Bioinformatics and Mathematical Modelling

Head of Department

Corr. Memb. Prof. Krassimir Atanassov, DSc. DSc.

  • E-mail: kratbas.bg
  • Phone: (359 2) 9793602
  • Fax: (359 2) 8723787
  • Address: “Acad. G. Bonchev” Str., Block 105, Room 205
    Sofia 1113, Bulgaria

Staff

Main research topics

  • Development of the theory of Generalized Nets and the theory of Intuitionistic Fuzzy Sets, and their application in medicine and biology.
  • Implementation of contemporary information technologies and development of intelligent systems supporting the diagnostic and therapeutic processes of healthcare.
  • Modelling of pathological processes, patients databases, knowledge formalization for diagnostic and therapeutic decision making.
  • Development of systems for health screening and monitoring.
  • Application of methods for contemporary system analysis, engineering, mathematical and computer-based methods and tools for modelling, optimization and management of pharmacy-related, food-related and other industrial systems.

Research projects

Current projects

  1. Intercriteria Analysis – A New Approach to Decision Making
    Bulgarian National Science Fund, № DFNI-I-02/5, 2014–
  2. Generalized net modelling of processes from the field of artificial intelligence
    Budgetary subsidy, 2014-2016
    Coordinator for IBPhBME: Assoc. Prof. Olympia Roeva
  3. Intuitionistic fuzzy sets and logics
    Budgetary subsidy, 2014-2016
    Coordinator for IBPhBME: Sen. Assist. Prof. Peter Vassilev
  4. Index matrices: theory and applications
    Budgetary subsidy, 2014
    Coordinator for IBPhBME: Corr. Memb. Prof. Krassimir Atanassov
  5. Intuitionistic fuzzy sets, intuitionistic fuzzy optimization – theory and applications in medicine, ecology and other areas
    Bilateral cooperation – Poland. Institute of System Research, PAS, 2012-2014
    Coordinator for IBPhBME: Corr. Memb. Prof. Krassimir Atanassov
  6. Intuitionistic fuzzy sets – theory and applications
    Bilateral cooperation – Slovakia. Institute of Mathematics, 2012-2014.
  7. Simulating the behaviour of forest and field fires
    Bulgarian National Science Fund, № DFNI-I-01/0006, 2012–2014
    Coordinator for IBPhBME: Corr. Memb. Prof. Krassimir Atanassov
  8. Management and modelling of biomedical processes and information with the application of generalized nets and linked data
    Bulgarian National Science Fund, № DMU-03-38, 2011–2014
    Coordinator: Dr. Pavel Tcheshmedjiev
  9. Design and development of intuitionistic fuzzy logic tools in information technologies (webpage)
    Bulgarian National Science Fund, № BIn-02-09, 2009–2014
    Coordinator: Corr. Memb. Prof. Krassimir Atanassov

Past projects

  1. Generalized net modelling of processes, related the scene analysis, machine learning, data-mining environments, genetic algorithms and neural networks
    Budgetary subsidy, 2011-2013.
  2. Intuitionistic fuzzy sets and logics
    Budgetary subsidy, 2011-2013
    Coordinator: Corr. Member Prof. Krassimir Atanassov
  3. High quality control of biotechnological processes with application of modified conventional and metaheuristic methods
    Bulgarian Science Fund, № ДМУ 02/4, 2009–2013
    Coordinator: Assoc. Prof. Olympia Roeva
  4. Generalized net models and intuitionistic fuzzy sets in intelligent systems
    Royal Society International Joint Project, № JP100372, 2010–2012.
  5. System for computer aid of the decisions for weaning critically ill ventilator dependent from mechanical ventilation
    Bulgarian National Science Fund, № DTK-02-48, 2009–2013
  6. Models for ageing and technological solutions for improving and enhancing the quality of life (MATSIQEL)
    Marie Curie International Research Staff Exchange Scheme, № GA–2009–247541
    Coordinator: Corr. Memb. Prof. Krassimir Atanassov
  7. High quality control of biotechnological processes with application of modified conventional and metaheuristics methods
    Bulgarian National Science Fund, № DMU 02/4, 2009–2013
    Coordinator: Assoc. Prof. Olympia Roeva
  8. Modelling of processes with fixed development rules (webpage)
    Bulgarian National Science Fund, № DID-02-29, 2009–2013
    Coordinator: Corr. Memb. Prof. Krassimir Atanassov
  9. Generalised net models and intuitionistic fuzzy sets in intelligent systems
    Royal Society International Joint Project, № JP100372, 2010–2012
    Coordinator: Prof. Krassimir Atanassov
  10. Knowledge representation with intuitionistic fuzzy logic for the purpose of medical diagnosis
    Bulgarian National Science Fund, № И – 1303/2003, 2003-2007.
  11. The Implementation of Research Potential of the Latvian State Institute of Wood Chemistry in the European Research Area (WOOD-NET): TP 10: Development of process control systems: functional state mathematical modeling, programming and optimization of bioreactor’s design both for solid state (including composting) and submerged fermentations
    FP7, №203459, FP7 call: FP7-REGPOT-2007-1, 01.06.2008– 31.05.2011
  12. Integration of the Latvian State Institute of Wood Chemistry in the European
    Research Area (WOOD-PRO), EU № QLK5-CT-2002-30360,
  13. Implementation of intelligent technologies for control of biotechnical processes based on flow injection measurements
    DFG, № 113/109, 2000 – 2001
  14. Functional state modelling of biotechnological processes and their high quality control in the class of variable structure systems
    DFG № 113/135, 2003 – 2005
  15. Modelling and Optimization of Stirred Tank Bioreactors
    Bulgarian National Science Fund, № TS-1314, 2003-2007.
  16. Development and testing of models for analysis, assessment and prognosis of the river systems pollution. Application to the basin of River Struma
    Bulgarian National Science Fund, Earth Sciences-Young Scientists № 1501, 2005 – 2008
  17. Modelling and establishment of a management system for a new kind of poultry form
    Bulgarian National Science Fund, SS-71, 1997-2000.
  18. Modelling and variable-structured management of a fermentation process
    Thracian University – Stara Zagora, №03-1046/2003, 2003
  19. Development of the theory and practical application of variable structure systems for management of fermentation processes
    Bulgarian National Science Fund, №ТН-647, 1996-1999.
  20. Modelling and optimization of biotechnological enterprise in the food industry
    Bulgarian National Science Fund, № СС-338, 1993-1996.
  21. Management of biotechnological and ecological systems
    Bulgarian National Science Fund, № 7903, 1990-1994.
  22. Model of integrated management for water quality and preservation of ecosystems
    МОНТ, №5049, 5th FP of EC “Environment and Sustainable Development” Programme, 1998-2000.
  23. Development of a conceptual model for integrated water quality management. Application to the basin of River Struma
    МОСВ, №5407, 2006-2007
  24. Modelling of the functional states of fermentation processes, aiming at their high quality management
    Bulgarian National Science Fund, № МИ-1505, 2005-2009.

International collaboration

  • Systems Research Institute, Polish Academy of Sciences, Warsaw, Poland
  • University of Westminster, London, UK
  • Northumbria University, Newcastle, UK
  • Durham University, UK
  • Matej Bel University, Banska Bystricá, Slovakia
  • Optimization of Bioprocess Systems and Institute оf Technical Chemistry – University Hannover, Germany
  • Institute of Microbiology and Biotechnology, University of Latvia, Latvia
  • Australian Institute of High Energetic Materials

Awards

  • 2014 – Olympia Roeva – Diploma for excellent scientific achievements in Engineering Sciences, Union of Scientists in Bulgaria
  • 2013 – Stefan Hadjitodorov – Award “Marin Drinov” Honorary Decoration with Ribbon of the Bulgarian Academy of Sciences
  • 2013 – Peter Vassilev – Award “Marin Drinov” of the Bulgarian Academy of Sciences
  • 2013 – Krassimir Atanassov – Fellow of International Fuzzy Systems Association
  • 2012 – Krassimir Atanassov – Prize “Pythagoras” of the Ministry of Science and Education for excellence in the field of Technical Sciences
  • 2011 – Vassia Atanassova – Award “Ivan Evstratiev Geshov” of the Bulgarian Academy of Sciences
  • 2010 – Vassia Atanassova – Second award on the 8th Youth session of the Federation of Scientific-Technical Unions
  • 2008 – Olympia Roeva – Diploma for excellent scientific achievements for young researchers, Union of Scientists in Bulgaria
  • 2008 – Olympia Roeva – Award on the 6th Youth session of the Federation of Scientific-Technical Unions
  • 2007 – Olympia Roeva – Award on the 5th Youth session of the Federation of Scientific-Technical Unions
  • 2004 – Krassimir Atanassov – Honorary Fellow of the KvB Institute of Technology, Sydney
  • 2001 – Stefan Hadjitodorov – 2nd Award of the National Science Fund for Achievements in the development of the research project “Contemporary methods for objective analysis of voice signals and screening of laryngeal diseases”, 8th concourse session 1998-2001
  • 1999 – Olympia Roeva – Award on the Youth session of the Federation of Scientific-Technical Unions
  • 1998 – Mitko Petrov and Tatiana Ilkova – 2nd Award on the Youth session of the Federation of Scientific-Technical Unions
  • 1997 – Mitko Petrov and Tatiana Ilkova – 2nd Award on the Youth session of the Federation of Scientific-Technical Unions
  • 1995 – Krassimir Atanassov – Honorary Fellow of the University of Technology, Sydney

Lecture courses

  • Generalized Nets – Burgas Free University, since 2006
  • Generalized Nets – Faculty of Mathematics and Informatics, Sofia University, 1988-1993, 2004-2009
  • Generalized Nets – Technical University of Sofia, since 1998
  • Generalized Nets – University “Prof. A. Zlatarov” of Burgas, since 2007
  • Fuzzy Sets – University “Prof. A. Zlatarov” of Burgas, 2011/2012
  • Intuitionistic Fuzzy Sets – Faculty of Mathematics and Informatics, Sofia University, 2004-2009
  • Intuitionistic Fuzzy Sets – New Bulgarian University, 2007-2009
  • Mathematics – University “Prof. A. Zlatarov” of Burgas, 1998-2006

Selected publications

Monographs

  1. Atanassov, K. Generalized Nets. World Scientific, Singapore, 1991.
  2. Atanassov, K. Intuitionistic Fuzzy Sets. Springer, Heidelberg, 1999.
  3. Atanassov, K. On Generalized Nets Theory. Prof. M. Drinov Academic Publ. House, Sofia, 2007.
  4. Atanassov, K., G. Gluhchev, S. Hadjitodorov, A. Shannon, V. Vassilev, Generalized Nets and Pattern Recognition. KvB Visual Concepts Pty Ltd, Monograph No. 6, Sydney, 2003.
  5. Atanassov, K., G. Gluhchev, S. Hadjitodorov, J. Kacprzyk, A. Shannon, E. Szmidt, V. Vassilev. Generalized Nets Decision Making and Pattern Recognition. Warsaw School of Information Technology, Warszawa, 2006.
  6. Илкова Т., Приложение на динамичното и невро-динамичното програмиране за оптимално управление на ферментационни процеси, Авангард Прима, София, 2008, ISBN 978-954-323-420-2
  7. Pencheva T., O. Roeva, I. Hristozov, Functional State Approach to Fermentation Processes Modelling, Tzonkov S., Hitzmann B. (Eds.), Prof. Marin Drinov Academic Publishing House, Sofia, 2006, ISBN-10: 954-322-170-7, ISBN-13: 978-954-322-170-7.
  8. Shannon A., O. Roeva, T. Pencheva, K. Atanassov, Generalized Nets Modelling of Biotechnological Processes, “Marin Drinov” Publishing House of Bulgarian Academy of Sciences, Sofia, 2004, ISBN 954-322-039-5.
  9. Viesturs, U., I. Simeonov, T. Pencheva, J. Vanags, M. Petrov, Y. Pavlov, O. Roeva, T. Ilkova, M. Vishkins, I. Hristozov. Contemporary Approaches to Modelling, Optimisation and Control of Biotechnological Processes. Prof. M. Drinov Academic Publ. House, Sofia, 2010, p. 242, figs. 68, ISBN 978-954-322-384-8.

Papers

  1. Petrov M., T. Ilkova, A Combined Algorithm for Multi-objective Fuzzy Optimization of Whey Fermentation, Chem. Biochem. Eng. Q., 2009, 23(2), 152-160.
  2. Petrov M., T. Ilkova, Fuzzy Optimization of Biosynthesis of L-lysine, Chem. Biochem. Eng. Q., 2005, 19(3), 283-289.
  3. Petrov M., Investigation of Power Characteristics of Small Scale Stirred Tank Bioreactor, Biotechnol. & Biotechnol. EQ., 2005, 19(1), 205-209.
  4. Ilkova T., M. Petrov, St. Tzonkov, An Approach for Optimal Control of Fed-Batch Fermentation Process with Multi Control Variables, Biotechnol. & Biotechnol. EQ., 2004, 18(2), 201-205.
  5. Petrov M., T. Ilkova, Modeling and Fuzzy Optimization of Fed-Batch Fermentation Process, Chem. Biochem. Eng. Q., 2002, 16(4), 173-178.
  6. Petrov M., St. Tzonkov, Modelling of Mass Transfer and Optimization of Stirred Bioreactors, Bioprocess Engineering, 1999, 21(1), 61-63.
  7. Petrov M., Fuzzy Optimization of Mass Transfer in Stirred Tank Bioreactors, Biotechnology & Biotechnological Equipment, 1998, 12(1), 120-124.
  8. Roeva O., Ts. Slavov, Fed-batch Cultivation Control based on Genetic Algorithm PID Controller Tuning, Lecture Notes on Computer Science, Springer-Verlag Berlin Heidelberg, 6046, 2011, 289-296.
  9. Roeva O., Feed Rate Profiles Synthesis using Genetic Algorithms, Lecture Notes in Artificial Intelligence, Springer-Verlag Berlin Heidelberg, 6304, 2010, 281-282. ISSN: 0302-9743.
  10. Roeva O., Parameter Estimation of a Monod-type Model based on Genetic Algorithms and Sensitivity Analysis, Lecture Notes on Computer Science, Springer-Verlag Berlin Heidelberg, 4818, 2008, 601-608.
  11. Roeva O., Multipopulation genetic algorithm: A tool for parameter optimization of cultivation processes models, Lecture Notes on Computer Science, Springer-Verlag Berlin Heidelberg, 4310, 2007, 255-262.
  12. Roeva O., A Modified Genetic Algorithm for a Parameter Identification of Fermentation Processes, Biotechnology and Biotechnological Equipment, 20(1), 2006, 202-209.
  13. Roeva O., T. Pencheva, Y. Georgieva, B. Hitzmann, S. Tzonkov, Implementation of Functional State Approach for Modelling of Escherichia coli Fed-Batch Cultivation, Biotechnology and Biotechnological Equipment, 2004, 18(3), 207-214.
  14. Kissiov, V.T., S. T. Hadjitodorov. A Fuzzy  Version  of  K-NN  Method. Fuzzy Sets and Systems, vol.49, 1992, pp. 323-329.
  15. Hadjitodorov S., Boyanov B., T. Ivanov, N. Dalakchieva. Text – Independent Speaker Identification Using Neural Nets and AR-Vector Models. Electronics letters, IEE Publ., UK, vol.30, No 11, 1994, pp.838-840.
  16. Boyanov B., S. Hadjitodorov. Acoustic analysis of pathological voices. IEEE Engineering in Medicine and Biology Magazine, vol.16, No 4, 1997, pp.74-82.
  17. Hadjitodorov,S., B.Boyanov, B.Teston. Laryngeal pathology detection by means of class-specific neural maps. IEEE Trans.on Information Technology in Biomedicine, vol. 4, No 1,  2000, pp. 68-73.
  18. Hadjitodorov, S.T.An intuitionistic fuzzy version of the nearest prototype classification method based on a moving-of-pattern procedure”, International Journal of General Systems: Special issue of “Trends in Fuzzy Systems”, vol.30 (2), 2001, pp.155-165.
  19. Hadjitodorov S. ,  L. I. Kuncheva , L. P. Todorova.  Moderate Diversity for Better Cluster Ensembles. Information Fusion J. , Vol 7/3, 2006, pp. 264-275.
  20. Hadjitodorov, S., L. Todorova. Consultation System for Determining The Patients’ Readiness for Weaning from Long-Term Mechanical Ventilation,  Computer Methods and Programs in Biomedicine,  Vol. 100(1), Oct. 2010, pp.59-68.
  21. Atanassov K., Intuitionistic  fuzzy  sets,  Fuzzy sets and Systems, Vol. 20, 1986, No. 1, 87-96.
  22. Atanassov K., Gargov G., Interval valued intuitionistic fuzzy sets, Fuzzy Sets and Systems, Vol. 31, 1989, No. 3, 343-349.
  23. Atanassov K., More on intuitionistic fuzzy sets, Fuzzy Sets and Systems, Vol. 33, 1989, No. 1, 37-45.
  24. Atanassov K., New operations, defined over the intuitionistic fuzzy sets. Fuzzy Sets and Systems, Vol. 61, 1994, No. 2, 137-142.
  25. Atanassov, K., G. Pasi and R. Yager. Intuitionistic fuzzy interpretations of multi-criteria multi-person and multi-measurement tool decision making. International Journal of Systems Science, Vol. 36, 2005, No. 14, 859-868.
  26. Todorova, L., A. Temelkov, MD. Weaning from long-term mechanical ventilation: a nonpulmonary weaning index. Journal of Clinical Monitoring and Computing, 2004; 18: 275 – 281.

History

The Department of Bioinformatics and Mathematical Modelling in the present Institute of Biophysics and Biomedical Engineering is a union of two departments from the former Centre of Biomedical Engineering:

  • Biomedical Informatics, head Prof. Krassimir Atanassov
  • Modelling and Optimization of Bioprocess Systems, head Prof. Stoyan Tzonkov

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