Jacob Barhak

My research interests are: Computational Disease Modeling, Artificial Intelligence, Machine Learning, High Performance Computing, Intellectual Property, Computer Aided Design, Computer Graphics, Geometric Reconstruction, Computational Geometry, Computational Methods, Information Technology, Inspection Systems, Computer Vision.

My Research In Pictures and Videos:

Lessons Learned from Modeling COVID-19: Steps to Take at the Start of the Next Pandemic

AI and Legal Aspects

The Reference Model for COVID-19 attempts to explain USA data

A Space Debris Risk Analysis Tool (skip to timestamp 31:30)

ClinicalUnitMapping.Com Takes a Small Step Towards Machine Comprehension of Clinical Trial Data

The Reference Model for Disease Progression: Explaining COVID-19

Open Source, Sustainability, and CC0

The Reference Model for COVID-19 attempts to explain USA data

The Reference Model for COVID-19 - The First Multi-Scale Ensemble Disease Model

Using Python HoloViz Technologies to Create Interactive Presentations

The Reference Model Accumulates Knowledge With Human Interpretation

Visualizing Machine Learning of Units of Measure using PyViz

Standardizing Clinical Data with Python

Clinical Data Modeling with Python

Evolutionary Computation Examples with Inspyred

The Reference Model: A Decade of Healthcare Predictive Analytics with Python

The Reference Model for Disease Progression and Latest Developments in the MIST

 The Reference Model for Disease Progression uses MIST to find data fitness

 MIST: Micro-Simulation Tool to Support Disease Modeling

 The Reference Model for disease progression 

 Statistical / Economic Chronic Disease Modeling

Automotive Interior Personalization to Customer Taste 

Automatic Computational Alignment of Complex Shapes for Inspection using Registration Algorithms:

  The Reconfigurable Array for Machine Vision Inspection (RAMVI):

Geometric Reconstruction using Neural Network Techniques:

Academic degrees:

• • 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).

Patents:

• J. Barhak, Reference model for disease progression - United States Patent 9,858,390, January 2, 2018 . On Google Patents

• J. Barhak, Analysis and Verification of Models Derived from Clinical Trials Data Extracted from a Database, U.S. Patent Number 10,923,234, February 16, 2021 . On Google Patents

Software Published:

• • MIcro Simulation Tool (MIST). Python code to support Micro Simulation in High Performance Computing (HPC) environment - helpful for Disease modeling. Available for download under GNU General Public License (GNU GPL) from the GitHub project web page: https://github.com/Jacob-Barhak/MIST or from the SimTK web portal: https://simtk.org/home/mist. Latest version of MIST available in https://github.com/Jacob-Barhak/MIST

  • The Indirect Estimation and Simulation Tool (IEST): Python code available for download under the GNU General Public License (GNU GPL). Download IEST (Ver 0.85.0.0, 27-Feb-2012) : InstallIEST_0_85_0_0.zip. 

  • The Indirect Estimation Prototype: Matlab code available for download under the GNU General Public License (GNU GPL). Download the Indirect Estimation Prototype for Matlab (Ver 0.39, 09-Dec-2009) : IndirectEstimationPrototype_Release_Ver0_39.zip. 

  • The BIM project: The BIM software was developed at the NSF (ERC/RMS) at the University of Michigan. This is a non commercial release of the source code. For questions regarding possible commercial use please contact Prof. Yoram Koren. Latest version of the BIM project is available in: https://github.com/Jacob-Barhak/BIM 

  • NN (Neural Network): This is code was written as part of the Ph.D. thesis. The code implements several types of self organizing Neural Networks for the purpose of reconstructing meshes from point clouds. The software was developed at the CAD Lab at the Technion. This is a non commercial release of the source code. For questions regarding possible commercial use please contact the Technion Industry Liaison Office. Latest version of NN are available in: https://github.com/Jacob-Barhak/NN 

  • My Github Account https://github.com/Jacob-Barhak contains some of the above software tools alongside many other smaller software projects

Ph.D. Thesis:

• • J. Barhak, “Reconstruction of Freeform Objects with Arbitrary Topology from Multi Range Images”, Ph.D. Thesis, Mechanical Engineering faculty, Technion - Israel institute of technology, Haifa, Israel, 2003. Seminar on the subject presented on October 24th 2002.

Publications:

• Lessons Learned from Modeling COVID-19: Steps to Take at the Start of the Next Pandemic

  • Webinar  MIDAS Network 2025 Mar 28th, Virtual.  Presentation:  https://www.clinicalunitmapping.com/show/Lessons_Learned_COVID19_Latest.pdf  Video: https://youtu.be/xvmehz_pnUo?si=ExuKpFdUq0mPgxS-  

  • Glorioso, C., Castiglione, F., Oshinubi, K., Chharia, A., & Barhak, J. (2024). Lessons Learned from Modeling COVID-19: Steps to Take at the Start of the Next Pandemic. Preprints. https://doi.org/10.20944/preprints202411.2193.v1 

• Jacob Barhak, The Reference Model for COVID-19 attempts to explain USA data.   Presentation: https://www.clinicalunitmapping.com/show/COVID19_Ensemble_Latest.html

  • Keynote, CHRONIC DISEASES & INFECTIOUS DISEASES 24-NOV-2022, Paris, France. https://www.chronicdiseases.scientexconference.com/

  • PyData Chicago on 15-Dec-2022, https://www.meetup.com/pydatachi/events/289899473/         Video: https://youtu.be/1M645o5gWrc

  • San Diego Python Users Group Monthly Meetup 27-April-2023, https://www.meetup.com/pythonsd/events/292436501/ Video:  https://www.youtube.com/live/U9jSxbyJU0I?feature=share&t=1773

  • MODSIM World 2023 May 22-23 booth, https://modsimworld.org/  

  • 2023 MSM Consortium Meeting - Past2Future, NIH Campus, Natcher Conference Center, Bethesda MD, 28-29 June 2023, https://www.imagwiki.nibib.nih.gov/imag-events/2023-MSM-Meeting

  • CAFCW23 Computational Approaches for Cancer Workshop November 12, 2023. https://ncihub.cancer.gov/groups/cafcw/cafcw23/cafcw23_program

  • MODSIM World 2024 May 20-22 booth, https://modsimworld.org/  

  • 2nd Global Congress on Healthcare & Patient Safety Berlin, July 29 - 30, 2024. https://healthcareconference.pagicle.com/

  • Code Mavens January 27, 2025. https://www.meetup.com/code-mavens/events/305357268/ . Video: https://youtu.be/Ea_e6xI48Ik?si=KNers3doU2djKE6a

  • Holon Institute of Technology March 16, 2025

• Jacob Barhak, AI and Legal Aspects, https://www.clinicalunitmapping.com/show/AI_legal_Latest.pdf 

  •   Austin Python Meetup, 2025 March 12th

    •  Video: https://youtu.be/e19cYzXR0aA?si=8D7pXwUSG5Cx4Blv 

  • Anaconda, 2025 Jan 9th, 17th

  • GE Healthcare Paper Club 2024 Sep 2nd Haifa

  • AI Makerspace Community Session 2024 Aug 24th, Sep 4th Virtual

    • Video 1: https://www.loom.com/share/a90ee4974a1643a9afebcd66122db510?sid=8de5eebd-6c56-415f-8048-a75117545f13

    • Video 2: https://www.loom.com/share/f6a0adcd0f88466392aeba897a189bc3?sid=ef4e5920-dd79-4219-819b-a427c09b1ef4

• Jacob Barhak, Joe Guzman, A Space Debris Risk Analysis Tool. https://app.box.com/s/5jqlyai4in6r7a4eqtlcreap91iutvou San Diego Python meetup https://www.youtube.com/live/rh8M90OztTM?si=7pfXRA1S9gNNIZFZ&t=1890

• Jacob Barhak & Joshua Schertz, ClinicalUnitMapping.Com Takes a Small Step Towards Machine Comprehension of Clinical Trial Data. Presentation: https://www.clinicalunitmapping.com/show/Unit_Mapping_Latest.html 

  • Keynote, CHRONIC DISEASES & INFECTIOUS DISEASES 25-NOV-2022, Paris, France.  https://www.chronicdiseases.scientexconference.com/ 

  • MODSIM World 2023 May 22-23 booth, https://modsimworld.org/  

  • 2023 MSM Consortium Meeting - Past2Future, NIH Campus, Natcher Conference Center, Bethesda MD, 28-29 June 2023, https://www.imagwiki.nibib.nih.gov/imag-events/2023-MSM-Meeting

  • CAFCW23 Computational Approaches for Cancer Workshop November 12, 2023. https://ncihub.cancer.gov/groups/cafcw/cafcw23/cafcw23_program

  • Austin Python Meetup - January 10, 2024 https://www.meetup.com/austinpython/events/297392368/.  Video: https://youtu.be/d4qB9xaPU-U?si=MkPfADDtJuyK4T90

  • MODSIM World 2024 May 20-22 booth, https://modsimworld.org/  

  • 2nd Global Congress on Healthcare & Patient Safety Berlin, July 29 - 30, 2024. https://healthcareconference.pagicle.com/

• Jacob Barhak, The Reference Model for Disease Progression: Explaining COVID-19 - SCITUBE May 11, 2023 : https://scitube.io/dr-jacob-barhak-the-reference-model-for-disease-progression-explaining-covid-19/  - youtube video: https://youtu.be/s9L-qFF84Ew

• Jacob Barhak, "Open Source, Sustainability, and CC0" August Penguin 3-Mar-2023, Tel Aviv, Israel. Presentation: https://jacob-barhak.github.io/PenguinIsrael2023_OpenSource_2023_03_02.pdf , Video: https://youtu.be/Bhli5L4qskU

• Jacob Barhak, The Reference Model is a Multi-Scale Ensemble Model of COVID-19. Self Published Interactive Manuscript. Publication Date: 27-May-2021  http://doi.org/10.34235/b7eaa32b-1a6b-444f-9848-76f83f5a733c

•  Jacob Barhak: The Reference Model for COVID-19 - The First Multi-Scale Ensemble Disease Model, MIDAS Webinar - 28 May 2021,  https://jacob-barhak.github.io/COVID19_Ensemble_MIDAS_Webinar.html  Video: https://youtu.be/-z8N40TdKDk?t=1860

•  Jacob Barhak, Demonstration of Data or Software Resource: The MIcro Simulation Tool (MIST) used for disease modeling and population generation. MIDAS Annual Meeting 2021 May10-13.  https://event.midas2021.exordo.com/presentation/33/the-micro-simulation-tool-mist-used-for-disease-modeling-and-population-generation    Presentation material: https://github.com/Jacob-Barhak/Presentations/tree/master/MIDAS2021_MIST

• Jacob. Barhak, The Reference Model for COVID-19 is Now a Multi-Scale Ensemble Model. MIDAS Annual Meeting 2021 May10-13, Virtual. https://event.midas2021.exordo.com/presentation/32/the-reference-model-for-covid-19-is-now-a-multi-scale-ensemble-model . Interactive Poster: https://jacob-barhak.github.io/Poster_COVID19_Ensemble_2021.html

• Jacob Barhak, James Bednar, Using Python HoloViz Technologies to Create Interactive Presentations. PyCon Israel 2021 May 2-3. Presentation: https://jacob-barhak.github.io/Presentation_PyConIL2021_HoloViz.html  Video: https://youtu.be/YSdQ50SFLpM

•  Jacob. Barhak, Open Source and Sustainability, COMBINE 2020 October 5-9. Video: https://drive.google.com/drive/folders/1actGnx6FwvoCcPrrF3qbnO0AmHt10WN6  starting from minute 13:10.  Presentation:  https://jacob-barhak.github.io/COMBINE2020_OpenSource_upload_2020_10_04.odp

• Jacob Barhak, The Reference Model for Disease Progression Handles Human Interpretation, MODSIM World 2020. Paper: https://www.modsimworld.org/papers/2020/MODSIM_2020_paper_42_.pdf  Interactive Results: https://jacob-barhak.netlify.app/thereferencemodel/results_2020_03_21_visual_2020_03_23/CombinedPlot.html

•  Jacob Barhak, The Reference Model Accumulates Knowledge With Human Interpretation. Interagency Modeling and Analysis Group - IMAG wiki - MODELS, TOOLS & DATABASES Uploaded 16 March 2020.  Poster: https://jacob-barhak.github.io/Poster_MSM_IMAG_2020.html  Code:  https://github.com/Jacob-Barhak/Presentations/tree/master/MSM_IMAG2020

•  Jacob Barhak, Joshua Schertz, Visualizing Machine Learning of Units of Measure using PyViz . PyData Austin 2019 , 6-7 December 2019, Galvanize Austin. Presentation: https://jacob-barhak.github.io/Presentation_PyData_Austin_2019.html   Video: https://youtu.be/KS-sRpUvnD0

•  Jacob Barhak, Joshua Schertz, Supervised Learning of Units of Measure . ML-MSM/IMAG meeting. IMAG Multiscale Modeling (MSM) Consortium Meeting October 24-25, 2019 @ NIH, Bethesda, MD . Poster: https://jacob-barhak.github.io/Poster_MSM_ML_IMAG_2019.html

•  Jacob Barhak, Joshua Schertz, Clinical Unit Mapping with Multiple Standards, 2019 CDISC U.S. Interchange, San Diego, CA, 16 - 17 October 2019. Poster: https://jacob-barhak.github.io/Poster_CDISC2019.html 

•  Jacob Barhak, Joshua Schertz, Standardizing Clinical Data with Python . PyCon Israel 3-5 June 2019, Video: https://youtu.be/vDXyCb60L5s  Presentation: https://jacob-barhak.github.io/Presentation_PyConIsrael2019.html 

•  Jacob Barhak, Aaron Garrett, Anselm Blumer, Olaf Dammann, Population Disease Occurrence Models Using Evolutionary Computation. MODSIM World 2019, April 22-24, 2019, Norfolk, VA Paper: https://www.modsimworld.org/papers/2019/MODSIM_2019_paper_14.pdf code: https://github.com/Jacob-Barhak/PopDOM , Presentation: https://jacob-barhak.github.io/Presentation_MODSIM_2019.html

•  Jacob Barhak, Clinical Data Modeling with Python, AnacondaCon , Austin, Texas,  April 3-5, 2019. Video: https://youtu.be/fQIYMf5wKGE , Presentation: https://jacob-barhak.github.io/AnacondaCon_2019.html 

•  Jacob Barhak, The Reference Model is the most validated diabetes cardiovascular model known. MSM/IMAG meeting. IMAG Multiscale Modeling (MSM) Consortium Meeting March 6-7, 2019 @ NIH, Bethesda, MD . Poster: https://jacob-barhak.github.io/InteractivePoster_MSM_IMAG_2019.html Poster Code: https://github.com/Jacob-Barhak/Presentations/tree/master/PosterIMAG2019 

•  Jacob Barhak, Joshua Schertz, Clinical Unit Mapping for Standardization of ClinicalTrials.Gov . MSM/IMAG meeting. IMAG Multiscale Modeling (MSM) Consortium Meeting March 6-7, 2019 @ NIH, Bethesda, MD . Poster: https://jacob-barhak.github.io/InteractivePoster_MSM_IMAG_2019.html Poster Code: https://github.com/Jacob-Barhak/Presentations/tree/master/PosterIMAG2019

•  Jacob Barhak, Joshua Schertz - Natural Language Processing and Web Tools for Mapping Units from ClinicalTrials.Gov - Simulation Interchangeability Standards Organization (SISO) 2019 Simulation Innovation Workshop.  11 - 15 February 2019 Orlando, Florida. Web link: ClinicalUnitMapping.com   , Presentation: https://www.sisostds.org/DigitalLibrary.aspx?Command=Core_Download&EntryId=49580   Paper: https://www.sisostds.org/DesktopModules/Bring2mind/DMX/API/Entries/Download?Command=Core_Download&EntryId=49686&PortalId=0&TabId=105

• Jacob Barhak, Python Based Standardization Tools for ClinicalTrials.Gov. Combine 2018 . Boston University. October 8-12, 2018.  Poster: http://co.mbine.org/system/files/COMBINE_2018_Barhak.pdf

• Jacob Barhak, Chris Myers, Leandro Watanabe, Lucian Smith, Maciek Jacek Swat , Healthcare Data and Models Need Standards. Simulation Interchangeability Standards Organization (SISO) 2018 Fall Innovation Workshop.  9-14 Sep 2018 Orlando, Florida.  Presentation: https://www.sisostds.org/DesktopModules/Bring2mind/DMX/API/Entries/Download?Command=Core_Download&EntryId=47969&PortalId=0&TabId=105 and https://jacob-barhak.github.io/old/SISO_SIW_2018_08_14.pptx

•  J. Barhak, A. Garrett, Evolutionary Computation Examples with Inspyred. PyCon Israel Bar Ilan University, June 4-5, 2018, Abstract:  https://il.pycon.org/2018/schedule/presentation/38/  Presentation: https://jacob-barhak.github.io/old/PyConIsrael_2018_06_04.odp  Video: https://youtu.be/PPpmUq8ueiY 

• J. Barhak, Visualization and Pre-Processing of Intensive Care Unit Data Using Python Data Science Tools. MODSIM world 2018. 24-26 Apr. Norfolk,Virginia. Paper: http://www.modsimworld.org/papers/2018/MODSIM_2018_Barhak.pdf   Presentation: https://jacob-barhak.github.io/old/BarhakMODSIM_2018_04_25.odp   GitHub: https://github.com/Jacob-Barhak/VisICU   Results: https://jacob-barhak.github.io/VisualICU.html  

•  J. Barhak, The Reference Model Visualizes Gaps in Computational Understanding of Clinical Trials, 2018 IMAG Futures Meeting March 21-22, 2018 @ NIH, Bethesda, MD. https://jacob-barhak.github.io/old/Poster_IMAG_MSM2018_Map_Upload_2018_03_17.pdf 

• J. Barhak, The Reference Model: A Decade of Healthcare Predictive Analytics with Python, PyTexas 2017, Nov 18-19, 2017, Galvanize, Austin TX.  Presentation: https://jacob-barhak.github.io/old/PyTexas2017_Upload_2017_11_18.pptx Video: https://youtu.be/Pj_N4izLmsI 

• J. Barhak, The Reference Model Models ClinicalTrials.Gov. SummerSim 2017 July 9-12, Bellevue, WA. Paper: https://doi.org/10.22360/SummerSim.2017.SCSC.022   http://dl.acm.org/citation.cfm?id=3140087 Presentation: https://jacob-barhak.github.io/old/SummerSim2017_Upload_2017_07_09.pptx 

• J. Barhak, The Reference Model Predicting Life Expectancy for Diabetics, MODSIM world 2017. 26-28 Apr, Virginia Beach Convention Center, Virginia Beach, VA. Paper: https://www.modsimworld.org/papers/2017/The_Reference_Model_Predicts_Life_Expectancy_for_Diabetics.pdf  Presentation:   https://jacob-barhak.github.io/old/MODSIM2017_Submit_2017_04_25.pptx 

• J. Barhak, The Reference Model Estimates Medical Practice Improvement in Diabetic Populations. SpringSim 2017 April 12 - 15, Alexandria, VA, USA. Paper: https://doi.org/10.22360/SpringSim.2017.MSM.006       http://dl.acm.org/citation.cfm?id=3108762   Presentation:   https://jacob-barhak.github.io/old/SpringSim2017_Present_2017_04_25.pptx    

•  J. Barhak, The Reference Model Interface with ClinicalTrials.Gov  , IMAG Multiscale Modeling (MSM) Consortium Meeting March 22-24, 2017 @ NIH, Bethesda, MD. https://jacob-barhak.github.io/old/PosterImportClinicalTrialsGov_IMAG_MSM2017_Upload_2017_03_18.pdf 

• 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: https://jacob-barhak.github.io/old/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: https://jacob-barhak.github.io/old/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. Paper:  http://dl.acm.org/citation.cfm?id=3015579  https://doi.org/10.22360/SummerSim.2016.SCSC.010 Presentation: https://jacob-barhak.github.io/old/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: https://www.modsimworld.org/papers/2016/Optimizing_Model_Combinations.pdf  Presentation: https://jacob-barhak.github.io/old/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: https://jacob-barhak.github.io/old/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:  https://jacob-barhak.github.io/old/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: https://jacob-barhak.github.io/old/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: https://jacob-barhak.github.io/old/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: https://modsimworld.org/papers/2015/Object_Oriented_Population_Generation.pdf Presentation: https://jacob-barhak.github.io/old/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: https://jacob-barhak.github.io/old/PosterPopulationGenerationMIST_IMAG_MSM2014_Upload_2014_08_31.pdf 

• J. Barhak, The Reference Model for Disease Progression – Data Quality Control. SummerSim 6-10 July 2014, Monterey CA. Paper: http://dl.acm.org/citation.cfm?id=2685666  Presentation: https://jacob-barhak.github.io/old/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: https://jacob-barhak.github.io/old/MH2014TheReferenceModel_Submit_2014_06_15.pptx 

• J. Barhak, The Reference Model for Disease Progression uses MIST to find data fitness.  PyData Silicon Valley 2014 held at Facebook Headquarters: Abstract: http://pydata.org/sv2014/abstracts/#195_  Presentation: https://jacob-barhak.github.io/old/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: https://jacob-barhak.github.io/old/MODSIM2014_MIST_INSPYRED_Paper_Submit_2014_03_10.pdf   Presentation: https://jacob-barhak.github.io/old/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: https://jacob-barhak.github.io/old/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: https://jacob-barhak.github.io/old/SciPy2013_MIST_Presented_2013_06_26.pptx Video of Talk: https://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. https://jacob-barhak.github.io/old/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: https://jacob-barhak.github.io/old/MODSIM_World2013_Submitted_04Apr2013.pdf , Presentation: https://jacob-barhak.github.io/old/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:  http://www2.cs.uh.edu/~cosine/talks_cosine4/monday/MultidisciplinaryTalks/2_JacobBarhak.pptx  Slides Copy: https://jacob-barhak.github.io/old/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: https://jacob-barhak.github.io/old/PosterTheReferenceModel_IMAGE_MSM_Submit_2012_10_17.pdf 

• J. Barhak, The Reference Model for Disease Progression. SciPy 2012, Austin Tx, 18-19 July 2012. Paper: http://dx.doi.org/10.25080/Majora-54c7f2c8-007 ,  https://github.com/Jacob-Barhak/scipy_proceedings/blob/2012/papers/Jacob_Barhak/TheReferenceModelSciPy2012.rst, Poster: https://jacob-barhak.github.io/old/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.

• 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:

• Jacob Barhak, The Reference Model for COVID-19 attempts to explain US data. Orlando Machine Learning and Data Science 18 June 2022,  https://www.meetup.com/orlando-mlds/events/286278255/. Presentation: https://jacob-barhak.github.io/COVID19_Ensemble_Latest.html 

• Jacob Barhak, The Reference Model for COVID-19 attempts to explain US data. Austin Python meetup, 13 April 2022, https://www.meetup.com/austinpython/events/lgrbmqydcgbrb/  , Video: https://youtu.be/BXVbvDCD4lk 

• Jacob Barhak. How Dask Helped Model Diseases and Specifically COVID-19. Blog at Coiled. June 23, 2021 https://coiled.io/how-dask-helped-model-diseases-and-specifically-covid-19/

• Jacob Barhak, The Reference Model Accumulates Knowledge With Human Interpretation. MSM Working Group on MULTISCALE MODELING AND VIRAL PANDEMICS. Miniseminar, Dec 3, 2020. Video: https://youtu.be/aTB8-XEZheU  , Presentation: https://jacob-barhak.github.io/Poster_MSM_IMAG_2020.html 

• J. Barhak, J. Bednar, Using Python HoloViz Technologies to Create Interactive Presentations, COMBINE 2020 October 5-9. Presentation:  https://jacob-barhak.github.io/Presentation_COMBINE2020_HoloViz.html  Video: https://youtu.be/a0IWsCNvlgA 

• Christine Mary, Doreen Darsh, Lisbeth Garassino, Jacob Bahak. Improved Disease Modeling Tools for Populations . Pandemic Response Hackathon.  Online: March 27-29 2020,  https://devpost.com/software/improved-disease-modeling-tools-for-populations

• J. Barhak, J. Schertz. Evolutionary Computation. Austin Algorithms MeetupClustering and Self Organization, 10 Feb 2020,  https://www.meetup.com/Austin-Algorithms-Meetup/events/267755116/ Presentation: https://jacob-barhak.github.io/Presentation_Galvanize_Austin_2019_01.html 

• J. Barhak, J. Schertz. Visualizing Machine Learning for Healthcare using HoloViz. Austin Data Science, Galvanize 28 Jan 2020. https://www.meetup.com/Austin-Data-Science/events/267700544/

• Comment from Jacob Barhak Posted by the Food and Drug Administration on May 16, 2019 - https://beta.regulations.gov/document/FDA-2019-N-1185-0031 

• J. Barhak, A. Garrett, A. Blumer, O. Dammann. Evolutionary Computation. Austin Algorithms Meetup, 9 Dec 2019,  https://www.meetup.com/Austin-Algorithms-Meetup/events/263929782/

• J. Barhak, The Reference Model for Disease Progression & Clinical Unit Standardization. SISO ENGTAM Webinar 7th May 2019. Video: https://www.youtube.com/watch?v=t8AAWpaMMVI

• J. Barhak, The Reference Model and Associated Technologies Towards Computational Accumulation of Medical Knowledge, GE Healthcare Sepsis Journal Club 20th August 2019. Presentation: https://jacob-barhak.github.io/Presentation_GE_Healthcare2019.html Video: https://zoom.us/recording/share/Ccr2V6Z7hFfIXUAQOHfBODFbAVRDWD4ZEThkVYa0LcywIumekTziMw  

• J. Barhak, 50 Summers of Computer Simulation (Panel) - Seasons of Disease Modeling, Austin, Texas, SummerSim 2018, July 9-12, 2018 Bordeaux, France. https://jacob-barhak.github.io/old/SummerSim2018_Panel_2018_07_09.pdf 

• J. Barhak, The MIcro Simulation Tool (MIST) used for Disease Modeling and Population Generation – Tutorial. SummerSim 2017 July 9-12, Bellevue, WA. https://jacob-barhak.github.io/old/SummerSim_Tutorial_MIST_Upload_2017_07_09.pptx 

• J. Barhak, The MIcro Simulation Tool (MIST) - The MIcro Simulation Tool (MIST) used for Disease Modeling and Population Generation – Tutorial. SummerSim 2016 9-12 July, Bellevue, WA. 

• J. Barhak, The Reference Model for Disease Progression, Healthcare Predictive Analytics Meetup, Austin, Texas, 19-Jan-2017.  https://jacob-barhak.github.io/old/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, The MIcro Simulation Tool (MIST) - How to create basic disease models – Tutorial. SummerSim 2016 24-27 July, Montreal, CA. Presentation: https://jacob-barhak.github.io/old/SummerSim_Tutorial_MIST_Given_2016_07_24.pptx 

• J. Barhak, StarCluster Demo at the Austin Web Python Users Group: https://www.meetup.com/austinwebpythonusergroup/events/231188161/ Video: https://www.youtube.com/watch?v=wpfw8POx-wI 

• 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:  https://inscightpodcast.wordpress.com/2013/10/19/episode-32-code-reproducibility-and-open-source/

• J. Barhak, Austin Machine Learning Group presentation 31-July-2013: https://jacob-barhak.github.io/old/AustinMachineLearningMeetup_Present_2013_07_31.pptx 

• 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: https://jacob-barhak.github.io/old/PublicResponseLetterToModelingGoodResearchPracticesTaskForce_Upload_17Apr2013.pdf 

• Barhak J., The Reference Model in the Mount Hood #6-2012 validation challenge and the uncertainty challenge. The Mt hood challenge 6, June 7-8, 2012. Johns Hopkins Mt. Washington Conference Center.

• Herman W.H., Barhak J., Brown M.B., Lee J.M., Prosser L.A., Ye W., Presented the Michigan Model on behalf of the Michigan Modeling team in the Mount Hood 5 validation challenge and the uncertainty challenge. The Mt hood challenge 5, September 18-19, 2010, Malmo, Sweden.

• J. Barhak: Python in Science: Chronic Disease Modeling Software. Lightning talk in PyOhio, Colombus, OH, USA, 25-July-2009, available online at https://www.blip.tv/file/2517728   (near the end of the video)

• J. Barhak: Python in Science: Chronic Disease Modeling Software.  Michigan Python Users Group, Ann Arbor, MI, USA, 6-August-2009

• J. Barhak: Chronic Disease Modeling Software and the Michigan Model for Diabetes.  University of Alberta, Edmonton, AL, Canada, 21-August-2009

• J. Barhak: Chronic Disease Modeling Software and the Michigan Model for Diabetes. University of California Merced, Merced, CA, USA, 28-August-2009

• J. Barhak: Chronic Disease Modeling Software and the Michigan Model for Diabetes.  Cornell University. Ithaca, NY, USA, 2-Nov-2009 

• J. Barhak, D.J.M. Isaman, Software for Statistical Estimation and Simulation of Chronic Disease Progression Using Markov Models. January 30th 2008, IOE 899 Seminar Series, Industrial and Operations Engineering, University Of Michigan

• Yoram Koren, Jacob Barhak, Zbigniew Pasek, Method and apparatus for re-configurable vehicle interior design and business transaction , US Patent Application: US 20070156540 A1. https://www.google.com/patents/US20070156540 

• J. Barhak, A. Fischer, Parameterization and Surface Fitting Of Range Images, Israeli Computer Graphics Forum, Tel Aviv, Israel, February 18th 2000.

• J. Barhak, A. Fischer, Reconstruction of Freeform Objects with 3D SOM Neural Networks. CGGC seminar, Haifa - Israel, March 20th 2002.

• J. Barhak, A. Fischer, F. L. Krause, N. Gross, Artificial Neural Network Techniques for Reverse Engineering. CIRP general assembly, STC - Dn, Montreal Canada, August 29th 2003.

• J. Barhak, Geometry Approximation and Topology Detection Using Neural Networks. CGGC seminar, Haifa - Israel, December 1st 2004.

• J. Barhak, Event Report - GRAPP 2006 International Conference on Computer Graphics Theory and Applications. Computer Graphics Forum, Vol 25, No 4. pp. 837, 2006. Online: https://dx.doi.org/10.1111/j.1467-8659.2006.01001.x 

Old style Journal Publications:

• Karr Jonathan, Malik-Sheriff Rahuman S., Osborne James, Gonzalez-Parra Gilberto, Forgoston Eric, Bowness Ruth, Liu Yaling, Thompson Robin, Garira Winston, Barhak Jacob, Rice John, Torres Marcella, Dobrovolny Hana M., Tang Tingting, Waites William, Glazier James A., Faeder James R., Kulesza Alexander.  Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility. Frontiers in Systems Biology, Vol 2. 2022. https://doi.org/10.3389/fsysb.2022.822606

• Barhak J , The Reference Model Initial Use Case for COVID-19. Cureus.  https://dx.doi.org/10.7759/cureus.9455 , Online: https://www.cureus.com/articles/36677-the-reference-model-an-initial-use-case-for-covid-19 . PMCID: PMC7392354 , PMID: 32760637 , Interactive Results: https://jacob-barhak.netlify.app/thereferencemodel/results_covid19_2020_06_27/combinedplot 

• L. Watanabe, J. Barhak, C. Myers, Towards Reproducible Disease Models using the Systems Biology Markup Language.  Simulation 2018.  https://dx.doi.org/10.1177/0037549718793214  Accompanying Source code: https://github.com/Jacob-Barhak/DiseaseModelsSBML 

• 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. https://dx.doi.org/10.1177/0037549716673729 

• W. Ye., J. Barhak, 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, https://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, https://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: https://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:  https://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: https://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: https://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: https://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: https://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: https://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: https://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: https://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: https://doi.ieeecomputersociety.org/10.1109/2945.910817 

Book Chapters:

• Authors: Umut Durak, Andrea D’Ambrogio, Andreas Tolk, Saikou Diallo, Gregory Zacharewicz, José L. Risco-Martín, Jacob Barhak, Ralph Coolidge Huntsinger, M. S. Raunak, 50 Summers of Computer Simulation. Summer of Simulation, pp.1-24, 2019, 10.1007/978-3-030-17164-3_1. hal-02126923f  https://doi.org/10.1007/978-3-030-17164-3 and https://hal.archives-ouvertes.fr/hal-02126923 

Technical Reports:

• • 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.

Teaching:

• • Lecturer: ME454 “Computer Aided Mechanical Design”, University of Michigan (2006).

  • Lecturer: 35003 “Interactive Computer Graphics and Introduction to CAD”, Technion (2002).

Now 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: