature. Springer Natural Computing Series, Springer-Verlag. Order information.
  • Handl, J. and Knowles, J. (2008) Modes of Problem Solving with Multiobjective Optimization: Implications for Interpreting the Pareto Set and for Decision Making. In Multiobjective Problem Solving from Nature. Springer Natural Computing Series, Springer-Verlag, pp. 131-151. SpringerLink
  • Jin, Y., Knowles, J., Hongmei, L., Yizeng, L. and Kell, D.B. (2008) The landscape adaptive particle swarm optimizer. Applied Soft Computing, 8 (1): 295-304. PDF.
  • Ludtke, N., Panzeri, S., Brown, M., Broomhead, D., Knowles, J., Montemurro, M.A. and Kell, D.B. (2008) Information-theoretic sensitivity analysis: a general method for credit assignment in complex networks. Journal of the Royal Society Interface. 5 (19): 223-235.

2007

  • Handl, J., Kell, D. and Knowles, J. (2007) Multiobjective optimization in computational biology and bioinformatics. IEEE Transactions on Computational Biology and Bioinformatics, 4(2):279-292. PDF
  • Corne, D. and Knowles, J. (2007) Techniques for Highly Multiobjective Optimisation: Some Nondominated Points are Better than Others. Proceedings of the 9th Annual Conference on Genetic and Evolutionary Computation (GECCO), pp. 773-780. ACM Press, New York. Preprint
  • Knowles, J. and Corne, D. (2007) Quantifying the Effects of Objective Space Dimension in Evolutionary Multiobjective Optimization. Evolutionary Multi-Criterion Optimization, LNCS 4403, pp 757-771. PDF from Springer Link
  • Handl, J. and Knowles, J. (2007) An evolutionary approach to multiobjective clustering. IEEE Transactions on Evolutionary Computation 11(1):56-76. Draft version - PDF and Link to IEEE Xplore version.
  • O'Hagan, S., Dunn, W.B., Knowles, J.D., Broadhurst, D., Williams, R. Ashworth, J.J., Cameron, M., Kell, D.B. (2007) Closed-Loop, Multiobjective Optimization of Two-Dimensional Gas Chromatography/Mass Spectrometry for Serum Metabolomics. Analytical Chemistry 79 (2): 464-476. PDF.

2006

  • Yue, H., M. Brown, J. Knowles, H. Wang, D.S. Broomhead and D.B. Kell (2006) Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of an NF-kB signaling pathway. Molecular Biosystems, 2 (12): 640-649. DOI: 10.1039/b609442b.
  • Knowles, J. and Corne, D. (2006) Evolutionary Multiobjective Optimization. Semi-plenary talk at the 7th International Conference on Multi-Objective Programming and Goal Programming (MOPGP). Extended abstract.
  • Handl, J. and Knowles, J. (2006) An investigation of representations and operators for evolutionary data clustering with a variable number of clusters. Proceedings of IXth International Conference on Parallel Problem Solving from Nature (PPSN IX), pp. 839-849. SpringerLink
  • Handl, J. and Knowles, J. (2006) Semi-supervised feature selection via multiobjective optimization. International Joint Conference on Neural Networks (IJCNN 2006). Proc WCCI 2006, pp 6351-6358, IEEE Press. PDF
  • Rowe, W., Corne, D.W. and Knowles, J. (2006) Predicting Stochastic Search Algorithm Performance using Landscape State Machines. IEEE Congress on Evolutionary Computation (CEC 2006). Proc WCCI 2006, pp 9849-9856. IEEE Press. PDF(local) PDF(official)
  • Handl, J. and Knowles, J. (2006) On semi-supervised clustering via multiobjective optimization. Genetic and Evolutionary Computation Conference (GECCO-2006), pp 1465-1472. ACM Press. PDF
  • Handl, J., Kell, D.B. and Knowles, J. (2006) Multiobjective optimization in bioinformatics and computational biology. Technical report TR-COMPSYSBIO-2006-04. PDF A shorter version will now appear in TCBB (see above).
  • Handl, J. and Knowles, J. (2006) Feature subset selection in unsupervised learning via multiobjective optimization. International Journal of Computational Intelligence Research, 2 (3): 217-238. PDF Available online
  • Knowles, J. D., Thiele, L. and Zitzler, E. A tutorial on the performance assessment of stochastive multiobjective optimizers. TIK-Report No. 214, Computer Engineering and Networks Laboratory, ETH Zurich, February 2006 (Revised version. First version, January 2005). PDF
  • Knowles, J. (2006). The assignment of referees to WSC10 submissions: An evolutionary approach. In A. Tiwari et al, editors, Applications of Soft Computing: Recent Trends. Springer-Verlag.
  • A. Tiwari, J. Knowles, E. Avineri, K. Dahal and R. Roy (2006) Applications of Soft Computing: Recent Trends. Springer-Verlag. ISBN 3-540-29123-7.
  • Handl, J. and Knowles, J. (2006) Multiobjective clustering and cluster validation. Yaochu Jin (editor) Multiobjective Machine Learning. Studies in Computational Intelligence 16, pp 21-47. Springer. PDF Book from Springer
  • Kell, D.B. and Knowles, J. (2006) The role of modeling in systems biology. Z. Szallasi, V. Periwal, J. Stelling (editors) System Modeling in Cellular Biology: From Concepts to Nuts and Bolts, pp 3-18. MIT Press, Cambridge, MA. PDF Book from MIT Press
  • Knowles, J. (2006) ParEGO: A hybrid algorithm with on-line landscape approximation for expensive multiobjective optimization problems. IEEE Transactions on Evolutionary Computation. 10 (1): 50-66. Preprint version: PDF (981 KB) Published version from IEEE Explore. BibTeX
  • Handl, J., Knowles, J. and Dorigo, M. (2006) Ant-based clustering and topographic mapping. Artificial Life 12(1). PDF

2005

  • Handl, J. and Knowles, J. (2005) Improvements to the scalability of multiobjective clustering. IEEE Congress on Evolutionary Computation, pp. 438-445. IEEE Press. PDF
  • Handl, J. and Knowles, J. (2005) Multiobjective clustering around medoids. IEEE Congress on Evolutionary Computation, pp. 550-557. IEEE Press. PDF
  • Handl, J., Knowles, J., and Kell, D.B. (2005) Computational cluster validation in post-genomic data analysis. Bioinformatics, 21: 3201-3212. Abstract Full text Supplementary material including color figures
  • Fonseca, C. M., Knowles, J., Thiele, L. and Zitzler, E. (2005) A tutorial on the performance assessment of stochastic multiobjective optimizers. Slides from a tutorial presented by J. Knowles at EMO 2005. PDF (2.5 MB)
  • Knowles, J. (2005) A summary-attainment-surface plotting method for visualizing the performance of stochastic multiobjective optimizers. Proceedings of the Fifth International Conference on Intelligent Systems Design and Applications (ISDA V). For more information and paper download, click here.
  • Brown, M., Dunn, W.B., Ellis, D.I., Goodacre, R., Handl, J., Knowles, J.D., O'Hagan, S., Spasic, I. and Kell, D.B. (2005) A metabolome pipeline: from concept to data to knowledge. Metabolomics 1 (1), 39-51.
  • O'Hagan, S., Dunn, W. B., Brown, M., Knowles, J. D. and Kell, D. B. (2005) Closed-loop, multiobjective optimization of analytical instrumentation: gas chromatography/time-of-flight mass spectrometry of the metabolomes of human serum and of yeast fermentations. Analytical Chemistry 77 (1) pp. 290-303. January. Available online here.
  • Knowles, J. and Hughes, E. J. (2005) Multiobjective optimization on a budget of 250 evaluations. Evolutionary Multi-Criterion Optimization (EMO 2005), LNCS 3410, pp. 176-190. Springer-Verlag. PDF and supporting material
  • Handl, J. and Knowles, J. (2005) Exploiting the trade-off - the benefits of multiple objectives in data clustering. Evolutionary Multi-Criterion Optimization (EMO 2005), LNCS 3410, pp. 547-560. Springer-Verlag. PDF
  • Bianchi, L., Knowles, J., and Bowler, N. (2005) Local search for the probabilistic traveling salesman problem: correction to the 2-p-opt and 1-shift algorithms. European Journal of Operational Research, 162 (1), pp. 206-219. April. Copyright owned by Elsevier. Downloadable pre-print version in PDF

2004

  • Knowles, J. (2004) ParEGO: A hybrid algorithm with on-line landscape approximation for expensive multiobjective optimization problems. Technical report TR-COMPSYSBIO-2004-01, University of Manchester, Manchester, UK. September 2004. Abstract, paper and supporting material available here.
  • Handl, J. and Knowles, J. (2004) Multiobjective clustering with automatic determination of the number of clusters. Technical report TR-COMPSYSBIO-2004-02, UMIST, Manchester, UK. August 2004. Abstract and paper available here.
  • Knowles, J. and Corne, D. (2004) Memetic algorithms for multiobjective optimization: issues, methods and prospects. In Recent Advances in Memetic Algorithms. Krasnogor, N., Smith, J.E., and Hart, W.E. (eds). pp. 313-352. Springer. PDF and Info on the book
  • Knowles, J.D. and Corne, D.W. (2004) Bounded Pareto archiving: theory and practice. X. Gandibleux, M. Sevaux, K. Sorensen and V. T'kindt (Eds.), Metaheuristics for Multiobjective Optimisation, Lecture Notes in Economics and Mathematical Systems, Volume 535, Springer. pp. 39-64. Click here for more info on this book. BibTeX Abstract PDF
  • Handl, J. and Knowles, J. (2004) Evolutionary multiobjective clustering. Parallel Problem Solving From Nature (PPSN VIII). Pages 1081-1091. LNCS 3242. Copyright Springer-Verlag. Paper and all supporting material available here.

2003

  • Corne, D.W., Deb, K., Fleming, P.J., Knowles, J.D. (2003) The Good of the Many Outweights the Good of the One: Evolutionary Multiobjective Optimizations, coNNectionS, 1(1): 9-13, ISSN 1543-4281. (Feature article in first issue of coNNectionS, the quarterly newsletter of the IEEE Neural Networks Society. Pre-print Word document (sorry!). Copyright IEEE Press.
  • Handl, J., Knowles, J., and Dorigo, M. (2003) Strategies for the increased robustness of ant-based clustering. Self-Organising Applications: Issues, challenges and trends. Pages 90-104. LNCS 2977. Springer-Verlag. PDF
  • Handl, J., Knowles, J., and Dorigo, M. (2003) On the performance of ant-based clustering. Design and application of hybrid intelligent systems. Frontiers in Artificial intelligence and Applications 104. Pages 204-213. Copyright IOS Press. PDF
  • Knowles, J.D. and Corne, D.W. (2003) Properties of an adaptive archiving algorithm for storing nondominated vectors. IEEE Transactions on Evolutionary Computation, 7(2), pp. 100-116. April. Draft version. Original available from IEEE Press.
  • Knowles, J.D. and Corne, D.W. and Fleischer, M. (2003) Bounded archiving using the Lebesgue measure. Proceedings of the IEEE Congress on Evolutionary Computation. Volume 4, pp. 2490-2497. IEEE Press. BibTeX Abstract PDF
    Note: the Lebesgue measure archive as described in this paper does not have the time complexity stated. Lyndon While recently proved that Fleischer's Lebesgue measure computation algorithm has complexity exponential in the number of objectives, not polynomial as originally claimed. However this does not substantially change the conclusions drawn in this paper.
  • Corne, D.W. and Knowles, J.D. (2003) Some multiobjective optimizers are better than others. Proceedings of the IEEE Congress on Evolutionary Computation. Volume 4, pp. 2506-2512. IEEE Press. BibTeX Abstract PDF
  • Rossi-Doria, O., Sampels, M., Birattari, M., Chiarandini, M., Dorigo, M., Gambardella, L.M., Knowles, J., Manfrin, M., Mastrolilli, M., Paechter, B., Paquete, L., Stützle T. (2003) A comparison of the performance of different metaheuristics on the timetabling problem. Practice and Theory of Automated Timetabling IV: 4th International Conference, PATAT 2002, Selected Revised Papers. LNCS 2740. pp. 329-351. Springer. PDF
  • Knowles, J.D. and Corne, D.W. (2003) Instance generators and test suites for the multiobjective quadratic assignment problem. Evolutionary Multi-Criterion Optimization (EMO 2003) Second International Conference, Faro, Portugal, April 2003, Proceedings, pp. 295-310. BibTeX Abstract PDF - corrected version - (Copyright Springer). To see why this paper has been corrected, click here.
  • Corne, D.W. and Knowles, J.D. (2003) No free lunch and free leftovers theorems for multiobjective optimization problems. Evolutionary Multi-Criterion Optimization (EMO 2003) Second International Conference, Faro, Portugal, April 2003, Proceedings, pp. 327-341. BibTeX Abstract PDF (Copyright Springer)

2002

  • Knowles, J.D. (2002) Local-Search and Hybrid Evolutionary Algorithms for Pareto Optimization. PhD thesis. Department of Computer Science, University of Reading, UK. January. (Examiners: Prof. Kalyanmoy Deb and Prof. Kevin Warwick) Abstract and PDF
  • Knowles, J.D. and Corne, D.W. (2002) A Memetic Method for Multiobjective Optimisation. International Application Published Under the Patent Corporation Treaty (PCT), International Application Number PCT/GB00/03482, International Publication Number WO 02/03716 A1, January 10. Priority Data: EP00305549.8, 30th June 2000.
  • Knowles, J.D., Corne, D.W. (2002) Enumeration of Pareto optimal multi-criteria spanning trees - a proof of the incorrectness of Zhou and Gen's proposed algorithm. European Journal of Operational Research, Volume 143, Issue 3, 16 December 2002, Pages 543-547. Pre-print version
  • Knowles, J.D. and Corne, D.W. (2002) Towards landscape analyses to inform the design of a hybrid local search for the multiobjective quadratic assignment problem. In A. Abraham, J. Ruiz-del-Solar, M. Koppen (eds.), Soft Computing Systems: Design, Management and Applications, IOS Press, Amsterdam, pp. 271-279, ISBN 1-58603-297-6 BibTeX Abstract PDF
  • Socha, K., Knowles, J. and Sampels, M. (2002) A MAX-MIN ant system for the university course timetabling problem. In M. Dorigo, G. Di Caro and M. Sampels (Eds.) Ant Algorithms Third International Workshop, ANTS 2002, Brussels, Belgium, September 12-14. LNCS 2463. Springer-Verlag. pp. 1-13. (Also Technical Report TR/IRIDIA/2002-18.) PDF
  • Knowles, J.D. and Watson, R.A. (2002) On the utility of redundant encodings in mutation-based evolutionary search. In J.J. Merelo Guervos et al. (Eds.) Parallel Problem Solving from Nature - PPSN VII . Seventh International Conference, Granada, Spain, September 7-11. LNCS 2439. Copyright Springer-Verlag. pp. 88-98. Download: Postscript, PDF
  • Knowles, J.D. and Corne, D.W. (2002) On metrics for comparing non-dominated sets. In Proceedings of the 2002 Congress on Evolutionary Computation Conference (CEC02), pp. 711-716. IEEE Press. PS
  • Bianchi, L. and Knowles, J.D. (2002) Local search for the probabilistic traveling salesman problem: a proof of the incorrectness of Bertsimas' proposed 2-p-opt and 1-shift algorithms. TR/IRIDIA/2002-21 August. Submitted to European Journal of Operational Research
  • Knowles, J.D. and Corne, D.W. (2002) Properties of an Adaptive Archiving Algorithm for Storing Nondominated Vectors Technical Report TR/IRIDIA/2002-14, June.
  • Blum, C., Knowles, J., Paechter, B., Rossi-Doria, O., Sampels, M., Socha, K. (2002) A local search for the timetabling problem Technical Report TR/IRIDIA/2002-16. Presented at the 4th International Conference for the Practice and Theory of Automated Timetabling (PATAT '02). PDF
  • Rossi-Doria, O., Sampels, M., Birattari, M., Chiarandini, M., Dorigo, M., Gambardella, L. M., Knowles, J., Manfrin, M., Mastrolilli, M., Paechter, B., Paquete, L., Stützle, T. (2002) A comparison of the performance of different metaheuristics on the timetabling problem Technical Report TR/IRIDIA/2002-17. PDF Presented at the 4th International Conference for the Practice and Theory of Automated Timetabling (PATAT '02).

2001

  • Knowles, J.D. and Corne, D.W. (2001) Benchmark problem generators and results for the multiobjective degree-constrained minimum spanning tree problem. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001), pp. 424-431, Morgan Kaufmann Publishers. Download PS
  • Corne, D.W., Jerram, N.R., Knowles, J.D., and Oates, M.J. (2001) PESA-II: region-based selection in evolutionary multiobjective optimization. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2001), pp. 283-290, Morgan Kaufmann Publishers. Download PS
  • Knowles, J.D. and Corne, D.W. (2001) A comparison of encodings and algorithms for multiobjective spanning tree problems. In Proceedings of the 2001 Congress on Evolutionary Computation (CEC01), pp. 544-551, IEEE Press. Download PS
  • Knowles, J.D., Watson, R.A., Corne, D.W. (2001) Reducing local optima in single-objective problems by multi-objectivization. In Proceedings of the First International Conference on Evolutionary Multi-criterion Optimization (EMO'01), pp. 269-283, copyright Springer-Verlag. PDF(local) PDF(Springer)
  • Knowles, J.D., Corne, D.W. (2001) A comparative assessment of memetic, evolutionary, and constructive algorithms for the multiobjective d-MST problem. In Proceedings of the 2001 Genetic and Evolutionary Computation Conference Workshop Program. Presented at WOMA II. Download PS

2000

  • Knowles, J.D., Corne, D.W. (2000) Evolving neural networks for cancer radiotherapy. In The Practical Handbook of Genetic Algorithms: Applications, Second Edition, Lance D. Chambers (Ed.), Chapman and Hall/CRC, Boca Raton, Florida 33431, pp. 443 - 488. View it at Amazon now!
  • Knowles, J.D., Oates, M.J., Corne, D.W. (2000) Advanced multiobjective evolutionary algorithms applied to two problems in telecommunications. BT Technology Journal, 18(4), pp. 51-65. Draft. (Source code for the ADDMP evaluation function available here)
  • Knowles, J.D., Corne, D.W. (2000) Approximating the nondominated front using the Pareto archived evolution strategy. Evolutionary Computation, 8(2), pp. 149-172. Draft version. Final version obtainable from MIT press.
  • Knowles, J.D., Corne, D.W. (2000) A new evolutionary approach to the degree-constrained minimum spanning tree problem. IEEE Transactions on Evolutionary Computation, 4(2), pp. 125-134, July. Draft version
  • Knowles, J.D., Corne, D.W., Oates, M.J. (2000) On the assessment of multiobjective approaches to the adaptive distributed database management problem. In Proceedings of the Sixth International Conference on Parallel Problem Solving from Nature (PPSN VI), pp. 869-878, Springer, Berlin. Download PS. Source code for the ADDMP evaluation function available here
  • Corne, D.W., Knowles, J.D. (2000) The Pareto-envelope based selection algorithm for multiobjective optimization. In Proceedings of the Sixth International Conference on Parallel Problem Solving from Nature (PPSN VI), pp. 839-848, Springer, Berlin. Download PS
  • Knowles, J.D., Corne, D.W. (2000) M-PAES: a memetic algorithm for multiobjective optimization. In Proceedings of the Congress on Evolutionary Computation (CEC00), pages 325-332, IEEE Press, Piscataway, NJ. Download PS
  • Knowles, J. and Corne, D. (2000) Heuristics for evolutionary off-line routing in telecommunications networks. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2000), pages 574-581, Morgan Kaufmann. Download PS
  • Knowles, J.D., Corne, D.W. (2000) Multiobjective approaches to the adaptive distributed database management problem. The SAB/PPSN Workshops: Joint Workshops of SAB 2000 and PPSN 2000 September 16th, Paris. Evolutionary Computation in Telecommunications section. Download PS
  • Knowles, J.D., Corne, D.W. (2000) A comparison of diverse approaches to memetic multiobjective combinatorial optimization. In Proceedings of the 2000 Genetic and Evolutionary Computation Conference Workshop Program, pages 103-108. Download PS
  • Knowles, J.D., Corne, D.W. (2000) Benchmarking a new memetic algorithm for Pareto multiobjective optimization. Submitted to Knowledge and Information Systems (following nomination of CEC 2000 paper for submission to a `selected papers' conference edition of the journal) September 15, 2000. NB: No nominated papers were eventually reviewed or published. Download PS

1996-1999

  • Knowles, J.D., Corne, D.W., Oates, M.J. (1999) A new evolutionary approach to the degree constrained minimum spanning tree problem. In Proceedings of Genetic and Evolutionary Computation Conference (GECCO 99), page 794. Online version Download PS
  • Knowles, J.D., Corne, D.W. (1999) The Pareto archived evolution strategy : a new baseline algorithm for Pareto multiobjective optimisation. In Proceedings of the 1999 Congress on Evolutionary Computation (CEC'99), Volume 1, pages 98-105. Download PS
  • Knowles, J.D., Corne, D.W., Bishop, M. (1998) Evolutionary Training of Artificial Neural Networks for Radiotherapy Treatment of Cancers. In Proceedings of 1998 International Conference on Evolutionary Computation (ICEC'98), pages 398-403.
  • Knowles, J.D., Corne, D.W.(1999) Evolutionary approaches to off-line routing in backbone communications networks.Technical Report RUCS/1999/TR/007/A.
  • Knowles, J.D., Corne, D.W. (1999) Approximating the nondominated front using the Pareto archived evolution strategy. Technical Report RUCS/1999/TR/005/A, June 1999.
  • Knowles, J.D. (1998) PRISM : Identifying pages of interest on the Web. Copyright BT Labs, Martlesham Heath, October 1998.
  • Knowles, J.D. (1997) Fast Radiation Therapy Treatment Planning using Artificial Neural Networks. M.Sc. Dissertation. University of Reading, UK.
  • Knowles, J.D., Corne, D.W. (1999) Local search, multiobjective optimization and the Pareto archived evolution strategy. In Proceedings of the Third Australia-Japan Joint Workshop on Intelligent and Evolutionary Systems, ISBN 0 7317 0503 3, pages 209-216. Download PS
  • Knowles, J.D., Corne, D.W. (1999) Assessing the performance of the Pareto archived avolution strategy. In Proceedings of the 1999 Genetic and Evolutionary Computation Conference Workshop Program, pages 123-124.More info
  • Knowles, J.D. (1997) Fast Radiation Therapy Treatment Planning using Artificial Neural Networks. MSc Dissertation. Departments of Computer Science and Cybernetics, University of Reading, UK. September.

Joshua D. Knowles
Last modified: Jan 2011