[Population Modeling] PopModWkGrpIMAG-news Digest, Vol 12, Issue 1

Thu Oct 1 09:52:51 PDT 2015

Swimming in deep water for me, but ....
There may be many assumptions.  Some are inserts to the model but others may be omissions.  Omissions by choice or by oversight. The later may be most problematic since they may be oversights of which the modeler is just not aware. (These become objects to be discovered and disclosed in peer review and testing).  

MOST IMPORTANT is that the potential for reuse of any models requires that ALL consciousness assumptions of inclusion or omission be DOCUMENTED in great detail.   

One can see the code and make a decision that it is creditable for ones reuse or adaptation.  But if all assumptions know to the model's creator are not documented, the models creditability  for reuse becomes difficult if not impossible to establish.  

Although the cost (time and attention) required to capture all assumptions of new models is not trivial, experience of the Defense Department's failed model repositories showed that the cost of retroactively capturing, understanding and considering assumptions after models were complete was far greater, most often resulting in paying for new models as less expensive and safer.

At a minimum, even for the original model developer, clearly documents assumptions call attention to the need for new data/facts to gradually replace the original assumptions.

An all inclusive taxonomy for simply classifying different kinds of assumptions might be helpful.  It could be extremely beneficial if there were some kind of "meta-code" for capturing, and communicating model assumption to other potential users of a model or even to somehow communicate assumptions to other computational environments in ways that would call attention to possibly flawed assumption in the reuse application.  

John

Typed with two thumbs on my iPhone.  (757) 318-0671

The master in the art of living makes little distinction between his work and his play, ,,, He simply pursues his vision of excellence at whatever he does, leaving others to decide whether he is working or playing."
James A. Michener (1907 – 1997)

> On Oct 1, 2015, at 5:05, popmodwkgrpimag-news-request at simtk.org wrote:
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> Today's Topics:
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>   1. Re: Parameter estimation for population models (Jacob Barhak)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 30 Sep 2015 17:52:34 -0500
> From: Jacob Barhak <jacob.barhak at gmail.com>
> To: Matthias Chung <mcchung at vt.edu>
> Cc: "IMAG \(popmodwkgrpimag-news at simtk.org\)"
>    <popmodwkgrpimag-news at simtk.org>
> Subject: Re: [Population Modeling] Parameter estimation for population
>    models
> Message-ID:
>    <CAM_y+3QXjthdodTJ-UTBaQ=JRpBoJTxRQVzo0O5cWR4p49kFxg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Thanks Mattias,
> 
> Estimation of model parameters is an important topic. You will find that
> most of us in the list, had to deal with such issues.
> 
> It is commendable that you decided to share code - model reproducibility is
> important. You may want to follow the discussion on the data and model
> sharing group they have interesting ways of coding differential equation
> models that help sharing those. This may be helpful in the future,
> 
> Glancing at the paper, I see you took an approach of simplifying the
> problem to allow solution. Many of us use assumptions. In fact,  the model
> structure we use is an assumption as well. So there is a level of human
> judgment embedded in the estimation method. Although in your case it is
> small.
> 
> I am curious how other people in the list estimate model parameters. I
> encountered several approaches in the past that build a spectrum of
> estimation techniques that can be characterized by amount of human decision
> making.
> 
> One interesting end of the spectrum was reported by Steve Leff, where human
> experts go thorough a controlled process to determine parameters. Steve may
> want to elaborate on this technique. And I also know he used other
> techniques in the past as well from other sides of this estimation spectrum.
> 
> In the middle of the spectrum some modelers just picking numbers reported
> in the literature to drive models.
> 
> On the other extreme spectrum end, there are robust mathematical estimation
> techniques that rely on computation once the model is defined. The paper
> Matthias attached falls near this end of the spectrum.
> 
> Where do modelers in this group find themselves? Do you rely more on human
> judgment for estimation? Or do you find yourself on the end of relying on
> numerical techniques?
> 
> I hope people choose to share experiences and insights.
> 
>                Jacob
> 
> 
>> On Wed, Sep 30, 2015 at 9:42 AM, Matthias Chung <mcchung at vt.edu> wrote:
>> 
>> Hi everyone,
>> 
>> Some of you might be interested in parameter estimation in population
>> dynamic models. We developed a new efficient and robust estimation code in
>> Matlab to ?match? data with a differential equation model. We provide the
>> code here:
>> 
>> http://www.math.vt.edu/people/mcchung/resources/Continuous_Shooting.zip.
>> 
>> The associated preprint can be found here:
>> http://arxiv.org/abs/1509.06926
>> 
>> Thanks,
>> 
>> Matthias Chung
>> 
>> ------
>> Matthias Chung
>> 
>> Department of Mathematics, Virginia Tech
>> McBryde, RM 474
>> 225 Stanger Street
>> Blacksburg, VA 24061
>> 
>> Phone: +1 (540) 231-3446
>> Fax : +1 (540) 231-5960
>> www.math.vt.edu/people/mcchung
>> 
>> 
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