[Vp-reproduce-subgroup] White paper revision

Mon May 24 09:33:16 PDT 2021

Apologies John,

I misunderstood you and got worried - we are on the same page.

Thanks for clarifying.

           Jacob

On Mon, May 24, 2021 at 10:40 AM John Gennari <gennari at uw.edu> wrote:

>
> No, no no. I don't want to delete the table either!!
>
> There are now two copies of the table in the paper. I just meant that
> we'll eventually delete the older out-of-order table.
>
> -jhg
>
>
> On 5/24/2021 1:32 AM, Jacob Barhak wrote:
>
> And John,
>
> One more important thing,
>
> You mentioned deleting the table. I strongly object. Please keep the table
> in the paper - it's ok to have sections,yet the table is not a repetition,
> it is a necessary quick summary for those readers who do not have time to
> read the entire paper. In one table we summarize the issues and the
> potential solutions, so please do keep it - you can rephrase the text
> there, yet I think that it is important just like the image we have.
>
> Hopefully you now see the importance.
>
>            Jacob
>
> On Mon, May 24, 2021 at 3:07 AM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
>
>> Thanks John,
>>
>> Since you decided to work on the version you started from integration, I
>> repeat my request to secure the document and only allow editing by
>> permission from you.
>>
>> This means that people will have to use their accounts to view the
>> content of comments and make edits and you will need to to approve each and
>> every person in the list to edit by sharing the document with them, yet it
>> also means that you will be able to trace back edits to source - also it
>> will prevent malicious acts - remember that all the links to the document
>> are public so anyone can potentially edit without restriction and google
>> docs does not allow removal of a version. So I ask you to secure this. Not
>> that there is a high chance of anything bad happening, yet I witnessed
>> malicious changes in the past and securing the document is relatively easy
>> - only a few clicks for you in the share options.
>>
>> Also, should people add themselves to the sections they want? You missed
>> some of the communications in the email list - for example I wanted to be
>> added in sections 2,.9, 10. I have some text that I want to be kept and I
>> do want to contribute new text following new developments to one of the
>> sections. I looked at what Eric did to section 10 and it seems the content
>> I am interested in being kept is still there, so I have no issues there I
>> see now, yet this section was reduced in size and I have not traced back to
>> original contributions, so I am not sure about what else was eliminated and
>> still want to keep an eye on it in the future - this is why it is important
>> that people declare the sections they have interest in - to help you trace
>> back their contributions and those were not necessarily made in a way that
>> is easily detected by the original author - there was a lot of moving
>> around of text from original contribution.
>>
>> You mentioned section 3.8 - You merged 3 sub sections into this new
>> section when you changed the order. Those were written by many people - it
>> is hard to trace back all contributions, yet this section has many
>> important ideas. I can recognize contributions by  John Rice, Jonathan
>> Karr, and myself at the first part before subsections yet I am not sure
>> about text under the "Evaluating Model Credibility" and "Model Validation
>> Barriers" subtitles. If I recall correctly, and I may be mistaken, a lot
>> of  the text under "Evaluating Model Credibility" is from Jonathan Karr
>> with some text from James Glazier. Yet I am pretty sure there were several
>> other contributors and to my regret I am not sure who they were without
>> going through revisions of the original versions. Perhaps since we did not
>> suggest a solution to "Model Validation Barriers"   this section should be
>> moved  to an open questions section or an appendix at the end - yet I
>> really do not recall who originally wrote the text there so I cannot verify
>> with that person what they prefer. Note that those contributions can be
>> traced back in time to see who added what text - yet this process is time
>> consuming - I did this once when I assembled the combined version and it
>> was a time sink. I understand your desire to compress the section, yet I
>> also know it will be difficult to be honest to all contributors unless they
>> identify themselves - one possible way is that contributors identify
>> themselves through references they recognize adding.  Please let me know
>> what you think should be done in that section the way you assembled it - I
>> am reluctant to make edits unless contributors help trace back their
>> contributions.  Yet it is important do keep the first part of this section
>> intact as much as possible - it has important concepts. I personally am
>> interested keeping the paragraph about ensemble models - I think this is an
>> important glimpse to the future.
>>
>> So John, do you want us to write our own names at the top of each section
>> we have interest in, or do you intend to trace back contributions and
>> manage those?
>>
>> Yet please do secure the document. I know it seems harmless, yet I will
>> personally feel much easier if you do.
>>
>>                   Jacob
>>
>>
>>
>>
>> On Mon, May 24, 2021 at 1:14 AM John Gennari <gennari at uw.edu> wrote:
>>
>>>
>>> All:
>>>
>>> We've all now had a week to work on (or at least think about) the paper
>>> and the emails that have been sent around. As I listed on Monday, we're
>>> suggesting a re-ordering of the 12 (or 13?) challenges, and for each
>>> challenge, we are trying to assign a point person. That person doesn't
>>> need to be solely responsible for the content in the subsection (other
>>> authors can certainly chime in), but the point person(s) can act as a
>>> gatekeeper for consistency, length considerations, inclusion of ideas,
>>> etc.
>>>
>>> The challenge (as usual) is to actually get some writing done. (Of
>>> course, I'm just as guilty as others, having done not much of this
>>> either.)
>>>
>>> Over the last week, I saw some nice contributions by Alexander Kulesza
>>> (thank you!), so I've added his name to the author list. Otherwise, all
>>> I saw was some editing and some additions by Hana D and a few thoughts
>>> by James G.
>>>
>>> I also wanted to highlight that we have one section (the 12th
>>> challenge,  on model applications and real-world use) without a point
>>> person.
>>>
>>> I did go ahead and re-order the sections in the order listed in my email
>>> of May 17. This means that I also re-ordered (and numbered) the rows in
>>> Table 1. Because there were comments attached to some of these table
>>> rows, I also left the old table in the document. Obviously, we'll delete
>>> this table once folk are satisfied that their ideas have been
>>> incorporated or at least discussed by the group.
>>>
>>> Similarly, there are now two copies of the 12 sections -- once in the
>>> new order and with numbers, and then again in the old order.
>>>
>>> In the new ordering, I've listed the point person (or persons) at the
>>> beginning, and I also have a few notes about the sections. Since there
>>> are a couple of sections that I am the point person for, these will be
>>> my "homework". I did want to highlight that section 3.8 (on model
>>> validity and credibility) needs to be significantly reduced. One way to
>>> do this might be to move some of this content earlier, into the
>>> introduction, or perhaps into "reproducibility crisis" section.
>>>
>>> Hoping this email inspires some folk to do some writing. I'll keep
>>> plugging away at "my" sections. The document is in the same location:
>>>
>>> https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?ts=60a294c2
>>>
>>> -John G.
>>>
>>>
>>>
>>>
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