Email: jacob dot barhak at gmail dot com
Researcher / Developer / Disease Modeler
Welcome to my home page. I am a Researcher/Developer with multidisciplinary background. This includes Engineering and Computer Science and recently HealthCare. I am particularly interested in combinations of different disciplines.
Multimedia presentations describing my research can be viewed by clicking on the links and images below. These are followed by a short professional biography summary and by my publications - also see My Citations in Google Scholar.
First for the Fun part:
My mom and I translated a classic Pushkin fairy tale to English and Manuel Soto illustrated the E-book. You can get a copy from Amazon by clicking here
And now the serious part:
My research interests are: Computational Disease Modeling, High Performance Computing, Computer Aided Design, Computer Graphics, Geometric Reconstruction, Machine Learning, Computational Geometry, Computational Methods, Information Technology, Inspection Systems, Computer Vision.
My Research In Pictures and Videos:
Statistical / Economic Chronic Disease Modeling
- B.A. in Computer science from the Technion - Israel institute of technology (1993).
- B.Sc. in Mechanical engineering from the Technion - Israel institute of technology (1993).
- M.A. for completing the requirements for the Masters degree during the Ph.D. studies from the Technion - Israel institute of technology (2000).
- Ph.D. from the Technion Israel institute of technology, Mechanical Engineering department. Research subject: “Reconstruction of Freeform Objects with Arbitrary Topology from Multi Range Images” (2003).
- J. Barhak, The Reference Model for Disease Progression Combines Disease Models. I/IITSEC 2016 28 Nov – 2 Dec Orlando Florida. Paper: http://www.iitsecdocs.com/volumes/2016 Presentation: http://sites.google.com/site/jacobbarhak/home/IITSEC2016_Upload_2016_11_05.pptx
- J. Barhak, The Mount Hood Diabetes Challenge 2016. The Reference Model for Disease Progression - participated in challenges 1 and 2. 17-18 Sep 2016, St. Gallen Switzerland 2016. Program: http://media.wix.com/ugd/4e5824_36cb1fd0aca94f1980d8a2228cf7e6e8.pdf Presentations and results: http://sites.google.com/site/jacobbarhak/home/TheReferenceModel_MH2016_Submit_2016_09_04.zip
- L. Smith, M. J. Swat, J.Barhak . Sharing Formats for Disease Models. SummerSim 2016 24-27 July, Montreal, CA. Presentation: http://sites.google.com/site/jacobbarhak/home/SummerSim2016_SharingDiseaseModels_Given_2016_07_26.pptx
- J. Barhak, A. Garrett, W. A. Pruett, Optimizing Model Combinations, MODSIM world 2016. 26-28 Apr, Virginia Beach Convention Center, Virginia Beach, VA. Paper: http://www.modsimworld.org/papers/2016/Optimizing_Model_Combinations.pdf Presentation: http://sites.google.com/site/jacobbarhak/home/MODSIM2016_Submit_2016_04_25.pptx
- J. Barhak, The Reference Model for Disease Progression and Latest Developments in the MIST, PyTexas 2015. College Station, TX, 26-Sep-2015. Presentation: http://sites.google.com/site/jacobbarhak/home/PyTexas2015_Upload_2015_09_26.pptx Video: https://www.youtube.com/watch?v=htGRRjia-QQ
- J. Barhak, The Reference Model Uses Modular Population Generation! Object Oriented Population Generation on the Fly with MIST. IMAG Multiscale Modeling (MSM) Consortium Meeting 9-10 September 2015. Poster: http://sites.google.com/site/jacobbarhak/home/PosterModularPopulationGeneration_IMAG_MSM2015_Upload_2015_09_03.pdf
- J. Barhak, The Reference Model uses Object Oriented Population Generation. SummerSim 2015 July 26-29, Chicago IL, USA. Paper: http://dl.acm.org/citation.cfm?id=2874946 Presentation: http://sites.google.com/site/jacobbarhak/home/SummerSim2015_Upload_2015_07_26.pptx
- J. Barhak, Modeling Clinical Data from Publications, SpringSim 2015. April 12 - 15, Alexandria, VA, USA. Paper: http://dl.acm.org/citation.cfm?id=2873011&CFID=575392711&CFTOKEN=46270544 Presentation: http://sites.google.com/site/jacobbarhak/home/SpringSim2015ModelingDataFromPublications_Present_2015_04_13.pptx
- J. Barhak, Object Oriented Population Generation, MODSIM world 2015. 31 Mar – 2 Apr, Virginia Beach Convention Center, Virginia Beach, VA. Paper: http://modsimworld.org/papers/2015/Object_Oriented_Population_Generation.pdf Presentation: http://sites.google.com/site/jacobbarhak/home/MODSIM2015_Submit_Jacob_Barhak_2015_03_29.pptx
- J. Barhak, Generating Populations for Micro Simulation from Publicly Available Data - Populations in the MIST! IMAG Multiscale Modeling (MSM) Consortium Meeting 3-4 September 2014. Poster: http://sites.google.com/site/jacobbarhak/home/PosterPopulationGenerationMIST_IMAG_MSM2014_Upload_2014_08_31.pdf
- J. Barhak, The Reference Model for Disease Progression – Data Quality Control. 6-10 July 2014, Monterey CA. Paper: http://dl.acm.org/citation.cfm?id=2685666 Presentation: http://sites.google.com/site/jacobbarhak/home/SummerSim2014_Upload_2014_07_06.pptx
- J. Barhak, The Mount Hood Diabetes Challenge 2014. The Reference Model for Disease Progression - participated in the challenge. 17-19 June 2014, Stanford. Presentation: http://sites.google.com/site/jacobbarhak/home/MH2014TheReferenceModel_Submit_2014_06_15.pptx
- J. Barhak, The Reference Model for Disease Progression uses MIST to find data fitness. PyData Silicon Valley 2014: Abstract: http://pydata.org/sv2014/abstracts/#195_ Presentation: http://sites.google.com/site/jacobbarhak/home/PyData_SV_2014_Upload_2014_05_02.pptx Video: https://www.youtube.com/watch?v=vyvxiljc5vA
- J. Barhak, A. Garrett, Population Generation from Statistics Using Genetic Algorithms with MIST + INSPYRED. MODSIM World 2014, April 15 - 17, Hampton Roads Convention Center in Hampton, VA. Paper: http://sites.google.com/site/jacobbarhak/home/MODSIM2014_MIST_INSPYRED_Paper_Submit_2014_03_10.pdf Presentation: http://sites.google.com/site/jacobbarhak/home/MODSIM_World_2014_Submit_2014_04_11.pptx
- J. Barhak, The Reference Model for Disease Progression Sensitivity to Bio-Marker Correlation in Base Population - The Reference Model Runs with MIST Over the Cloud! 2013 IMAG Multiscale Modeling (MSM) Consortium Meeting, October 2-3, 2013, Poster: http://sites.google.com/site/jacobbarhak/home/PosterTheReferenceModel_IMAG_MSM2013_Submit_2013_09_23.pdf
- J. Barhak, MIST: Micro-Simulation Tool to Support Disease Modeling. SciPy, 2013, Bioinformatics track, https://github.com/scipy/scipy2013_talks/tree/master/talks/jacob_barhak, Presentation also available at: http://sites.google.com/site/jacobbarhak/home/SciPy2013_MIST_Presented_2013_06_26.pptx Video of Talk: http://www.youtube.com/watch?v=AD896WakR94
- J. Barhak, The Reference Model Scores Fitness of Models and Populations. Poster Presentation. ISPOR 18th Annual International Meeting, May 18-22, 2013, Sheraton New Orleans, New Orleans. Poster Presentation. http://sites.google.com/site/jacobbarhak/home/PosterTheReferenceModel_ISPOR_Submit_2013_05_14.pdf
- J. Barhak, H.S. Leff, Modeling a Chronic Disease Model and a Mental Health Model Using the Same Modeling Tools, MODSIM World 2013, April 30 - May 2nd, Hampton Roads Convention Center in Hampton, VA. Paper: http://sites.google.com/site/jacobbarhak/home/MODSIM_World2013_Submitted_04Apr2013.pdf , Presentation: http://sites.google.com/site/jacobbarhak/home/MODSIM_World_Presented_2013_05_2.pptx
- J. Barhak, The Reference Model: Improvement in Treatment Through Time in Diabetic Populations, The Fourth International Conference in Computational Surgery and Dual Training. The Joseph B. Martin Conference Center at Harvard Medical School. Boston, MA, USA. December 9-10-11, 2012. Video: http://web.cs.uh.edu/~cosine/?q=node/140 , Presentation slides: http://www2.cs.uh.edu/~cosine/talks_cosine4/monday/MultidisciplinaryTalks/2_JacobBarhak.pptx , Slides Copy: http://sites.google.com/site/ComputationalSurgery_Presneted_2012_12_LateUploadToOwnWebSite_2014_2_27.pptx
- J. Barhak, The Reference Model for Chronic Disease Progression. 2012 Multiscale Modeling (MSM) Consortium Meeting, October 22-23, 2012, Poster: http://sites.google.com/site/jacobbarhak/home/PosterTheReferenceModel_IMAGE_MSM_Submit_2012_10_17.pdf
- J. Barhak, The Reference Model for Disease Progression. Poster presentation, SciPy 2012, Austin Tx, 18-19 July 2012. Paper: https://github.com/Jacob-Barhak/scipy_proceedings/blob/2012/papers/Jacob_Barhak/TheReferenceModelSciPy2012.rst, Poster: http://sites.google.com/site/jacobbarhak/home/PosterTheReferenceModel_SciPy2012_Submit_2012_07_14.pdf
- J. Barhak, Using computing power to aid chronic disease modeling. The Mt hood challenge 6, June 7-8, 2012. Johns Hopkins Mt. Washington Conference Centre. Presentation: http://sites.google.com/site/jacobbarhak/home/ComputingPower_Presented_MountHood_7Jun2012.pptx
- J. Barhak, M.B. Brown, W.H. Herman, J.M. Lee, L.A. Prosser, W. Ye, The Michigan Model for Diabetes. The Mt hood challenge 5, September 18-19, 2010, Malmo, Sweden.
- W. Ye, J. Barhak, M. B. Brown, W. H. Herman, The Michigan Model For Diabetes. Poster presentation, American Diabetes Association, 69th Scientific Sessions, June 5 - 9, 2009, New Orleans, Louisiana
- J. Barhak, D.J.M. Isaman, W. Ye, Use of Secondary Data Analysis and Instantaneous States in a Discrete-State Model of Diabetic Heart Disease. Poster presentation, ENAR 2009 Spring Meetings, March 15-18, 2009, Grand Hyatt San Antonio, San Antonio, TX
- X. Li, I. Guskov, J. Barhak, Robust Alignment of Multi-view Range Data to CAD model. the International Conference on Shape Modeling and Applications 2006. SMI'06. Matsushima, JAPAN, 14-16th June, 2006. Online: http://dx.doi.org/10.1109/SMI.2006.32
- Y. Koren, J. Barhak, Automobile Interior Personalization Trends and Analysis, MCPC 2007 World Conference on Mass Customization & Personalization, October 7-9, 2007 at the Massachusetts Institute of Technology. http://scg.mit.edu/images/MCPC_Conference_proceedings/site/papers/MCPC-143-2007.pdf
- P. Spicer, K. Bohl, G. Abramovich, J. Barhak, Robust Calibration of a Reconfigurable Camera Array For Machine Vision Inspection (RAMVI) Using Rule-Based Colour Recognition. VISAPP International Conference on Computer Vision Theory and Applications, 25 - 28 February, 2006, Setúbal, Portugal.
- P. Spicer, J. Barhak, Applied Reconfigurability in Inspection Machines. The 17th IMACS world congress, Scientific Computation, Applied Mathematics and Simulation. Paris, France, July 11-15, 2005.
- G. Abramovich, J. Barhak, P. Spicer, Reconfigurable Array for Machine Vision Inspection (RAMVI).The 2005 CIRP 3rd International Conference on Reconfigurable Manufacturing, May 10-12, Ann Arbor, Michigan.
- J. Barhak, Utilizing Computing Power to Simplify the Inspection Process of Complex Shapes. The 2004 Israel-Italy Bi-National Conference on Measurements and Uncertainty Evaluation in Coordinate Measuring Machine (CMM) and Scanners and their Implication on Design and Reverse Engineering. Haifa, Israel, November 29-30, 2004.
- L. Zhu, J. Barhak, V. Srivatsan, R. Katz, Error Analysis and Simulation for Four-Axis Optical Inspection System, Digital Enterprise Technology, September 13-15, 2004, Seattle, Washington, USA.
- J. Barhak, R. Katz, Rapid Non-Contact Measurements of Engine Cylinder Heads with the Reconfigurable Inspection Machine, 4th CIRP international seminar on Intelligent Computation in Manufacturing Engineering, Sorrento, Italy, June 30th to July 4th 2004.
- J. Barhak, R. Katz, Interpretation of Laser Measurements Produced by the Reconfigurable Inspection Machine Using the Virtual Ball Method. CIRP 2nd International Conference on Reconfigurable Manufacturing August 20-21 2003, Ann Arbor, Michigan, USA.
- J. Barhak, A. Fischer, Adaptive Reconstruction of Freeform Objects with 3D SOM Neural Network Grid, Pacific Graphics 2001, October 16-18, Tokyo, Japan . Online: http://doi.ieeecomputersociety.org/10.1109/PCCGA.2001.962862
- Fischer, A. Manor, J. Barhak, Adaptive Parameterization for Reconstruction of 3D Freeform Objects from Laser-Scanned Data, IEEE Pacific Graphics'99, Seoul, Korea, October 5-7, 1999. Online: http://doi.ieeecomputersociety.org/10.1109/PCCGA.1999.803362
Selected Other Publications/Appearances/Talks/Posts:
- J. Barhak, The Reference Model for Disease Progression, Healthcare Predictive Analytics Meetup, Austin, Texas, 19-Jan-2017. http://sites.google.com/site/jacobbarhak/home/PredictiveHealthAnalyticsMeetup_Upload_2017_01_19.pptx
- J. Barhak, Death by clinical data: A model that accumulates medical knowledge for more comprehensive reporting. Data Driven Journalism, 11/1/2017. Online: http://datadrivenjournalism.net/news_and_analysis/death_by_clinical_data_a_model_that_accumulates_medical_knowledge_for_more
- J. Barhak, StarCluster Demo at the Austin Web Python Users Group: http://www.meetup.com/austinwebpythonusergroup/events/231188161/ Video: https://www.youtube.com/watch?v=wpfw8POx-wI
- J. Barhak, The MIcro Simulation Tool (MIST) - How to create basic disease models – Tutorial. SummerSim 2016 24-27 July, Montreal, CA. Presentation: http://sites.google.com/site/jacobbarhak/home/SummerSim_Tutorial_MIST_Given_2016_07_24.pptx
- Population Modeling Workgroup, Population Modeling by Examples (WIP) - SpringSim 2015 , April 12 - 15, Alexandria, VA, USA. Paper: http://dl.acm.org/citation.cfm?id=2887741&CFID=764108956&CFTOKEN=12623832, Also on: https://simtk.org/docman/view.php/962/1892/PopModExample_Submit_2015_03_04.doc Presentation: https://simtk.org/docman/view.php/962/1897/SpringSim2015PopMod_Upload_2015_04_10.pptx
- Lealem Mulugeta, Anthony Scopatz, Jacob Barhak, inSCIght, The Scientific Computing Podcast, Episode 32: Code Reproducibility and Open Source, Posted on 2013/10/19, Online: http://inscight.org/2013/10/19/episode-32-code-reproducibility-and-open-source/
- J. Barhak, H. S. Leff, Public Response Letter to the Authors of: Modeling good research practices: a report of the ISPOR-SMDM Modeling Good Research Practices Task Force. Online Public letter published with the LinkedIn ISPOR Discussion Group. Here is a link to the PDF version of the letter: http://sites.google.com/site/jacobbarhak/home/PublicResponseLetterToModelingGoodResearchPracticesTaskForce_Upload_17Apr2013.pdf
- J. Barhak, Technological innovation at ISPOR 18th annual meeting 2013 - Topic 4: Budget Impact Analysis Good Practices II Task Force trend towards not publishing models. Online Public post published with the LinkedIn ISPOR Discussion Group.
- J. Barhak, Austin Machine Learning Group presentation 31-July-2013: http://sites.google.com/site/jacobbarhak/home/AustinMachineLearningMeetup_Present_2013_07_31.pptx
- J. Barhak, Estimation of a disease model based on a discrete time Markov model using secondary data with transitions based on multi-dimensional tables. Simulation: Transactions of the Society for Modeling and Simulation International 1–23. http://dx.doi.org/10.1177/0037549716673729
- W. Ye., J. Barhak J., D.J.M. Isaman, Use of Secondary Data to Estimate Instantaneous Model Parameters of Diabetic Heart Disease: Lemonade Method. Information Fusion Volume 13, Issue 2, April 2012, Pages 137-145, http://dx.doi.org/10.1016/j.inffus.2010.08.003
- Barhak J., Isaman D.J.M., Ye W., Lee D.: Chronic disease modeling and simulation software. Journal of Biomedical Informatics, Volume 43, Issue 5, October 2010, Pages 791-799, http://dx.doi.org/10.1016/j.jbi.2010.06.003
- D.J.M. Isaman, J. Barhak, W. Ye: Indirect Estimation of a Discrete-State Discrete-time model using Secondary Data Analysis of Regression Data. Statistics in Medicine Volume 28, Number 16, Pages 2095 - 2115, 2009. Online: http://dx.doi.org/10.1002/sim.3599
- X. Li, I. Guskov, J. Barhak, Feature-based alignment of range scan data to CAD model. International Journal of Shape Modeling Vol. 13, No. 1 (June 2007) Online: http://dx.doi.org/10.1142/S0218654307000920
- X. Li, J. Barhak, I. Guskov, G. W. Blake, Automatic registration for inspection of complex shapes. Virtual and Physical Prototyping, Volume 2, Issue 2 June 2007, pages 75 - 88. Online: http://dx.doi.org/10.1080/17452750701374339
- L. Zhu, J. Barhak, V. Srivatsan, R. Katz, Efficient Registration for Precision Inspection of Free-Form Surfaces, the International Journal of Advanced Manufacturing Technology. Published Online, March 18, 2006. Online: http://dx.doi.org/10.1007/s00170-005-0370-9
- J. Barhak, D. Djurdjanovic, P. Spicer, R. Katz, Integration of Reconfigurable Inspection with Stream of Variations Methodology. International Journal of Machine Tools and Manufacture, Vol. 45, Issues 4-5, April 2005, p. 407-419. Online: http://dx.doi.org/10.1016/j.ijmachtools.2004.09.011
- F. L. Krause, A. Fischer, N. Gross, J. Barhak, Reconstruction of Freeform Objects with Arbitrary Topology Using Neural Networks and Subdivision Techniques, CIRP Annals, STC Dn, 52/1/2003, p.125, 2003. Online: http://dx.doi.org/10.1016/S0007-8506(07)60547-2
- J. Barhak, A. Fischer, Adaptive Reconstruction of Freeform Objects with 3D SOM Neural Network Grids, Special Issue on Geometrical Modeling and Computer Graphics, in Journal of Computers & Graphics, vol. 26, no. 5, 2002. Online: http://dx.doi.org/10.1016/S0097-8493(02)00129-2
- A. Fischer, J. Barhak, Tele Design for Manufacturing, CIRP Annals, STC Dn, 50/1/2001, p.77, 2001. Online: http://dx.doi.org/10.1016/S0007-8506(07)62075-7
- J. Barhak, A. Fischer, Multi - Reconstruction of a 3D Freeform Object From Range Images, The International Journal for Manufacturing Science & Production Vol 3. Nos. 2-4, 2000. Appears also in CIRP Seminar on Design with Manufacturing: Intelligent Design Concepts Methods and Algorithms, Haifa, Israel, May 16-18, 2000.
- J. Barhak, A. Fischer, Adaptive Parameterization for Reconstruction of 3D Freeform Objects from Laser-Scanned Data based on a PDE approach, The Visual Computer Vol. 17 No. 6, August 2001 p. 351-369. Online: http://www.springerlink.com/content/ut801y7f5nre835c/
- J. Barhak, A. Fischer, Parameterization and Reconstruction from 3D Scattered Points Based on Neural Network and PDE Techniques, IEEE Transactions on Visualization & Computer Graphics, Vol. 7, No.1, January-march, 2001 p.1-16. Online: http://doi.ieeecomputersociety.org/10.1109/2945.910817
- J. Barhak, A. Fischer, “B-Spline Surface Reconstruction from Single Range Image using Parameterization based on PDE Solution”, TME 461, Mechanical Engineering, Technion, Haifa, Israel, March 1999.
- J. Barhak, R. Katz, “Alignment and Measurement Extraction Procedures for the Reconfigurable Inspection Machine”. ERC/RMS Technical Report TR-052-04, University of Michigan, July 21st 2004.
- Lecturer: ME454 “Computer Aided Mechanical Design”, University of Michigan (2006).
- Lecturer: 35003 “Interactive Computer Graphics and Introduction to CAD”, Technion (2002).