Prof. Ofer Shir

Ofer Shir
Associate Professor of Computer Science
Principal Investigator
Research Group Leader
PhD
Phone
972-4-6489923

Lab Website

Full CV (PDF)
Research Interests:

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

Quote
You are the outcome of 3.8 billion years of evolutionary success. Act like it.

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. Our research interests encompass in general the following topics:

  • AI-Driven Scientific Research and Algorithmically-Guided Experimentation
  • Artificial General Intelligence, Deep Learning, Self-Supervised Learning
  • Combinatorial Optimization (White/Grey/Black-box, including physical systems in the lab)
  • Quantum Computing
     

Our current activities include Experimental Combinatorial Optimization (with Dr. Dan Gamrasni and Dr. Or Shahar), Multi-Objective Mixed-Integer Quadratic Models (with Prof. Michael Emmerich), Effective Detection of Foliage Diseases in Vineyards (with Dr. Rakefet Sharon), and Deep Learning of Enzymes' Functionality (with Dr. Livnat Jurnou and Dr. Itai Sharon).

CV

Education

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

2022-2023 Visiting Associate Professor, Faculty of Mathematics, Technion - Israel Institute of Technology
2020- Associate Professor, Computer Science Department, Tel-Hai College
2013- Principal Investigator, MIGAL-Galilee Research Institute

Previously

2019-2022 Head, Computer Science Department, Tel-Hai College
2012-2020 Lecturer and Senior Lecturer, Computer Science Department, Tel-Hai College
2010-2013, Research Staff Member, IBM-Research

Funding
  1. [M.O.S.T.] An innovative AI-driven approach for the development of environmentally-friendly postharvest volatile fungicides (with Dr. Gamrasni/Migal)
  2. [M.O.A.G.] Innovative AI-driven approach for the development of postharvest protocols (with Dr. Gamrasni/Migal)
  3. [Migal-internal] Automated identification of enzymes with desirable traits for agriculture use in extreme climate conditions using machine learning (with Dr. I. Sharon and Dr. Afriat-Jurnou)

Scientific Publications

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
2017

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
2016

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
2016

Multilevel Evolution Strategies for Multigrid Problems.

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

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
2015

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
2014

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
2014

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
2013

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
2013

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
2012

Niching in Evolutionary Algorithms

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

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
2012

Fidelity Between Unitary Operators and the Generation of Gates, Robust Against Off-Resonance Perturbations.

Cabrera, R., Shir, O.M., Wu, R., Rabitz, H.
Journal of Physics A: Mathematical and Theoretical 2011 Volume 44 Issue 9 Pages 095302
2011

Multiobjective Adaptive Feedback Control of Two-Photon Absorption Coupled with Propagation through a Dispersive Medium.

Laforge, F.O., Roslund, J., Shir, O.M., Rabitz, H.
Physical Review A 2011 Volume 84 Issue 1 Pages 013401
2011

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
2011

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
2011

Forced Optimal Covariance Adaptive Learning: Modified CMA-ES for Efficient Hessian Determination.

Shir, O.M., Roslund, J., Rabitz, H.
In Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2010 ,2010, Ed. ,ACM Press New York, NY, USA, Pages 421?422
2010

A Reduced-Cost SMS-EMOA Using Kriging, Self-Adaptation, and Parallelization.

Klinkenberg, J.W., Emmerich, M., Deutz, A., Shir, O.M., Bäck, T.
In Multiple Criteria Decision Making for Sustainable Energy and Transportation Systems: Volume 634 of Lecture Notes in Economics and Mathematical Systems. ,2010, Ed. ,Springer Berlin Heidelberg , Pages 301?311
2010

Adaptive Niche-Radii and Niche-Shapes Approaches for Niching with the CMA-ES

Shir, O.M., Emmerich, M., Bäck, T.
Evolutionary Computation 2010 Volume 18 Issue 1
2010

Niching with Derandomized Evolution Strategies in Artificial and Real-World Landscapes.

Shir, O.M., Bäck, T.
Natural Computing: An International Journal 2009 Volume 8 Issue 1 Pages 171?196
2009

Accelerated Optimization and Automated Discovery with Covariance Matrix Adaptation for Experimental Quantum Control

Roslund, J., Shir, O.M., Bäck, T., Rabitz, H.
Physical Review A (Atomic, Molecular, and Optical Physics) 2009 Volume 80 Issue 4 Pages 043415
2009

Enhancing Decision Space Diversity in Evolutionary Multiobjective Algorithms.

Shir, O.M., Preuss, M., Naujoks, B., Emmerich, M.
In Proceedings of Evolutionary Multi-Criterion Optimization: Fifth International Conference (EMO 2009). Volume 5467 of Lecture Notes in Computer Science. ,2009, Ed. ,Springer , Pages 95?109
2009

Evolutionary Multi-Objective Quantum Control Experiments with the Covariance Matrix Adaptation.

Shir, O.M., Roslund, J., Rabitz, H.
In Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2009 ,2009, Ed. ,ACM Press New York, NY, USA, Pages 659?666
2009

Niching Methods: Speciation Theory Applied for Multi-modal Function Optimization

Shir, O.M., Bäck, T.
In Algorithmic BioProcesses ,2009, Anne Condon, David Harel, Joost N. Kok, Arto Salomaa, Erik Winfree Ed. ,Springer Berlin Heidelberg , Pages 705-729
2009