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p.MsoNormal,p.MsoNoSpacing{margin:0}</style></head><body><div style="font-family:Arial;">Marcus said, "Imagine if everyone had full genome sequencing and every viral sample was deep sequenced." Iceland has something close to this already.<br></div><div style="font-family:Arial;"><br></div><div style="font-family:Arial;">davew<br></div><div style="font-family:Arial;"><br></div><div>On Sun, Apr 19, 2020, at 10:34 AM, Marcus Daniels wrote:<br></div><blockquote type="cite" id="qt"><div style="font-family:Calibri, Arial, Helvetica, sans-serif;font-size:12pt;color:rgb(0, 0, 0);">Steve writes:<br></div><div style="font-family:Calibri, Arial, Helvetica, sans-serif;font-size:12pt;color:rgb(0, 0, 0);"><br></div><div style="font-family:Calibri, Arial, Helvetica, sans-serif;font-size:12pt;color:rgb(0, 0, 0);">< The whole world is responding to what is *roughly* the same virus with *roughly* what is the same human phenotype/metabolism in a myriad of *roughly* the same modes of human organization. ><br></div><div style="font-family:Calibri, Arial, Helvetica, sans-serif;font-size:12pt;color:rgb(0, 0, 0);"><br></div><div style="font-family:Calibri, Arial, Helvetica, sans-serif;font-size:12pt;color:rgb(0, 0, 0);">There are hundreds of common HLA alleles across humans. In a diverse country like the US, with hundreds of thousands of positive cases and tens of thousands of deaths the hundreds of alleles would be well sampled. Too bad our medical surveillance is so
bad, and made worse by the moron. Imagine if everyone had full genome sequencing and every viral sample was deep sequenced. <br></div><div style="font-family:Calibri, Arial, Helvetica, sans-serif;font-size:12pt;color:rgb(0, 0, 0);"><br></div><div style="font-family:Calibri, Arial, Helvetica, sans-serif;font-size:12pt;color:rgb(0, 0, 0);">Marcus<br></div><div id="qt-appendonsend"><br></div><div><hr style="display:inline-block;width:98%;"><br></div><div id="qt-divRplyFwdMsg" dir="ltr"><div><span class="font" style="font-family:Calibri, sans-serif;"><span class="colour" style="color:rgb(0, 0, 0);"><b>From:</b> Friam <friam-bounces@redfish.com> on behalf of Steven A Smith <sasmyth@swcp.com><br> <b>Sent:</b> Sunday, April 19, 2020 10:11 AM<br> <b>To:</b> friam@redfish.com <friam@redfish.com><br> <b>Subject:</b> Re: [FRIAM] Judea Pearl: Book of Why</span></span> </div><div> <br></div></div><div><div><br></div><blockquote type="cite"><pre class="qt-x_moz-quote-pre">One way to address the N/A issue is to repeatedly perturb the real-world system so as to elicit those correlations. When that is practical.. <br></pre></blockquote><div><br></div><p>We are, in a time of real-world system perturbation, right now. The whole world is responding to what is *roughly* the same virus with *roughly* what is the same human phenotype/metabolism in a myriad of *roughly* the same modes of human organization.
This IS a testbed of human (-system?) response to a widespread, somewhat invisible threat. From Wuhan to Singapore to Italy to Iran to Sweden to Germany to NYC to WA State to the Navajo Nation to Florida's beaches, this IS a huge coupled systems dynamics/agent-model
executed in real-time by real-people with real casualties and real consequences. <br></p><p>We are, to varying degrees (collectively) recording the results of these "experiments" and if we are lucky (or smart, or both) we will do some post-game analysis intended to understand more-better how best to (self-)organize around a (nearly) existential
world-scale threat. And to the extent this is a game that will never end, we have to begin the analysis while we cope with it's consequences. Feels a bit like the models pof Physics Interreality.<br></p><p><a href="https://journals.aps.org/pre/abstract/10.1103/PhysRevE.75.057201"> https://journals.aps.org/pre/abstract/10.1103/PhysRevE.75.057201</a><br></p><p>Hanging too aggressive of a model on this (or collecting the data against too premature of a model) will reduce the utility of such data gathering and analysis. Whatever the dual of overfitting a model is? Overmodeling? Premature Modeling?<br></p><p>What I'm looking (askance) to(ward) Pearl for is a better way of rapidly constructing, maintaining, revising as generic of a model as possible in response to "this moment". Four months ago we should have been interested in models of how one limits a virus
such as COVID19 getting a foothold in this country. One month ago we should have been interested in how one limits COVID19 (with new understanding of it's virility, it's fatality, it's symptoms, it's mode of spread) once it HAS a foothold, now we are faced
with trying to understand how to cope with it once it is pervasive in our population whilst continuing/returning to "business as usual" and in another thread, I'm encouraging that we "try to plan/consider/think-about" what we want to do with this somewhat
"blank slate" (our ass?) we are having handed to us. <br></p><p>And how to think about this without premature modeling... what I think I was railing (whining/pushing-back) about with Dave on the Bellamyist thread earlier this morning.<br></p><p>- Steve<br></p><blockquote type="cite"><pre class="qt-x_moz-quote-pre"><br></pre><blockquote type="cite"><pre class="qt-x_moz-quote-pre">On Apr 19, 2020, at 8:33 AM, uǝlƃ ☣ <a class="qt-x_moz-txt-link-rfc2396E" href="mailto:gepropella@gmail.com"><gepropella@gmail.com></a> wrote:
Well, the argument I often end up making is that you can do a kind of face validation with the fake data. Show it to someone who's used to dealing with that sort of data and if the fake data looks a lot like the data they normally deal with, then maybe more data-taking isn't necessary. If it looks fake to the "expert", then more data-taking is definitely needed.
<br></pre><blockquote type="cite"><pre class="qt-x_moz-quote-pre">On 4/19/20 8:29 AM, Marcus Daniels wrote:
I have a hard time with this as a way to extend data. If it is high-dimensional it will be under-sampled. Seems better to me to measure or simulate more so that the joint distribution can be realistic. And if you can do that there is no reason to infer the joint distribution because you *have* it.
<br></pre><blockquote type="cite"><blockquote type="cite"><pre class="qt-x_moz-quote-pre">On Apr 19, 2020, at 8:18 AM, Frank Wimberly <a class="qt-x_moz-txt-link-rfc2396E" href="mailto:wimberly3@gmail.com"><wimberly3@gmail.com></a> wrote:
<br></pre></blockquote><pre class="qt-x_moz-quote-pre">
Going back and forth: If you infer the causal graph from observational data you can use that graph to simulate data with the same joint distribution as the original data.
<br></pre></blockquote></blockquote><pre class="qt-x_moz-quote-pre">--
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