research-article

The reference model uses object oriented population generation

Author:

Jacob BarhakAuthors Info & Claims

SummerSim '15: Proceedings of the Conference on Summer Computer Simulation

Pages 1 - 6

Published: 26 July 2015 Publication History

Abstract

The Reference Model for disease progression is a league of models attempting to explain published study data. The model cross references simulation results with observed clinical results for multiple population cohorts. The model has grown to contain 47 different cohorts from 9 diabetic populations. Each population contains -40 rules and ~45 objectives. Since there are many repetitions and replications in the code, it becomes hard to maintain and expand further. To support future expansion, code reusability is needed. This is accomplished by an object oriented approach that allows inheriting population generation building blocks. The presentation will discuss the reorganization of population generation using the MIcro Simulation Tool - MIST. Examples demonstrating the benefit from the transformation towards the object oriented approach are presented. Results demonstrate model stability after code transformation.

References

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Brown J. B., Palmer A. J., Bisgaard P., Chan W., Pedula K., Russell A. The Mt. Hood challenge: cross-testing two diabetes simulation models. Diabetes Research and Clinical Practice, Volume 50, Supplement 3, Pages S57-S64, November 2000. ://dx.doi.org/10.1016/S0168-8227(00)00217-

[2]

The Mount Hood 4 Modeling Group. Computer Modeling of Diabetes and Its Complications A report on the Fourth Mount Hood Challenge Meeting. Diabetes Care June 2007 vol. 30 no. 6 1638--1646. ://dx.doi.org/10.2337/dc07-

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Palmer A. J., The Mount Hood 5 Modeling Group. Computer Modeling of Diabetes and Its Complications: A Report on the Fifth Mount Hood Challenge Meeting, Value in Health - June 2013 Vol. 16, Issue 4, Pages 670--685, ://dx.doi.org/10.1016/j.jval.2013.01.

[4]

Barhak J., The Reference Model for Disease Progression -- Data Quality Control. 6-10 July 2014, Monterey CA. Paper: ://dl.acm.org/citation.cfm?id= Presentation: ://sites.google.com/site/jacobbarhak/home/SummerSim2014_Upload_2014_07_06.

[5]

Barhak J., The Mount Hood Diabetes Challenge 2014. The Reference Model for Disease Progression - participated in the challenge, Stanford. Presentation: ://sites.google.com/site/jacobbarhak/home/MH2014TheReferenceModel_Submit_2014_06_15.

[6]

Barhak J., The Reference Model for Disease Progression uses MIST to find data fitness. PyData Silicon Valley 2014: Abstract: ://pydata.org/sv2014/abstracts/#195_ Presentation: ://sites.google.com/site/jacobbarhak/home/PyData_V_2014_Upload_2014_05_02.pptx Video: ://www.youtube.com/watch?v=

[7]

Barhak J., 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, 2013, Poster: ://sites.google.com/site/jacobbarhak/home/PosterTheReferenceModel_IMAG_MSM2013_Submit_2013_09_23.

[8]

Barhak J., The Reference Model Scores Fitness of Models and Populations. Poster Presentation. ISPOR 18th Annual International Meeting, 2013, Poster Presentation. ://sites.google.com/site/jacobbarhak/home/PosterTheReferenceModel_ISPOR_Submit_2013_05_14.

[9]

Barhak J., 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, 2012. Slides: ://sites.google.com/site/ComputationalSurgery_Presneted_2012_12_LateUploadToOwnWebSite_2014_2_27.

[10]

Barhak J., The Reference Model for Chronic Disease Progression. 2012 Multiscale Modeling (MSM) Consortium Meeting, 2012, Poster: ://sites.google.com/site/jacobbarhak/home/PosterTheReferenceModel_IMAGE_MSM_Submit_2012_10_17.

[11]

Barhak J., The Reference Model for Disease Progression. SciPy 2012. Paper: ://github.com/Jacob-Barhak/scipy_proceedings/blob/2012/papers/Jacob_Barhak/TheReferenceModelSciPy2012., Poster: ://sites.google.com/site/jacobbarhak/home/PosterTheReferenceModel_SciPy2012_Submit_2012_07_14. Open Review: ://github.com/scipy-conference/scipy_proceedings_2012/issues/

[12]

Barhak J., MIST: Micro-Simulation Tool to Support Disease Modeling. SciPy, (2013), Bioinformatics track, ://github.com/scipy/scipy2013_talks/tree/master/talks/jacob_, Presentation: ://sites.google.com/site/jacobbarhak/home/SciPy2013_MIST_Presented_2013_06_26. Video: ://www.youtube.com/watch?v=

[13]

Barhak J., Garrett A., Population Generation from Statistics Using Genetic Algorithms with MIST + INSPYRED. MODSIM World 2014, April 15-17, Hampton, VA. Paper: ://sites.google.com/site/jacobbarhak/home/MODSIM2014_MIST_INSPYRED_Paper_Submit_2014_03_10. Presentation: ://sites.google.com/site/jacobbarhak/home/MODSIM_World_2014_Submit_2014_04_11.

[14]

MIcro Simulation Tool (MIST) in GitHub: ://github.com/Jacob-Barhak/

[15]

Barhak J., Isaman D. J. M., Ye W., Lee D. (2010), Chronic disease modeling and simulation software, Journal of Biomedical Informatics, 43(5) 791--799, ://dx.doi.org/10.1016/j.jbi.2010.06.

Digital Library

[16]

Barhak J., Object Oriented Population Generation, MODSIM world 2015. 31 Mar -- 2 Apr, Virginia Beach Convention Center, Virginia Beach, VA. Paper: ://modsimworld.org/papers/2015/Object_Oriented_Population_Generation. Presentation: ://sites.google.com/site/jacobbarhak/home/MODSIM2015_Submit_Jacob_Barhak_2015_03_29.

[17]

UKPDS: UK Prospective Diabetes Study UKPDS Group, Intensive blood-glucose control with sulphonylureas or insulin compared with conventional treatment and risk of complications in patients with type 2 diabetes UKPDS 33, Lancet 352 (1998) 837--853, ://dx.doi.org/10.1016/S0140-6736(98)07019-

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Hunt C. A., Ropella G. E. P., Lam T., Gewitz A. D., Relational grounding facilitates development of scientifically useful multiscale models. Theoretical Biology and Medical Modelling 2011, 8:35. Online: ://www.tbiomed.com/content/8/1/

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Petersen B. K., Ropella G. EP. Hunt C. A. Toward modular biological models: defining analog modules based on referent physiological mechanisms. BMC Systems Biology 2014, 8:95 ://www.biomedcentral.com/1752-0509/8/

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Eddy D. M., Schlessinger L., Archimedes: a trial-validated model of diabetes. Diabetes Care. Nov 2003;26 (11) 3093--101

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Schlessinger L., Eddy D. M., Archimedes: a new model for simulating health care systems: the mathematical formulation, Journal of Biomedical Informatics 2002, 35 37--50, ://dx.doi.org/10.1016/S1532-0464(02)00006-

Digital Library

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PyMC @ Github PyMC 3 on Github (Online). ://github.com/pymc-devs/pymc/tree/

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Modelica and the Modelica Association. Online: ://www.modelica.org/

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Esperon D. G., Mehlhase A. Karbe T. (2015), Appending Variable-Structure to Modelica Models (WIP). SummerSim 2015

Digital Library

Cited By

Barhak J(2017)The reference model models clinicaltrials.govProceedings of the Summer Simulation Multi-Conference10.5555/3140065.3140087(1-12)Online publication date: 9-Jul-2017
https://dl.acm.org/doi/10.5555/3140065.3140087
Barhak J(2017)The reference model estimates medical practice improvement in diabetic populationsProceedings of the Symposium on Modeling and Simulation in Medicine10.5555/3108760.3108762(1-12)Online publication date: 23-Apr-2017
https://dl.acm.org/doi/10.5555/3108760.3108762

Index Terms

The reference model uses object oriented population generation

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Information

Published In

cover image ACM Conferences

SummerSim '15: Proceedings of the Conference on Summer Computer Simulation

July 2015

549 pages

ISBN:9781510810594

Co-chair:
Floriano De Rango
University of Calabria, Italy
,
Editors:
Saurabh Mittal
Dunip Technologies, LLC, Colorado, USA
,
Il-Chul Moon
KAIST, Korea
,
Eugene Syriani
University of Montreal, Canada
,
Program Chair:
José Luis Risco Martín
Universidad Complutense de Madrid, Spain
,
Publications Chair:
Deniz Cetinkaya
Atilim University, Turkey

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SIGSIM: ACM Special Interest Group on Simulation and Modeling
SCS: Society for Modeling and Simulation International

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Society for Computer Simulation International

San Diego, CA, United States

Publication History

Published: 26 July 2015

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SummerSim '15

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SummerSim '15: 2015 Summer Simulation Multiconference

July 26 - 29, 2015

Illinois, Chicago

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Cited By

Barhak J(2017)The reference model models clinicaltrials.govProceedings of the Summer Simulation Multi-Conference10.5555/3140065.3140087(1-12)Online publication date: 9-Jul-2017
https://dl.acm.org/doi/10.5555/3140065.3140087
Barhak J(2017)The reference model estimates medical practice improvement in diabetic populationsProceedings of the Symposium on Modeling and Simulation in Medicine10.5555/3108760.3108762(1-12)Online publication date: 23-Apr-2017
https://dl.acm.org/doi/10.5555/3108760.3108762

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