IEEE CIS Task Force on Optimization Methods in Bioinformatics and Bioengineering (OMBB)
Members of the Task Force Group
What is our Mission as Task Force Group?
Our aim is to promote research on the design, application and theory of optimization methods in the field of bioinformatics and bioengineering.
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.
Where can I start to learn about Optimization Methods in/and Bioinformatics and Bioengineering?
Introductions to Bioinformatics and Bioengineering have been given by:
A tutorial on optimization in Bioinformatics can be found at:
Introductions to (multiobjective) optimization methods and their application to various problems in Bioinformatics and Bioengineering have been given by:
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:
Future events planned by our Task Force:
Some other important upcoming events related to optimization methods in Bioinformatics and Bioengineering are the following:
Events organized by our Task Force:
- Chairing and Organizing the IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2017) in Manchester
- General Chair: Richard Allmendinger
- Several chair roles were occupied by other members of this Task Force including Sanaz Mostaghim, Daniel and Wendy Ashlock, Juila Handl, Sheridan Houghten, and Joshua Knowles
- Special Session on Data-Driven Multiple Criteria Decision Making at the 24th International Conference on Multiple Criteria Decision Making (MCDM 2017)
- Organizers: Richard Allmendinger, Jussi Hakanen, Dmitry Podkopaev, and Karthik Sindhya
- Special Session on Optimization, Learning, and Decision-Making in Bioinformatics and Bioengineering (OLDBB) at the IEEE World Congress on Computational Intelligence 2016 (WCCI'16).
- Organizers: Richard Allmendinger, Daniel Ashlock, and Sanaz Mostaghim
- Special Session on Multiobjective Optimization in Bioinformatics, Computational Biology and Biomedical Engineering at the IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology 2016 (CIBCB 2016).
- Organizers: Richard Allmendinger, Julia Handl, and Laetitia Jourdan
- Special Session on Optimization Methods in Bioinformatics and Bioengineering at the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology 2015 (CIBCB'15).
- Organizers: Richard Allmendinger and Sanaz Mostaghim
- Special Session on Non-Standard Multiobjective Problems at the 27th European Conference on Operational Research (EURO'15).
- Organizers: Richard Allmendinger and Joshua Knowles
- Special Session on Multiobjective Optimization Methods in Bioinformatics and Bioengineering at the IEEE Symposium Series on Computational Intelligence (SSCI'14).
- Organizers: Richard Allmendinger, Anna Lavygina, and Sanaz Mostaghim
For additional information
If you want to know more about the activities of this working group, or you want to join us, please contact:
|Dr. Joseph Alexander Brown
Department of Computer Science
Innopolis, Republic of Tatarstan, Russia
||Dr. Richard Allmendinger
Alliance Manchester Business School
The University of Manchester