[Vp-integration-subgroup] About using a multi-scale mortality model in the ensemble

[Jacob Barhak]

Well Filippo,

Since the discussion is relevant to the comorbidities subgroup and to the
integration subgroup, you will find both mailing lists CCd. I suggest we
try to keep this discussion public and merge it with the working group
activities. I believe others will find interest in this discussion as it
may be relevant to their activities. I am copying the entire email
conversation below.

To your question about if I am suggesting to use your whole model to
simulate mortality?

The answer is: almost.

Your model has important utility towards calculating mortality. However, I
only need your output at this point. What I am asking for is the output of
your model as a function. Something like:

probability_death  = f (days since infection)

And at this initial point f does not have to be in functional form. It is
enough for simulation purposes to have an x,y table where x is from 0 to 60
in days for each day and the associated mortality probability.

And it is ok if you give me several assumptions with different cutoff
values in your model.

The ensemble model will balance those assumptions with other models and
assumptions. If the assumptions do not merge well with other
assumptions/models, the ensemble model should assign them less influence.

So if you can use the model you showed at the webinar to derive different
mortality functions and send those to me as a table - it will be great.

However, please also make sure you give me permission to use those for
commercial purposes - I do intend to monetize my technology and therefore
avoid using information that has restrictions. I did declare a conflict of
interest and I am making it public. However, I hope we can still
collaborate.

               Jacob

--
Jacob Barhak Ph.D.
Sole Proprietor, Software Developer, and Computational Disease Modeler
https://sites.google.com/view/jacob-barhak/home




On Sun, Dec 20, 2020 at 2:40 AM Filippo Castiglione <
filippo.castiglione at gmail.com> wrote:

> Dear Jacob, sure this conversation is open.
>
> Coming back to the mortality model question are you suggesting to use my
> whole model to simulate mortality? If yes, then It is possible at the
> condition that we define when the simulation should stop for “death”.
>
>
> Best
>
> --- Filippo (@iPhone)
>
> On 19 Dec 2020, at 21:48, Jacob Barhak <jacob.barhak at gmail.com> wrote:
>
> 
> Thanks Filippo,
>
> Yes, you are correct, the mortality models are not accurate. All models
> are assumptions - none of them are really accurate. The Reference Model was
> built to figure out how well they perform and provide a reference modelers
> can compare their models to.
>
> Your suggestions make sense and in fact I already have several mortality
> models plugged into my model. Yet those are simplified and not multi
> scale models.
>
> The value in your approach is that it makes this multi scale - if you
> would plug your model in the ensemble and the ensemble will prefer it to
> other models - this will give the multi scale model validation of sorts.
>
> And with your permission, I would like to add this conversation to the
> co-morbidities mailing list that I plan to create or to the integration
> mailing list in the integration working group portal:
> https://lists.simtk.org/pipermail/vp-integration-subgroup/
>
> Hopefully you are ok with making this conversation public and part of the
> working group discussions.
>
>              Jacob
>
>
>
> On Sat, Dec 19, 2020 at 2:48 AM Filippo Castiglione <
> f.castiglione at iac.cnr.it> wrote:
>
>> Hi Jacob.
>>
>> The only thing I feel to suggest is to use survival curves of covid
>> patients. I don’t know if you can recall them somewhere from clinical
>> available data (e.g.,
>> https://bmcpublichealth.biomedcentral.com/articles/10.1186/s12889-020-09721-2).
>>
>> You might be interested in age-related of such curves (Kaplan-Meier
>> curves plot 1-P(death)).
>>
>> I might calculated them starting from my simulations but they would be
>> inaccurate because based on an artificial definition of “death” that, of
>> course, I don’t have. Let me know if you want to try it anyway but I
>> suggest to look for them around.
>>
>> Another very simple stylised model of mortality would be to use a reverse
>> sigmoid function to represent the upside-down sigmoid shape (long right
>> tail) of a generic Kaplan-Meier plot centred around the "typical value”
>> time of death. For instance such t could be in the range 7-15 days, for
>> instance, 1-0.2/(1+exp(7-x)) where 1-0.2 is the asymptotic value and 7 is
>> the typical death t.
>>
>> Let me know if I expressed my thoughts clearly.
>>
>> All the best
>> Fil
>>
>> > On 18 Dec 2020, at 18:38, Jacob Barhak <jacob.barhak at gmail.com> wrote:
>> >
>> > Hi Filippo,
>> >
>> > Following your talk at the webinar yesterday, you may recall that I was
>> interested in a mortality model based on time.
>> >
>> > I wanted to communicate with you about it to see what is possible.
>> >
>> > I am looking for models to plug into my ensemble model. You can see
>> quickly how it looks in this video - I am pointing at the point where I
>> show some ensemble results:
>> > https://youtu.be/aTB8-XEZheU?t=1000
>> >
>> > I am actively looking for several types of models to integrate into my
>> model. One of the models can be mortality models.  Currently I use two
>> different models for mortality - one of overall risk and one for death. I
>> do not have a probability of death per day from infection and looking at
>> your plots I figured you may have something - even at a level of an
>> assumption.
>> >
>> > Do you think it is possible to get such models from you and if so,
>> under what terms?
>> >
>> > Hopefully you can help.
>> >
>> >                Jacob
>> >
>> >
>> >
>> > On Mon, Dec 7, 2020 at 7:57 AM Jacob Barhak <jacob.barhak at gmail.com>
>> wrote:
>> > Ok Filippo,
>> >
>> > You are in a similar situation to many others.
>> >
>> > Your situation is very common and well understood.
>> >
>> >         Jacob
>> >
>> > On Mon, Dec 7, 2020, 02:37 Filippo Castiglione <
>> f.castiglione at iac.cnr.it> wrote:
>> > Dear Jacob, sorry for the late response.
>> >
>> > I recently realised I had subscribed to too many groups to be
>> practically able to follow, so opted out from many of them included the
>> comorbidity. I asked Bruce to update the groups’ lists.
>> >
>> > All the best
>> > Fil
>> >
>> > > On 6 Dec 2020, at 06:23, Jacob Barhak <jacob.barhak at gmail.com> wrote:
>> > >
>> > > Hi Filippo,
>> > >
>> > > You were listed as interested in comorbidities within the viral
>> pandemic working group. I am going over each member personally to see why
>> they signed up.
>> > >
>> > > I looked at your web site:
>> > >
>> > > https://www.iac.cnr.it/~filippo/about-me.html
>> > >
>> > > Your interest in co-morbidities is visible directly from what you
>> state in your web site:
>> > > "particular interest in the immune system and related pathologies"
>> > >
>> > > I wonder why you did not respond to my email to step up and co-lead
>> this sub-working group. After all you have many publications and experience
>> in leadership.
>> > >
>> > > Hopefully my personal email will get a response.
>> > >
>> > >              Jacob
>> > >
>> > > --
>> > > Jacob Barhak Ph.D.
>> > > https://sites.google.com/view/jacob-barhak/home
>> > >
>> >
>>
>>
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