IEEE CIS Task Force on Optimization Methods in Bioinformatics and Bioengineering (OMBB)

The IEEE CIS Task Force on Optimization Methods in Bioinformatics and Bioengineering (OMBB) is a Task Force under the IEEE Bioinformatics and Bioengineering Technical Committee (BBTC).

Our Mission

Our aim is to promote research on the design, application and theory of optimization methods in the field of Bioinformatics and Bioengineering.

Upcoming Events

IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2025 (CIBCB 2025), Tainan, Taiwan.

What is Bioinformatics and Bioengineering?

Bioinformatics and Bioengineering are interdisciplinary scientific fields involving many branches of computer science, engineering, mathematics, and statistics.

Bioinformatics is concerned with the development and application of computational methods for the modeling, retrieving and analysis of biological data. There is a long list of problems in the field that can be formulated as optimization problems including, just to name a few, the optimization of biochemical processes, protein structure alignment and prediction, protein sequence alignment, directed evolution, drug design and discovery, and experimental design.

Whilst Bioinformatics uses computers to understand biology better, Bioengineering is the application of engineering techniques to biology so as to create usable and economically viable products. Typical problems in the field deal with the design of biological systems, optimization of manufacturing processes, material and equipment optimization, and biomedical equipment manufacturing.

Why a Task Force Group on Optimization Methods in Bioinformatics and Bioengineering?

Bioinformatics and Bioengineering are relatively new fields subject to different types of challenging optimization problems, urging the need for effective optimization methods due to several reasons:

Biological data sets are typically complex, very large, include noisy measurements, and may change over time, thus requiring advanced optimization approaches.
Problems can often be formulated as multiobjective optimization problems, and thus require optimization methods capable of discovering a set of trade-off solutions (i.e. Pareto optimal solutions) rather than a single solution.
Problems may involve time-consuming and expensive physical experiments and/or computer simulations, and thus require optimization methods that arrive at a robust solution as quickly as possible, whilst, potentially, needing to account for constraints, uncertainty, mixed-variable types, user preferences, and various resourcing issues.
Problems can be “black box” (i.e. lack gradient information) and thus call for derivative-free optimization methods, such as nature-inspired algorithms and heuristics.

Start Learning about Optimization Methods in/and Bioinformatics and Bioengineering

Introductions to Bioinformatics and Bioengineering have been given by:

J. Claverie and C. Notredame (2011): Bioinformatics for dummies. John Wiley & Sons.
J. Cohen (2004): Bioinformatics – An Introduction for Computer Scientists. ACM Computing Surveys, 36(2):122-158.
A. Nair (2007): Computational Biology & Bioinformatics: A Gentle Overview. Communications of the Computer Society of India.
S. Chien, P.C. Chen, and Y.C. Fung (2008): An introductory text to bioengineering. World Scientific.

A tutorial on optimization in Bioinformatics can be found at:

Optimization and Applications in Bioinformatics, presented Clarisse Dhaenens at the 5th IAPR International Conference on Pattern Recognition in Bioinformatics, 2010.

Introductions to (multiobjective) optimization methods and their application to various problems in Bioinformatics and Bioengineering have been given by:

G. Fogel, D.W. Corne, and Y. Pan (2007): Computational intelligence in bioinformatics. John Wiley & Sons.
J. Handl, D.B. Kell, and J. Knowles (2007): Multiobjective optimization in bioinformatics and computational biology. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 4(2): 279-292.
V. Cutello, G. Narzisi, and G. Nicosia (2006): A multi-objective evolutionary approach to the protein structure prediction problem. Journal of the Royal Society Interface 3(6):139-151.

If you want to test your own optimization method on Bioinformatics problems, then datasets as well as Bioinformatics software can be found at:

Literature focused in more detail on the topics evolutionary multiobjective optimization, evolutionary optimization in dynamic environments, and resourcing issues in experimental optimization include:

K. Deb (2001): Multi-Objective Optimization using Evolutionary Algorithms. John Wiley & Sons.
J. Branke (2002): Evolutionary optimization in dynamic environments. Kluwer Academic Publishers.
R. Allmendinger (2012): Tuning Evolutionary Search for Closed-Loop Optimization. PhD thesis. Department of Computer Science, University of Manchester, UK.

Past Events

IEEE Symposium on Computational Intelligence in Health and Medicine (IEEE CIHM) at the 2025 IEEE Symposium Series on Computational Intelligence (IEEE SSCI 2025), Trondheim, Norway.
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2024 (CIBCB 2024) in Natal, Brazil
Special Session on Advances in CI in Health and Medicine (ACIHM), IEEE World Congress on Computational Intelligence (IEEE WCCI 2024), Yokohama, Japan
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2023 (CIBCB 2023) in Eindhoven, The Netherlands
Special Session on Optimization Methods for Bioinformatics and Bioengineering, IEEE Congress on Evolutionary Computation (IEEE CEC 2023).
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2022 (CIBCB 2022) in Ottawa, Canada
Special Session on Explainable and Interpretable Deep Learning Approaches to Address Health Challenges, IEEE World Congress on Computational Intelligence (IEEE WCCI 2022).
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2021 (CIBCB 2021) in Melbourne, Australia
Special Session on Optimization, Learning and Decision-Making in Bioinformatics, IEEE Congress on Evolutionary Computation (IEEE CEC 2021).
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2020 (CIBCB 2020) in Santiago, Chile
Special Session on Optimization, Learning, and Decision-Making in Bioinformatics and Bioengineering, IEEE World Congress on Computational Intelligence (IEEE WCCI 2020).
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2019 (CIBCB 2019) in Siena, Italy
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2018 (CIBCB 2018) in Saint Louis, USA
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2017 (CIBCB 2017) in Manchester, UK
Special Session on Computational Intelligence in Bioinformatics, IEEE Congress on Evolutionary Computation (IEEE CEC 2017).
Special Session on Data-Driven Multiple Criteria Decision Making, International Conference on Multiple Criteria Decision Making (MCDM 2017)
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2016 (CIBCB 2016) in Chiang Mai, Thailand
Special Session on Optimization, Learning, and Decision-Making in Bioinformatics and Bioengineering (OLDBB), IEEE World Congress on Computational Intelligence 2016 (WCCI 2016)
Special Session on Multiobjective Optimization in Bioinformatics, Computational Biology and Biomedical Engineering, IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2016 (CIBCB 2016)
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2015 (CIBCB 2015) in Niagara Falls, Canada
Special Session on Optimization Methods in Bioinformatics and Bioengineering, IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology 2015 (CIBCB 2015)
Special Session on Computational Intelligence in Bioinformatics, IEEE Congress on Evolutionary Computation (IEEE CEC 2015).
Special Session on Non-Standard Multiobjective Problems, 27th European Conference on Operational Research (EURO 2015)
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2014 (CIBCB 2014) in Honolulu, USA
Hybrid Special Session on Computational Intelligence in Bioinformatics, IEEE World Congress on Computational Intelligence (IEEE WCCI 2014).
Special Session on Multiobjective Optimization Methods in Bioinformatics and Bioengineering, IEEE Symposium Series on Computational Intelligence (SSCI 2014)
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2013 (CIBCB 2013) in Singapore
Special Session on Computational Intelligence in Bioinformatics, IEEE Congress on Evolutionary Computation (IEEE CEC 2013).
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2012 (CIBCB 2012) in San Diego, USA
Hybrid Special Session on Computational Intelligence in Bioinformatics, IEEE World Congress on Computational Intelligence (IEEE WCCI 2012), Brisbane, Australia
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2011 (CIBCB 2011) in Paris, France
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2010 (CIBCB 2010) in Montreal, Canada
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2009 (CIBCB 2009) in Nashville, USA
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2008 (CIBCB 2008) in Sun Valley, USA
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2007 (CIBCB 2007) in Honolulu, USA
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2006 (CIBCB 2006) in Toronto, Canada
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2005 (CIBCB 2005) in La Jolla, USA
IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2004 (CIBCB 2004) in La Jolla, USA

OMBB Members

Contact

If you want to know more about the activities of our Task Force or you want to join us, please contact the IEEE OMBB Chair or Vice Chair:

Chair

Prof. Vassilis P. Plagianakos currently serves as the Dean of the School of Science at the University of Thessaly. He is the former President of the Hellenic National Organization for the Provision of Health Services (E.O.P.Y.Y.) and the former President of the European Healthcare Fraud & Corruption Network (EHFCN). He has served as the Chair of the Board of the Hellenic Artificial Intelligence Society and is the Founder of the Intelligent Systems Laboratory of the Department of Computer Science and Biomedical Informatics, University of Thessaly. Furthermore, he has more than 15 years of industrial experience, working as a systems and network engineer. His network expertise includes design, implementation and support of secure multi-protocol networks with high efficiency and guaranteed quality of service, design of security policies for computer networks, firewall administration and VPNs, as well as integration of data and voice networks. He is coauthor of more than 50 journal publications and more than 140 conference papers, and his published work has received more than 5000 citations (h-index 34). His research interests are in the areas of Machine Learning and Neural Networks, Data Science and Intelligent decision making, Data Mining, Bioinformatics, Clustering, Evolutionary and Genetic Algorithms, Parallel and Distributed computations, and real-world problem solving.

Vice Chair

Sotiris Tasoulis received his diploma in Mathematics in 2006 and his MSc in Mathematics of Computers and Decision Making in 2009 from University of Patras in Greece. In 2013 he received his PhD from the Department of Computer Science and Biomedical Informatics of the University of Thessaly in Greece. In the same year he joined Helsinki Institute for Information Technology (HIIT) and Department of Computer Science of the University of Helsinki in Finland as a post-doctoral researcher in Knowledge Discovery in Big Data. Next in September 2015 Sotiris was assigned as Lecturer (Assistant Professor) at the Department of Applied Mathematics of Liverpool John Moores University in UK. In June 2019 was assigned Assistant Professor in the Department of Computer Science and Biomedical Informatics of the University of Thessaly and in 2024 assigned Associate Professor in the same Department. His research focuses on the development of Statistical approaches able to cope with the central challenges associated with Data Analysis, and in particular Big Data, while his teaching concern courses on Data Mining, Artificial Intelligence and Deep Learning. He has organized several workshops regarding advances in High Dimensional Big Data and have received several funding and scholarship awards on the subject. He has participated in many EU–HORIZON2020 research projects, while, on many occasions Dr. Tasoulis has collaborated with the industry as a consultant in Machine Learning and Big Data applications.