Jiří Kléma - Curriculum Vitae

Born 1971, Czech nationality, married, 2 children

Current position:

associate professor in Artificial Intelligence at The Department of Computer Science, Czech Technical University in Prague (since 12/2013).

Before:

assistant professor at The Department of Cybernetics, Czech Technical University in Prague (since 4/2002), research fellow in The Gerstner Laboratory for Intelligent Decision Making and Control (since 12/1996).

Education:

Ph.D. in Artificial Intelligence and Biocybernetics at Czech Technical University (2002), thesis "Prototype Applications of Instance-Based Reasoning" (supervision: Prof. Olga Stepankova).

MSc. (Ing.) with honours in Computer Science at Czech Technical University (1994), diploma thesis on "Machine Learning as Diagnostic Tool" (supervision: Prof. Olga Stepankova).

Professional Interests:

Machine learning, data mining and decision support, bioinformatics.

Research Experience:

2017-20: AZV project "Long non-coding RNAs in pathogenesis of myelodysplastic syndromes".

2013-15: IGA MZ projects "XGENE.ORG - a public tool for integrated analysis of microarray, microRNA and methylation data" and "Prediction of the response to demethylation treatment in patients with myelodysplastic syndromes using integrative genomics".

2009-10: Research project "The Impact of Interaction between Genotype and Living Environment on Human Health", the Czech project with Department of Genetic Ecotoxicology, Institue of Experimental Medicine, Prague. The project aims to identify links between genetic polymorphisms and phenotype data.

2008-09: Research project "Heterogeneous Data Fusion for Genomic and Proteomic Knowledge Discovery", the Czech-French bilateral project, partners: GREYC laboratory, University of Caen, Center for Molecular and Cellular Genetics, the University Claude Bernard Lyon 1, France.

2005-06: Research project "Bases de donnees INductives et GenOmique (BINGO), the French national project on genomics and inductive databases, a one year post-doc position in Computer Science, Linguistic and Natural Language Processing aimed at utilization of textual resources in genomics, GREYC laboratory, Caen, France.

2004-05: Research project "MetaTool for Educational Tool Design (METOD)", the international project co-funded by EU in the frame of Leonardo da Vinci - Community Vocational Training Action Programme.

2000-03: Research project "Data Mining and Decision Support for Business Competitiveness: A European Virtual Enterprise" Co-funded project by EU, IST-1999-11.495, Sol-Eu-Net.

2000-03: Research project "Intelligent Medical Systems", partner University of Maribor, Faculty of Electrical Engineering and Computer Science, System Design Laboratory.

Practical Experience:

2007: Half a year research and development project "Fault Diagnostics and Prediction in Thermal Power Plant" with the industrial partner SKODA POWER, a.s., modeling and knowledge discovery to develop a robust fault diagnostic system of the steam turbine and its control system.

2004-05: Research and development project "Full rhythm classification" with the industrial partners CertiCon a.s. and VITATRON B.V., the project aimed to investigate and develop a sophisticated patient independent classifiers of the electrical activity of the heart.

2004: Half a year research and development project "Determination and Analysis of Critical Process Parameters" with the industrial partners Rockwell Automation and Abbott Laboratories, the data mining project aimed to identify critical process parameters resulting in optimization of production line manufacturing.

2000-01: 1.5 year research and development project "Intelligent pump diagnostics and control" with the industrial partner Grundfos A/S, the project focused on intelligent diagnostics of a specific application and the optimal pump control. One of the main aims in the project was to come up with new ideas, combine the ideas with the theoretical methods, and hand over the knowledge to the industrial partner.

1997-2004: Development project "Gas Consumption Prediction" with the industrial partner TDE GmbH, the project resulted in development of problem-oriented prediction systems SPS (Smart Prediction System) and OPS (Open Prediction System).

1998-00: Cooperative research with CZI MEDICON, Healthcare Informatics Center and Health Data Research, Inc. aimed at utilization of machine learning for preoperative prediction of patient's mortality after cardiology surgery.

1996-98: Research and development project "Fault Diagnostics of Intelligent Pump" with the industrial partner Rockwell Automation and University of Sussex aimed at non-invasive condition monitoring of induction motor driven pumps.

1996: Joint Allen-Bradley and Milwaukee School of Engineering, WI, project: Software Testing and Software Quality Management (WinRunner).

Academic Experience:

Lecturing in AI (responsibility for Statistical Data Analysis, Advanced Methods for Knowledge Representation, teaching in Foundations of Artificial Intelligence, Symbolic Machine Learning, Machine Learning and Data Mining), Biocybernetics and Bioinformatics (responsibility for Bioinformatics, Biological Data Processing, Biometry and Statistics), teaching in courses on Cybernetics and AI (Cybernetics and Artificial Intelligence Foundations), Programming Languages for AI (Prolog) and Expert Systems (Expert Systems' Foundations).

The course "Advances in Data Mining", University of Helsinki, May 2006, Socrates program, shared with Bruno Cremilleux.

Supervision of Filip Karel, the PhD thesis Quantitative Association Rule Mining defended in December 2009.

Supervision of Michael Andel, a PhD student in bioinfomatics.

Supervision of Vladimír Kunc, a PhD student in AI and bioinformatics.

Supervision of a number of master's and bachelor's theses.

Memberships, committees, reviews:

Board of the Open Informatics (since 2011), Presidium of The Czech Society for Cybernetics and Informatics (since 2007).

PC's of Bioinformatics (since 2012), ACM SAC DM (since 2006), IEEE SMC (2013), IDA (2009, 2010), IICAI (2009, 2011), IADIS e-Health (2009), HCI-KDD USAB (2011), IEEE CBMS (2007).

Reviewer for journals IEEE SMC C, IEEE SMC A, BMC Bioinfomatics, Control and Cybernetics, Knowledge and Information Systems, International Journal of Computer Mathematics, Advances in AI, Machine Learning, Journal of Biomedical Informatics, Methods.

Local chair of ILP 2008 (Inductive Logic Programming) and ECML PKDD 2013 (European Conf. on Machine Learning and Principles of Knowledge Discovery in Databases).

Selected Publications:

Klema, J., Malinka, F., Zelezny, F.: Semantic biclustering for finding local, interpretable and predictive expression patterns. BMC Genomics, Volume 18, 2017.

Andel, M., Klema, J., Krejcik, Z.: Network-Constrained Forest for Regularized Classification of Omics Data. Methods, Vol. 83, pp. 88–97, 15 July 2015.

Holec M., Klema J., Zelezny F., Tolar J.: Comparative Evaluation of Set-Level Techniques in Predictive Classification of Gene Expression Samples. BMC Bioinformatics, 13, Suppl. 10, S15, 2012.

Krejnik, M., Klema J.: Empirical Evidence of the Applicability of Functional Clustering through Gene Expression Classification. IEEE/ACM Transactions on Computational Biology and Bioinformatics,9:3, pp. 788-798, 2012.

Libalova, H., Uhlirova, K., Klema, J., Machala, M., Sram, R., Ciganek, M. and Topinka, J.: Global Gene Expression Changes in Human Embryonic Lung Fibroblasts Induced by Organic Extracts from Respirable Air Particles. Particle and Fibre Toxicology, 9:1, 2012.

Klema, J., Novakova, L., Karel, F., Stepankova, O., Zelezny, F.: Sequential Data Mining: A Comparative Case Study in Development of Atherosclerosis Risk Factors. IEEE Transactions on Systems, Man, and Cybernetics: Part C: Applications and Reviews, Vol. 38, no. 1, pp. 3--15, 2008.

Soulet, A., Klema J. and Cremilleux, B.: Efficient Mining Under Rich Constraints Derived from Various Datasets. In Dzeroski, S., Struyf, J. (eds.): Knowledge Discovery in Inductive Databases, Lecture Notes in Computer Science Volume 4747/2007, Springer Berlin / Heidelberg, pp. 223-239, 2007.

Klema, J., Soulet, A., Cremilleux, B., Blachon, S., Gandrilon, O.: Mining Plausible Patterns from Genomic Data. In Proceedings of Nineteenth IEEE International Symposium on Computer-Based Medical Systems. Los Alamitos: IEEE Computer Society Press, pp. 183-188, 2006.

Klema, J., Flek, O., Kout, J., Novakova, L.: Intelligent Diagnosis and Learning in Centrifugal Pumps. In Emerging Solutions for Future Manufacturing Systems. New York: Springer, pp. 513-522, 2004.

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