Dr. Jiri Ocenasek

	Optimization software development and consulting Jiriho z Podebrad 6 78701 Sumperk Czech Republic  Email:     jiri{at}ocenasek{dot}com

Research   -   CV   -   Publications   -   Former ETH projects   -   Download

Research and consulting fields

• Evolutionary Computation
• Probabilistic models
• Data mining
• Bayesian reasoning
• Artificial intelligence
• Neural networks
• Data classifiers & Pattern recognition
• Embedded systems

Curriculum Vitae

• Born: 1976 in Sumperk, Czech Republic
• MSc. in Computer Science, Brno University of Technology, Czech Republic, 1994-1999
• Ph.D. in Information Technology, Faculty of Electrical engineering and Computer Science and Faculty of Information Technology, Brno University of Technology, 1999–2002
• Postdoctoral researcher, CoLab, ETH Zürich, 2003-2004
• Senior software developer, Kimotion Technologies, 2005-2007
• Senior software developer, Magwel NV, since 2008

Publications

• Ocenasek, J., Cantú-Paz, E., Pelikan, M., Schwarz, J.: Design of Parallel Estimation of Distribution Algorithms. In: Pelikan et al. (Eds.): Scalable Optimization via Probabilistic Modeling: From Algorithms to Applications. Series: Studies in Computational Intelligence. Vol. 33, Springer, 2006, Chapter 8, ISBN 978-3-540-34953-2.
• Ocenasek, J.: Entropy-based Convergence Measurement in Discrete Estimation of Distribution Algorithms. In: Lozano et al. (Eds.): Towards a New Evolutionary Computation. Advances in Estimation of Distribution Algorithms. Series: Studies in Fuziness and Soft Computing, Vol. 192, Springer Verlag, 2006, pp. 39 - 50, ISBN 978-3-540-29006-3.
• Kobliha, M., Schwarz, J., Ocenasek, J.: Bayesian Optimization Algorithms for Dynamic Problems, In: Applications of Evolutionary Computing, Budapest, HU, Springer, 2006, pp. 800-804, ISBN 3-540-33237-5, ISSN 0302-9743
• Potthast, F., Ocenasek, J., Rutishauser, D., Pelikan, M., Schlapbach, R.: Database Independent Detection of Isotopically Labeled MS/MS Spectrum Peptide Pairs. Journal of Chromatography B, Volume 817, Issue 2, pp. 225 - 230, March 2005, ISSN 1570-0232. See abstract.
• Kobliha, M., Schwarz, J., Ocenasek, J.: Bayesian Optimization Algorithm in Dynamic Environment, In: Mendel 2005 11th Internacional Conference on Soft Computing, Brno, CZ, FSI VUT, 2005, pp. 15-20, ISBN 80-214-2961-5
• Schwarz, J., Ocenasek, J., Jaros, J.: Advanced Bayesian Optimization Algorithms Applied in Decomposition Problems, In: Proceedings of ECBS 2004, Los Alamitos, CA, US, IEEE CS, 2004, pp. 102-111, ISBN 0-7695-2125-8
• Ocenasek, J., Kern, S., Hansen, N., Müller, S., Koumoutsakos, P.: A Mixed Bayesian Optimization Algorithm with Variance Adaptation. Lecture Notes in Computer Science, 3242, Springer, 2004, pp.352 - 361. ISBN: 3-540-23092-0
  © Springer-Verlag. For LNCS series click here.
• Ocenasek, J., Pelikan, M.: Parallel Mixed Bayesian Optimization Algorithm: A Scaleup Analysis. In: GECCO-2004 workshop proceedings, 2004. Preprint arXiv:cs.NE/0406007
• Kern, S., Hansen, N., Müller, S., Büche, D., Ocenasek, J., Koumoutsakos, P.: Distributions in Continuous Evolutionary Algorithms – Review and Comparison. Natural Computing, Volume 3, Issue 1, 2004, pp. 77 - 112.
• Pelikan, M., Goldberg, D.E., Ocenasek, J., Trebst, S.: Robust and Scalable Black-Box Optimization, Hierarchy, and Ising Spin Glasses . IlliGAL report #2003019, 2003.
• Ocenasek, J., Schwarz, J., Pelikan, M.: Design of Multithreaded Estimation of Distribution Algorithms. In: Cantú-Paz et al. (Eds.): Genetic and Evolutionary Computation Conference - GECCO 2003. Springer Verlag: Berlin, 2003, pp. 1247-1258, ISBN 3-540-40603-4, ISSN 0303-9743.
  © Springer-Verlag. For complete proceedings click here.
• Ocenasek, J., Pelikan, M.: Parallel spin glass solving in hierarchical Bayesian optimization algorithm. In: Proceedings of the 9th International Conference on Soft Computing, Mendel 2003, Brno University of Technology, Brno, Czech Rep., 2003, pp. 120-125, ISBN 80-214-2411-7.
• Schwarz, J., Ocenasek, J.: Accelerated Bayesian Optimization Algorithms for advanced hypergraph partitioning. In: Proceedings of the 9th International Conference on Soft Computing, Mendel 2003, Brno University of Technology, Brno, Czech Rep., 2003, pp. 133-141, ISBN 80-214-2411-7.
• Ocenasek, J.: Parallel Estimation of Distribution Algorithms. Vutium, Brno, Czech Rep., 2003, ISBN 80-214-2329-3, ISSN 1213-4198.
• Ocenasek, J.: Parallel Estimation of Distribution Algorithms. PhD. Thesis, Faculty of Information Technology, Brno University of Technology, Brno, Czech Rep., 2002, pp. 1-154.
• Ocenasek, J., Schwarz, J.: Development system DEBOA for rapid prototyping of evolutionary applications. In: Proceedings of the 36th International Conference MOSIS'02, MARQ, Ostrava, Czech Rep., 2002, pp. 169-176, ISBN 80-85988-71-2.
• Ocenasek, J., Schwarz, J.: Estimation of Distribution Algorithm for mixed continuous-discrete optimization problems. In: 2nd Euro-International Symposium on Computational Intelligence, IOS Press, Kosice, Slovakia, 2002, pp. 227-232, ISBN 1-58603-256-9, ISSN 0922-6389.
• Laumanns, M., Ocenasek, J.: Bayesian Optimization Algorithms for Multi-Objective Optimization. In: Parallel Problem Solving From Nature - PPSN VII, Lecture Notes in Computer Science, Springer-Verlang, Granada, Spain, 2002, pp. 298-307, ISBN 3-540-444139-5, ISSN 0302-9743.
• Schwarz, J., Ocenasek, J.: Bayes-Dirichlet BDD as a probabilistic model for logic function and evolutionary circuit decomposer.. In: Proceedings of the 8th International Mendel Conference on Soft Computing, Mendel 2002, Brno University of Technology, Brno, Czech Rep., 2002, pp. 117-124, ISBN 80-214-2135-5.
• Schwarz, J., Ocenasek, J.: Ratio cut hypergraph partitioning using BDD based mBOA optimization algorithm. In: 5th IEEE Design and Diagnostics of Electronic Circuits and Systems Workshop 2002, Brno, Czech Rep., 2002, pp. 87-96, ISBN 80-214-2094-4.
• Ocenasek, J., Schwarz, J.: The Distributed Bayesian Optimization Algorithm for combinatorial optimization. In: EUROGEN 2001 - Evolutionary Methods for Design, Optimisation and Control, CIMNE, Athens, Greece, 2001, pp. 115-120, ISBN 84-89925-97-6.
• Schwarz, J., Ocenasek, J.: Evolutionary Multiobjective Bayesian Optimization Algorithm: Experimental Study. In: 35th Spring International Conference: Modelling and Simulation of Systems (MOSIS'01), MARQ, Hradec nad Moravici, Czech Rep., 2001, pp. 101-108, ISBN 80-85988-57-7.
• Schwarz, J., Ocenasek, J.: Multiobjective Bayesian Optimization Algorithm for Combinatorial Problems: Theory and Practice. In: NEURAL NETWORK WORLD, Vol. 11, No. 5, Czech Republic, pp. 423-441, ISSN 1210-0552.
• Schwarz, J., Ocenasek, J.: Pareto Bayesian Optimization Algorithm for the Multiobjective 0/1 Knapsack Problem. In: Proceedings of the 7th International Mendel Conference on Soft Computing, Mendel 2001, Brno University of Technology, Brno, Czech Rep., 2001, pp. 131-136, ISBN 80-214-1894-X.
• Ocenasek, J., Schwarz, J.: The Parallel Bayesian Optimization Algorithm. In: Proceedings of the European Symposium on Computational Inteligence, Physica-Verlag, Kosice, Slovak Rep., 2000, pp. 61-67, ISBN 3-7908-1322-2, ISSN 1615-3871.
• Schwarz, J., Ocenasek, J.: A problem knowledge-based evolutionary algorithm KBOA for hypergraph bisectioning. In: Proceedings of the Fourth Joint Conference on Knowledge-Based Software Engineering, IOS Press, Brno, Czech Rep., 2000, pp. 51-58, ISBN 1-58603-060-4.
• Schwarz, J., Ocenasek, J.: Partitioning-oriented placement using advanced genetic algorithm BOA. In: Proceedings of the 6th International Conference on Soft Computing, Mendel 2000, Brno University of Technology, Brno, Czech Rep., 2000, pp. 145-150, ISBN 80-214-1609-2.
• Ocenasek, J.: The Acceleration of Estimation of Distribution Algorithms, In: Sbornik praci studentu a doktorandu VI., CERM, Brno, Czech Rep., 2000, pp. 213-215, ISBN 80-7204-155-X.
• Schwarz, J., Ocenasek, J.: Experimental study: Hypergraph partitioning based on the simple and advanced genetic algorithms BMDA and BOA. In: Proceedings of the Mendel '99 conference, Brno University of Technology, Brno, Czech Rep., 1999, pp. 124-130, ISBN 80-214-1131-7.
• Ocenasek, J.: Implementation of advanced genetic algorithm, MSc. thesis, Department of Computer Science, FEI VUT Brno, Czech Rep., 1999, in czech (dean price award).
• Ocenasek, J.: Advanced genetic algorithms for hypergraph partitioning. In: Sbornik praci studentu a doktorandu V., CERM, Brno, Czech Rep., 1999, pp. 89-90, ISBN 80-214-1155-4, in czech.
• Ocenasek, J.: Genetic algorithm for task scheduling, In: Sbornik praci studentu a doktorandu IV., CERM, Brno, Czech Rep., 1998, pp. 53-54, ISBN 80-214-1141-4, in czech.

Former ETH projects

• Drug design: Development of an efficient optimizer for flexible ligand docking (extension of FFLD code; with Department of Biochemistry, University of Zurich).
• Proteomics: Automatic detection of isotopically labeled MS/MS pairs (development of ICATcher software; with Functional Genomics Center Zurich).
• Computational physics: Finding spin glass ground states (massively parallel MBOA running on Asgard Beowulf cluster). See the project description here.

Download of discontinued academic code

• Adaptive Mixed Bayesian Optimization Algorithm (AMBOA) (with variance adaptation in continuous domain).

• Mixed Bayesian Optimization Algorithm (MBOA). Contains both MBOA versions - sequential and distributed (MPI).
• TRANSIM source for simulating Multithreaded Mixed Bayesian Optimization Algorithm (MMBOA) - see GECCO'03 paper.