Dr. Ofer Shir

Dr. Ofer Shir
Research Group Leader
Senior Lecturer, Department Head
Experimental Optimization and Scientific Informatica
Research Interests:

Computational Intelligence, Experimental Optimization, Statistical Learning, Theory of Randomized Search Heuristics, Quantum ML

The advent of modern laboratory and field experiments, as well as of computerized systems, enables researchers to control experiments and analyze their big-data in high-speed rates. Yet, algorithmic design of intelligent experiments for optimization and learning of prescribed objectives may constitute the next level. Very little is known today about the general usefulness of optimization heuristics and statistical learning methods in laboratory experiments, about their strengths and weaknesses when compared to traditional Design-of-Experiments approaches, or about any kind of guidelines which approach to prefer, depending upon the dimensionality of the search-space, the levels of uncertainty and the number of available trials.

We are interested in learning and optimization questions related to systems within the Natural Sciences. In particular, Operational Research and Machine Learning aspects of experimental domains, that is, practical physical- and life-sciences problems whose computerized models are unavailable or too expensive to be executed, and thus necessitate real-world experiments toward the end of their global optimization.
We have specific interest in the realms of Chemistry and Bio-Molecules' Production; Our targeted family of methodologies stem from Computational Intelligence, and especially Natural Computing.

Our current activities include Experimental Combinatorial Optimization (with Dr. Noy), Benchmarking Randomized Search Heuristics (with Prof. Bäck and Dr. Doerr), Geo-Statistical Learning (with Prof. Litaor), Effective Detection of Foliage Diseases in Vineyards (with Dr. Sharon), and Deep Learning of a Complementary Ensemble of Sporadic Input Maps (with Prof. Linker and Dr. Chen).



2008-2010 Postdoctoral Research Associate, Princeton University, USA
2008 Ph.D., Computer Science, Leiden University, The Netherlands
2004 M.Sc., Computer Science, Leiden University, The Netherlands
2003 B.Sc., Physics and Computer Science, The Hebrew University of Jerusalem, Israel

Academic and research positions

2019- Head, Department of Computer Science, Tel-Hai College
2016- Senior Lecturer, Department of Computer Science, Tel-Hai College
2013- Principal Investigator, MIGAL-Galilee Research Institute
2012-2016, Faculty Lecturer, Department of Computer Science, Tel-Hai College
2010-2013, Research Staff Member, IBM-Research

Scientific Publications

Bayesian Performance Analysis for Black-Box Optimization Benchmarking.

Calvo, B., Shir, O.M., Ceberio, J., Doerr, C., Wang, H., Bäck, T., Lozano, J.A.
In Proceedings of the Genetic and Evolutionary Computation Conference Companion, GECCO-2019 ,2019, Ed. ,ACM Press New York, NY, USA, Pages 1789?1797

Benchmarking Discrete Optimization Heuristics with IOHprofiler.

Doerr, C., Ye, F., Horesh, N., Wang, H., Shir, O.M., Bäck, T.
In Proceedings of the Genetic and Evolutionary Computation Conference Companion, GECCO-2019 ,2019, Ed. ,ACM Press New York, NY, USA, Pages 1798?1806

On the Covariance-Hessian Relation in Evolution Strategies.

Shir, O.M., Yehudayoff, A.
Theoretical Computer Science 2019 Volume 801 Pages 157-174

Predict or Screen Your Expensive Assay? DoE vs. Surrogates in Experimental Combinatorial Optimization.

Horesh, N., Bäck, T., Shir, O.M.
In Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2019 ,2019, Ed. ,ACM Press New York, NY, USA, Pages 274?284

Statistical Learning in Soil Sampling Design Aided by Pareto Optimization.

Israeli, A., Emmerich, M., Litaor, M., Shir, O.M.
In Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2019 ,2019, Ed. ,ACM Press New York, NY, USA, Pages 1198?1205

Compiling A Benchmarking Test-Suite For Combinatorial Black-Box Optimization: A Position Paper.

Shir, O.M., Doerr, C., Bäck, T.
In Proceedings of the Genetic and Evolutionary Computation Conference Companion, GECCO-2018 ,2018, ACM Press Ed. , New York, NY, USA,, Pages 1753?1760

Evolution Strategies.

Emmerich, M.T.M., Shir, O.M., Wang, H.
In Handbook of Heuristics. ,2018, Martí R., Panos P., Resende M. Ed. ,Springer Cham , Pages 1-31

Searching for the Pareto frontier in multi-objective protein design.

Nanda, V., Belure, S.V., Shir, O.M.
Biophysical Reviews 2017 Volume 9 Issue 4 Pages 339?344

Solving Structures of Pigment-Protein Complexes as Inverse Optimization Problems using Decomposition.

Lahav, Y., Shir, O.M., Noy, D.
In Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2017, ,2017, Ed. ,ACM Press New York, NY, USA,, Pages 1169?1176

On the Statistical Learning Ability of Evolution Strategies

Shir, O.M., Yehudayoff, A.
In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms FOGA-2017 ,2017, ACM Press Ed. ,ACM Press New York, NY, US, Pages 127?138

Protein Design by Multiobjective Optimization: Evolutionary and Non-Evolutionary Approaches.

Belure, S.V., Shir, O.M., Nanda, V.
In Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2017 ,2017, Ed. ,ACM Press New York, USA, Pages 1081?1088

Efficient Isothermal Titration Calorimetry Technique Identifies Direct Interaction of Small Molecule Inhibitors with the Target Protein.

Gal, M., Bloch I., Shechter, N., Romanenko, O., Shir, O.M.
Comb Chem High Throughput Screen 2016 Volume 19 Issue 1 Pages 4-13

Genetic background and environmental conditions drive metabolic variation in wild type and transgenic soybean (Glycine max) seeds

Cohen H, Shir OM, Yu Y, Hou W, Sun S, Han T, Amir R.
Plant Cell and Environment 2016 Volume 39 Pages 1805-17

Multilevel Evolution Strategies for Multigrid Problems.

Shir, O.M.
ACM Press New York, NY, USA, ,2016

On the Capacity of Evolution Strategies to Statistically Learn the Landscape.

Shir, O.M., Roslund, J., Yehudayoff, A.
Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2016, 2016 Pages 151-152

Exploring the complexity of quantum control optimization trajectories.

Nanduri, A., Shir, O.M., Donovan, A., Ho, T.-S., Rabitz, H.
Physical Chemistry Chemical Physics 2015 Volume 17 Issue 1 Pages 334?347

Efficient retrieval of landscape Hessian: Forced optimal covariance adaptive learning

Shir, O.M., Roslund, J., Whitley, D., Rabitz, H.
Physical Review E 2014 Volume 89(6) 063306

Pareto Landscapes Analyses via Graph-Based Modeling for Interactive Decision-Making.

Shir, O.M., Chen, Sh., Amid, D., Margalit, O., Masin, M., Anaby-Tavor, A., Boaz, D.
In EVOLVE - A Bridge between Probability, Set Oriented Numerics, and Evolutionary Computation V. Advances in Intelligent Systems and Computing ,2014, Tantar AA. et al. Ed. ,Springer, Cham , Pages 97?113

Pareto Optimization and Tradeoff Analysis Applied to Meta-Learning of Multiple Simulation Criteria.

Shir, O.M., Moor, D., Chen, Sh., Amid, D., Boaz, D., Anaby-Tavor, A.
In Proceedings of the 2013 Winter Simulation Conference (INFORMS WSC-2013) ,2013, Ed. ,IEEE , Pages 89?100

Self-Organizing Maps for Multi-Objective Pareto Frontiers.

Chen, Sh., Amid, D., Shir, O.M., Boaz, D., Schreck, T., Limonad, L.
In Proceedings of the Pacific Visualization Symposium, PacificVis-2013 ,2013, IEEE Ed. ,IEEE Pacific , Pages 153?160

Algorithms for Finding Maximum Diversity of Design Variables in Multi-Objective Optimization.

Zadorojniy, A., Masin, M., Greenberg, L., Shir, O.M., Zeidner, L.
In Conference on Systems Engineering Research. Volume 8 of Procedia Computer Science. ,2012, Ed. ,Elsevier , Pages 171-176

Niching in Evolutionary Algorithms

Shir, O.M.
Handbook of Natural Computing: Theory, Experiments, and Applications 2012 Pages 1035?1069

Quantum Control Experiments as a Testbed for Evolutionary Multi-Objective Algorithms

Shir, O.M., Roslund, J., Leghtas, Z., Rabitz, H.
Genetic Programming and Evolvable Machines 2012 Volume 13 Issue 4 Pages 445?491

Control of Nirtomethane Photoionization Efficiency with Shaped Femtosecond Pulses.

Roslund, J., Shir, O.M., Dogariu, A., Miles, R., Rabitz, H.
The Journal of Chemical Physics 2011 Volume 134 Issue 15 Pages 154301

Evolutionary Optimization of Rotational Population Transfer.

Rouzée, A., Ghafur, O., Vidma, K., Gijsbertsen, A., Shir, O.M., Bäck, T., Meijer, A., van der Zande, W.J., Parker, D., Vrakking, M.J.J.
Physical Review A 2011 Volume 84 Issue 3 Pages 033415