[Vp-reproduce-subgroup] About taxonomies

Tue May 18 16:16:09 PDT 2021

Actually John,

There are taxonomies in some fields. Here is an older paper:
http://www.medicine.mcgill.ca/epidemiology/courses/EPIB654/Summer2010/Modeling/Brennan2006.pdf

Perhaps its time to renew it and add newer techniques and extend it to more
fields, yet taxonomies do exist.

        Jacob

On Tue, May 18, 2021 at 4:44 PM John Rice <john.rice at noboxes.org> wrote:

> Ah. TAXONOMIES!
>
> Which kind of models require how much of what?  But we don’t know what
> kinds of models exist.   And we don’t know what each other might be
> thinking about when we say “models need ….”
>
> I suspect a similar problem talking about “valid”.  What kind of validity:
>
>
> Content
>
> Construct
>
> Convergent
>
> Discriminant
>
> Predictive
>
> Diagnostic
>
> Face
>
> Experimental
>
> Criterion
>
> Internal
>
> External
>
> Concurrent
>
> Sample
>
> Representational
>
> Presentational
>
> Translational
>
> ????
>
>
> Just things to have to work around for A paper.
>
>
> Typed with two thumbs on my iPhone.  (757) 318-0671
>
> “Upon this gifted age, in its dark hour,
> Rains from the sky a meteoric shower
> Of facts . . . they lie unquestioned, uncombined.
> Wisdom enough to leech us of our ill
> Is daily spun; but there exists no loom
> To weave it into fabric.”
>
> –Edna St. Vincent Millay,
>
>
>
> On May 18, 2021, at 16:25, Jacob Barhak <jacob.barhak at gmail.com> wrote:
>
> 
> Yes William,
>
> Winston is right, there are multiple types of operator and those extend
> beyond math definition. In fact ensemble models use multiple compositions
> methods - your own simple example that you shown a few week ago on this
> mailing list needs to be extended to many more examples - I think
> composition methods are a topic for a paper on its own with many examples.
> For now allow me to be happy to see this conversation.
>
>              Jacob
>
> On Tue, May 18, 2021 at 3:19 PM William Waites <wwaites at ieee.org> wrote:
>
>> Winston, you have hit the nail on the head! Maybe we would want to think
>> of two basic kinds of combination operator, loosely, one that composes in
>> models series and one that does this in parallel. And maybe think of these
>> as a coproduct and product in a monoidal category. As you say, specifying
>> the object of that category precisely, and defining these operations
>> properly to be able to get an algebra of models (for at least some kinds of
>> model, and we do actually have this for some kinds) is the tricky bit.
>>
>> I’d also like to contribute to #9 and also the one about stochastic
>> models.
>>
>> Cheers,
>> -w
>>
>>
>> > On 18 May 2021, at 21:01, Winston Garira <Winston.Garira at univen.ac.za>
>> wrote:
>> >
>> > I could not attend the zoom meeting because there was another meeting
>> with graduate students at  the same time.  I have read through the
>> interesting communications that have been ongoing since yesterday from the
>> subgroup. I will be able to contribute and edit challenge 9:  "Environments
>> to adapt and integrate models". Already an interesting discussion has  been
>> initiated in the form of  the following statements:
>> >
>> > >If you separately accredit M1 and M2 for your purpose, and they fit
>> together like lego, it does not >automatically mean that M1 + M2 is
>> credible. One of the things we would like to know is, what >properties must
>> M1 and M2 have for us to safely believe that we understand what M1 + M2
>> does. We >only know this for a few special cases today.
>> >
>> > Two issues need consideration here. If M1and M2 are different models
>> describing phenomena at the same scale, then perhaps this is the few
>> special cases where we may know that  M1+M2 is credible. This is because
>> “+” is much easier to define in that case. However, if M1 and M2 describe
>> phenomena at different scales then  the problem of  defining  “+” becomes
>> even more challenging. Defining “+” involves defining methods for
>> linking/coupling/integrating  models from the different  scales.   For
>> multiscale modelling, the different  scales  indicate/represent
>> shifts/changes/transitions in  processes for the complex system under
>> consideration and we do not know in general how scale transition occurs.
>> For example in infectious disease dynamics there is usually pathogen
>> replication at the microscale scale and pathogen  transmission at the
>> macroscale [1].  There is no single unique  and widely acceptable
>> method/way of defining “+” or integrating models for a given M1 and M2.  In
>> the past, I have considered the different ways in which to define “+”
>>  when M1 and M2 describe infectious disease phenomena at different scales
>> (i.e the microscale and macroscale). This enabled me to come up with 5
>> different categories of multiscale  models of disease dynamics [2,3].  So
>> even if  M1 and M2  have the correct properties we may not safely  believe
>> what M1 + M2 does because there  is still an additional  challenge of
>> identifying  the correct “+” which turns out to be the greatest challenge
>> in multiscale modelling.
>> >
>> > [1.] Garira, W. (2019). The Replication-Transmission Relativity theory
>> for Multiscale Modelling of infectious Disease Systems. Scientific reports,
>> 9(1), 1-17.
>> > [2.] Garira, W. (2017). A complete categorization of multiscale models
>> of infectious disease systems. Journal of biological dynamics, 11(1),
>> 378-435.
>> > [3.] Garira, W. (2018). A primer on multiscale modelling of infectious
>> disease systems. Infectious Disease Modelling, 3, 176-191.
>> >
>> > Winston Garira, PhD
>> > DEPARTMENT OF MATHEMATICS AND APPLIED MATHEMATICS
>> > Modelling Health and Environmental Linkages Research Group (MHELRG)
>> > University of Venda, Private Bag X5050, Thohoyandou 0950, South
>> Africa.
>> > Email(1): winston.garira at univen.ac.za, Email(2): wgarira at gmail.com
>> >
>> > From: Jacob Barhak <jacob.barhak at gmail.com>
>> > Sent: Tuesday, 18 May 2021 17:17
>> > To: William Waites <wwaites at ieee.org>
>> > Cc: Tomas Helikar <thelikar2 at unl.edu>;
>> vp-reproduce-subgroup at lists.simtk.org <
>> vp-reproduce-subgroup at lists.simtk.org>;
>> vp-integration-subgroup at lists.simtk.org <
>> vp-integration-subgroup at lists.simtk.org>; Winston Garira <
>> Winston.Garira at univen.ac.za>; Faeder, James R <faeder at pitt.edu>
>> > Subject: Re: [Vp-integration-subgroup] [EXT] Re: White paper revision
>> >
>> > So William,
>> >
>> > For now, you should just claim the sections you wish to edit - I think
>> your name is mentioned already, yet check out the rest of the sections.
>> This will give John a picture of who he has to satisfy when he makes edits.
>> >
>> > Once he has a full picture we can start actual editing. He will decide
>> where edits go - I suggested using the existing version so changes are
>> reflected in one location and we will have a traceable track of changes -
>> if he prefers another link it's fine - yet I asked him to secure the
>> document and provide links to older versions the document is derived from.
>> It is after all a paper about reproducibility. And I did experience
>> security issues in the past in collaborative work that needed treatment, so
>> this is why I asked for those. You really do not want an anonymous animal
>> using your public document as it sees fit - remember that our conversations
>> are public as well as the links.
>> >
>> > He promised 2 weeks and I do not envy him if he has to go through the
>> history of contributions and locate authors who contributed to each
>> section, this is why we are declaring what sections are are interested in -
>> Sheriff suggested this yesterday. So please just look at the sections John
>> mentioned with his numbering and declare what you want to edit. Once we all
>> claimed sections, John can more easily decide what to edit and how without
>> facing potential objections.
>> >
>> > I hope this makes sense now and you know your next move.
>> >
>> >           Jacob
>> >
>> >
>> >
>> >
>> >
>> >
>> > On Tue, May 18, 2021 at 9:57 AM William Waites <wwaites at ieee.org>
>> wrote:
>> >
>> > > On 18 May 2021, at 15:30, Tomas Helikar <thelikar2 at unl.edu> wrote:
>> > >
>> > > Since John is taking the lead on the new version, my suggestion is to
>> let him do it the way that will be most efficient for him. I think
>> everyone, including John, have noted your concerns.
>> >
>> > I agree. But I am also now completely confused about which document it
>> is ok for who to edit when.
>> >
>> > -w
>>
>> _______________________________________________
> Vp-reproduce-subgroup mailing list
> Vp-reproduce-subgroup at lists.simtk.org
> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.simtk.org/pipermail/vp-reproduce-subgroup/attachments/20210518/fd859bab/attachment.html>