[Vp-reproduce-subgroup] [Vp-integration-subgroup] [EXT] Re: White paper revision

[William Waites]

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