Jaume Bacardit

Jaume Bacardit

Jaume Bacardit
Automated Scheduling, Optimization and Planning (ASAP) research group Multi-disciplinary Centre for Integrative Biology (MyCIB)
School of Computer Science School of Biosciences
University of Nottingham
Jubilee Campus, Wollaton Road Sutton Bonington, LE12 5RD, UK
Nottingham, NG8 1BB, UK
 
Tel: +44 115 846 7044 Tel: +44 115 951 6276
Fax: +44 115 846 7877 Fax: +44 115 951 6292

jaume dot bacardit at nottingham dot ac dot uk
Lecturer in Bioinformatics
PhD (Universitat Ramon Llull, Barcelona, Catalonia, Spain)
Room
C40 in Computer Science, B21 (Main Building) in Biosciences
Research Interests
Bioinformatics, learning classifier systems, evolutionary computation, genetics-based machine learning, data mining
Curriculum Vitae
cvJaumeBacardit.pdf
Hits
hits since March 1, 2005
Last refreshed at 20:25, Saturday, March 20, 2010


Academic role

My position as Lecturer in Bioinformatics has been jointly appointed between the Schools of Computer Science and Biosciences of the University of Nottingham. My role is to facilitate and encourage interdisciplinary research involving both schools.

Teaching duties

My teaching duties for the academic year 2009/2010 are the following:

Administrative duties

  • Careers officer of the School of Computer Science (web)
  • Industrial Placement officer of the School of Computer Science (web)

Research

In a nutshell, my research is mainly focused on Machine Learning and Data Mining, and their application to bioinformatics and, in general, to any class of biological domains. From the Computer Science point of view I am particularly interested in methods for large-scale data mining as well as the interpretability capacity of machine learning methods.

My PhD thesis dealt with the Pittburgh model of Learning Classifier Systems (LCS). Specifically, the thesis had the following objectives:

  • Improving the generalization capacity of the model
  • Reducing the run-time of the system
  • Proposing rule-based representations for real-valued attributes
You can download my thesis here

From 2005 to 2007 I worked as RA applying LCSs to protein structure prediction, in a project called Robust Prediction with Explanatory Power for Protein Structure and Related Prediction Problems

Here is the list externally funded projects where I am PI/CI:

  1. Principled Application of Learning Classifier Systems to Large-Scale Challenging Datasets (LCSxLCD)
    • Funding body: EPSRC (link to project)
    • Amount Awarded: £101,458
    • Principal Investigator: J. Bacardit
    • Awarded: 2/9/2009
    • Start date: 1/1/2010
    • End date: 31/3/2011
  2. Development of novel tools for characterisation of unique cell phenotypes using data mining and statistical analysis
    • Funding body: Feasibilty award granted by the EPSRC's Bridging the Gaps project awarded to the University of Nottingham
    • Amount Awarded: £9,379
    • Principal Investigator: J. Bacardit
    • Co-Investigators: Dr. A. Mobasheri and Prof. A. Wood
    • Awarded: 1/5/2009
    • Start date: 1/9/2009
    • End date: 15/12/2009
  3. Bioinformatics, Systems and Synthetic Biology Plant Science Summer School (ESF-2482)
    • Funding Body: European Science Foundation
    • Amount Awarded: €60435
    • Principal Investigator: Dr. N.Krasnogor
    • Co-Investigators: Dr. J. Bacardit and Prof. M. Bennett
    • Awarded: 18-3-2009
    • Start Daiite: 18-3-2009
    • End Date: 31-9-2009

Research team:

Professional activities

Right now I am a co-organizer of the Plant Bioinformatics, Systems and Synthetic Biology Summer School that will take place in Nottingham from the 27th to the 31st of July, 2009.

I am also co-organising the 12th International Workshop on Learning Classifier Systems that will take place on during the Genetic And Evolutionary Computation Conference - GECCO2009.
I was elected by the LCS community to organize the IWLCS first from 2007 to 2008 and again from 2009 to 2010

Reviewer for the following journals
  • IEEE Transactions on Evolutionary Computetion
  • IEEE Transactions on Systems, Man and Cybernetics Part-B
  • Evolutionary Computation Journal
  • International Journal of AI Tools
  • Soft Computing Journal
  • Expert Systems, the Journal of Knowledge Engineering
  • Frontiers in Bioscience
  • Journal of Artificial Evolution and Applications
  • Computers in Biology and Medicine
  • Evolutionary Intelligence
  • Natural Computing
  • Pattern Recognition Letters

Member of the program commitee of following conferences
  • Genetic and Evolutionary Computation Conference (GECCO) (since 2005)
  • Spanish Conference on meta-heuristics and evolutionary and bio-inspired algorithms (since 2005)
  • International Workshop on Learning Classifier Systems (since 2005)
  • ASME 2005 International Design Engineering Technical Conference
  • International Joint Conference on Neural Networks (IJCNN) (since 2006)
  • International Conference on Evolutionary Computation (CEC) (2008)
  • 2nd International Confernence on Bio-Inspired Computing: Theory and Applications (BIC-TA 2007)
  • International Workshop on Nature Inspired Cooperative Strategies for Optimization, NICSO (since 2007)
  • IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (2006-2007)
  • 2nd IAPR Workshop on Pattern Recognition in Bioinformatics (PRIB 2007)
  • 8th International Conference on Hybrid Intelligent Systems (HIS 2008)
  • The 11th Ibero-American Conference on Artificial Intelligence (IBERAMIA 2008)
  • Fifth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics


Readings

Here you can find the BibTeX references I have collected over the years

Publications

2009
A Mixed Discrete-Continuous Attribute List Representation for Large Scale Classification Domains
Bacardit, J. and Krasnogor, N.
In Proceedings of the 11th Annual Conference on Genetic and Evolutionary Computation (GECCO2009), pp. 1155-1162, ACM Press, 2009
p1155-bacardit.pdf

Automated Alphabet Reduction for Protein Datasets
J. Bacardit, M. Stout, J.D. Hirst, A. Valencia, R.E. Smith and N. Krasnogor
BMC Bioinformatics 10:6, 2009
Access to the paper

Improving the scalability of rule-based evolutionary learning
J. Bacardit, E.K. Burke and N. Krasnogor
Memetic Computing journal 1(1):55-67, 2009
paperAttListKR.pdf

Performance and Efficiency of Memetic Pittsburgh Learning Classifier Systems
J. Bacardit and N. Krasnogor
Evolutionary Computation Journal, 17(3):(to appear), 2009
paperMPLCS.pdf

Prediction of Topological Contacts in Proteins Using Learning Classifier Systems
Stout, M., Bacardit, J., Hirst, J.D., Smith, R.E. and Krasnogor, N.
Soft Computing Journal, 13(3):245-258, 2009
Access to the paper

KEEL: A Software Tool to Assess Evolutionary Algorithms for Data Mining Problems
Alcalá-Fdez, J., Sánchez, L., García S., del Jesus, M.J., Ventura, S., Garrell, J.M., Otera, J., Romero, C., Bacardit, J., Rivas, V.M. and Fernández, J.C.
Soft Computing Journal, 13(3):307-318, 2009.
Access to the paper

2008
Learning Classifier Systems. 10th International Workshop, IWLCS 2006, Seattle, MA, USA, July 8, 2006, and 11th International Workshop, IWLCS 2007, London, UK, July 8, 2007, Revised Selected Papers
Bacardit, J.; Bernadó-Mansilla, E.; Butz, M.V.; Kovacs, T.; Llorà, X.; Takadama, K., Editors
Lecture Notes in Artificial Intelligence 4998, Springer, 2008
Link to the book

Learning Classifier Systems: Looking Back and Glimsing Ahead
J. Bacardit, E. Bernaó-Mansilla, and M.V. Butz
Learning Classifier Systems. 10th International Workshop, IWLCS 2006, Seattle, MA, USA, July 8, 2006, and 11th International Workshop, IWLCS 2007, London, UK, July 8, 2007, Revised Selected Paper, LNAI 4998, pp. 1-21, 2008, Springer
LCS-Looking-Glimsing.pdf

Empirical evaluation of ensemble techniques for a Pittsburgh Learning Classifier System
J. Bacardit and N. Krasnogor
Learning Classifier Systems. 10th International Workshop, IWLCS 2006, Seattle, MA, USA, July 8, 2006, and 11th International Workshop, IWLCS 2007, London, UK, July 8, 2007, Revised Selected Paper, LNAI 4998, pp. 255-268, 2008, Springer
EnsemblesLCSbook.pdf

Learning classifier systems for optimization problems: A case study on the fractal travelling salesman problem
M. Tabacman, N. Krasnogor, J. Bacardit and I. Loiseau
Eleventh International Workshop on Learning Classifier Systems, IWLCS2008
iwlcs2008.pdf

Fast Rule Representation for Continuous Attributes in Genetics-Based Machine Learning
Bacardit, J. and Krasnogor, N.
In Proceedings of the 10th Annual Conference on Genetic and Evolutionary Computation (GECCO2008), pp. 2039-2046, ACM Press, 2008
gecco2008.pdf

Prediction of Recursive Convex Hull Class Assignments for Protein Residues
Stout, M., Bacardit, J., Hirst, J.D. and Krasnogor, N.
Bioinformatics, 24(7):916-923, 2008
Access to paper

Data Mining in Proteomics with Learning Classifier Systems
J. Bacardit, M. Stout, J.D. Hirst and N. Krasnogor
Bull, L., Bernado Mansilla, E. and Holmes, J. (eds), Learning Classifier Systems in Data Mining, pages 17-46, Springer, 2008
DataMiningLCS.pdf

2007

Data Mining in Learning Classifier Systems: Comparing XCS with GAssist
Bacardit, J. and Butz, M.V.
Learning Classifier Systems, Revised Selected Papers of the International Workshop on Learning Classifier Systems 2003-2005, Lecture Notes in Computer Science 4399, pp. 282-290, 2007, Springer
bacardit07data.pdf

Improving the Performance of a Pittsburgh Learning Classifier System Using a Default Rule
Bacardit, J., Goldberg D.E. and Butz, M.V.
Learning Classifier Systems, Revised Selected Papers of the International Workshop on Learning Classifier Systems 2003-2005, Lecture Notes in Computer Science 4399, pp. 291-307, 2007, Springer
bacardit07improving.pdf

Bloat control and generalization pressure using the minimum description length principle for a Pittsburgh approach Learning Classifier System
Bacardit, J. and Garrell, J.M.
Learning Classifier Systems, Revised Selected Papers of the International Workshop on Learning Classifier Systems 2003-2005, Lecture Notes in Computer Science 4399, pp. 59-79, 2007, Springer
bacardit07bloat.pdf

Automated Alphabet Reduction Method with Evolutionary Algorithms for Protein Structure Prediction
J. Bacardit, M. Stout, J.D. Hirst, K. Sastry, X. Llorà and N. Krasnogor
In Proceedings of the 9th Annual Conference on Genetic and Evolutionary Computation (GECCO2007), pp. 346-353, ACM Press, 2007
gecco2007-ar.pdf
2006

Empirical evaluation of ensemble techniques for a Pittsburgh Learning Classifier System
J. Bacardit and N. Krasnogor
Ninth International Workshop on Learning Classifier Systems, IWLCS2006
iwlcs2006.pdf

Smart Crossover operator with multiple parents for a Pittsburgh Learning Classifier System
J. Bacardit and N. Krasnogor
Genetic and Evolutionary Computation Conference 2006, GECCO'06
In Proceedings of the 8th Annual Conference on Genetic and Evolutionary Computation (GECCO2006), pp. 1441 - 1448, ACM Press, 2006
gecco2006-sx.pdf

Coordination number prediction using Learning Classifier Systems: Performance and interpretability
J. Bacardit, M. Stout, J.D. Hirst, N. Krasnogor and J. Blazewicz
In Proceedings of the 8th Annual Conference on Genetic and Evolutionary Computation (GECCO2006), pp. 247-254, ACM Press, 2006
gecco2006-cn.pdf

From HP Lattice Models to Real Proteins: coordination number prediction using Learning Classifier Systems
M. Stout, J. Bacardit, J.D. Hirst, N. Krasnogor and J. Blazewicz
4th European Workshop on Evolutionary Computation and Machine Learning in Bioinformatics 2006
Lecture Notes in Computer Science vol. 3907, pp. 208-220, Springer, 2006
evobio2006.pdf

Prediction of Residue Exposure and Contact Number for Simplified HP Lattice Model Proteins Using Learning Classifier Systems
M. Stout, J. Bacardit, J.D. Hirst, J. Blazewicz and N. Krasnogor
In D. a. Ruan, P. D'hondt, P. F. Fantoni, M. D. Cock, M. Nachtegael and E. E. Kerre, eds., 7th International FLINS Conference on Applied Artificial Intelligence,, World Scientific, 2006, pp. 601-608. CIBB2006.pdf

2005

Analysis of the Initialization Stage of a Pittsburgh Approach Learning Classifier System
Jaume Bacardit
Genetic and Evolutionary Computation Conference 2005, GECCO'05
gecco2005.pdf

2004

Pittsburgh Genetics-Based Machine Learning in the Data Mining era: Representations, generalization, and run-time
Jaume Bacardit
Doctoral disertation, Ramon Llull University, Barcelona, Catalonia, Spain
thesis.pdf

Speeding-up Pittsburgh Learning Classifier Systems: Modeling Time and Accuracy
Jaume Bacardit, David E. Goldberg, Martin V. Butz, Xavier Llorà and Josep M. Garrell
8th International Conference on Parallel Problem Solving from Nature - PPSN VIII
ppsn04.pdf

Data Mining in Learning Classifier Systems: Comparing XCS with GAssist
Jaume Bacardit and Martin V. Butz
Seventh International Workshop on Learning Classifier Systems (IWLCS-2004)
iwlcs2004b.ps.gz

Improving the Performance of a Pittsburgh Learning Classifier System Using a Default Rule
Jaume Bacardit, David E. Goldberg and Martin V. Butz
Seventh International Workshop on Learning Classifier Systems (IWLCS-2004)
iwlcs2004.ps.gz

Analysis and improvements of the Adaptive Discretization Intervals knowledge representation
Jaume Bacardit and Josep M. Garrell
Genetic and Evolutionary Computation Conference 2004, GECCO'04
gecco2004.ps.gz

Experimental Evaluation of Discretization Schemes for Rule Induction
Jesus Aguilar--Ruiz, Jaume Bacardit and Federico Divina
Genetic and Evolutionary Computation Conference 2004, GECCO'04
gecco2004b.ps.gz

Combinando multiples discretizadores para aprendizaje de reglas evolutivo con enfoque de Pittsburgh
Jaume Bacardit, Josep M. Garrell and Pere Miralles
Proceedings of the "Tercer Congreso Español de Metaheurísticas, Algoritmos Evolutivos y Bioinspirados", pages 192-202
maeb04.ps.gz

2003

Development of a Genetic Algorithm to Design and Identify Peptides that can Cross the Blood-Brain Barrier: Design and validation in silico
Teixidó, M., Belda, I., Rosell&ocaute;, X., Gonzàlez, S., Fabre, M., Llorà, X., Bacardit, J., Garrell, J.M., Vilaró, S., Albericio, F., and Giralt, E.
Journal of QSAR and Combinatorial Science. Vol. 22, No. 7, pp. 745--753, Wiley-VCH.

Comparison of training set reduction techniques for Pittsburgh approach Genetic Classifier Systems
Jaume Bacardit and Josep M. Garrell
X Conferencia de la Asociación Española para la Inteligencia Artificial (CAEPIA2003)
caepia2003.ps.gz

Bloat control and generalization pressure using the minimum description length principle for a Pittsburgh approach Learning Classifier System
Jaume Bacardit and Josep M. Garrell
Sixth International Workshop on Learning Classifier Systems (IWLCS-2003)
Chicago, July 2003
iwlcs03.ps.gz

Evolving multiple discretizations with adaptive intervals for a Pittsburgh Rule-Based Learning Classifier System
Jaume Bacardit and Josep M. Garrell
Genetic and Evolutionary Computation Conference 2003, GECCO'03
Lecture Notes in Computer Science 2724, pages 1818--1831, Springer-Verlag
gecco03.ps.gz

Incremental Learning for Pittsburgh Approach Classifier Systems
Jaume Bacardit and Josep M. Garrell
Proceedings of the "Segundo Congreso Español de Metaheurísticas, Algoritmos Evolutivos y Bioinspirados", pages 303-311
maeb03.ps.gz


2002

Evolution of Multi-Adaptive Discretization Intervals for a Rule-Based Genetic Learning System
Jaume Bacardit and Josep M. Garrell
Proceedings of the 7th Iberoamerican Conference on Artificial Intelligence (IBERAMIA2002)
LNAI vol. 2527, pages 350-360, Springer
iberamia02.ps.gz

The role of interval initialization in a GBML system with rule representation and adaptive discrete intervals
Jaume Bacardit and Josep M. Garrell
Proceedings of the 5th Catalan Conference on Artificial Intelligence (CCIA'2002)
LNAI vol. 2504, pages 184-195, Springer
ccia2002.ps.gz

Evolution of Adaptive Discretization Intervals for a Rule-Based Genetic Learning System
Jaume Bacardit and Josep M. Garrell
Proceedings of the 4th Genetic and Evolutionary Computation converence (GECCO-2002) page 677 (poster page)
gecco2002_abstract_page.ps.gz

Métodos de generalización para sistemas clasificadores de Pittsburgh
Jaume Bacardit and Josep M. Garrell
Proceedings of the "Primer Congreso Español de Algoritmos Evolutivos y Bioinspirados (AEB'02)", pages 486-493
aeb02_bacardit+garrell.ps.gz(spanish)


Pictures

Here you can find pictures of some place I have been over the years

Last updated Monday January 25, 2010.