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Code review of the Imperial College London Covid-19 modelling

73 点作者 jimmcslim大约 5 年前

13 条评论

spamizbad大约 5 年前
John Carmack&#x27;s response: <a href="https:&#x2F;&#x2F;twitter.com&#x2F;ID_AA_Carmack&#x2F;status&#x2F;1258192134752145412" rel="nofollow">https:&#x2F;&#x2F;twitter.com&#x2F;ID_AA_Carmack&#x2F;status&#x2F;1258192134752145412</a>
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dekhn大约 5 年前
I have pretty deep experience in modelling code across a wide range of dimensions (academic, industrial and government, supercomputing to microcontroller, internet ads to protein design). I&#x27;ve seen a lot of modelling codes, and run a bunch of them, written some of them, and helped people fix problems in them.<p>Throughout that time I&#x27;ve seen a wide range of modelling quality. Very few people can churn out really nice code that solves useful problem, update that software for a wide range of uses over the years, keep it documented, pay down technical debt, fix bugs, write great tests, and make sure the numerics are excellent. Often times these things are built by people who are experts, but spend most of their time in meetings explaining the situation to politicians, or running labs and publishing papers.<p>Having read this particular article, many of the problems I see being complained about are typical and happen in industry frequently, even in highly functional orgs with strong incentives to build high quality software. Further, it really just seems like the author had a very strong position about lockdowns, and tried to make a quantitative&#x2F;technie takedown of some code that was used to make some decisions. The article really drips of that kind of animosity. i see a number of technical errors and ambiguity which make it unconvincing.<p>That said, we <i>could</i> have far better codes. In principle, all the data and support libraries would be open, the pipelines to produce the data reproducible, maintainable, and well-tested, and anybody would be able to write a simple notebook that reproducibly model their hypotheses for large populations in a way that a large number of people could inspect and come to their own conclusions.
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HarryHirsch大约 5 年前
<i>Investigation reveals the truth: the code produces critically different results, even for identical starting seeds and parameters</i><p>The fellow claims to have been at Google, yet seems not to have heard about non-determinism in parallelized code? Are we supposed to throw away all molecular dynamics results that were not run on a single core?!<p>And what&#x27;s with the beef about the mathematics? Yes, it&#x27;s apparently poorly determined, but that is a feature, you can extract uncertainty from it. An engineer, even if it&#x27;s a software &quot;engineer&quot; should have heard about experimental error!
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rontoes大约 5 年前
This is an incredibly poor take. It&#x27;s well known that academic software doesn&#x27;t follow great software engineering practices. The model is an incredibly complex piece of software that attempts to model stochastic behaviour. That it isn&#x27;t fully deterministic (with a fixed random seed) doesn&#x27;t make thee research invalid and shouldn&#x27;t discredit research that builds on the model.<p>&gt;On a personal level, I’d go further and suggest that all academic epidemiology be defunded. This sort of work is best done by the insurance sector.<p>This is another level of crazy.
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hartator大约 5 年前
Actual code: <a href="https:&#x2F;&#x2F;github.com&#x2F;mrc-ide&#x2F;covid-sim" rel="nofollow">https:&#x2F;&#x2F;github.com&#x2F;mrc-ide&#x2F;covid-sim</a>
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scarmig大约 5 年前
It&#x27;s disappointing to see this flagged.<p>Imagine the Trump administration was using a model with similar code quality to justify reopening the economy. We would not be making excuses for it, or flagging articles that criticize it. In fact, if I told you today that I was running the model with a certain random seed and getting a result that said the US would have &lt;5k additional deaths in 2020, how would you even dispute that?<p>The biggest issue with this link is that it&#x27;s less a code review than a rant about the code quality, but the code is so badly written that it&#x27;s hard to know where to start doing a code review.
lbeltrame大约 5 年前
IMO this should be unflagged and the link changed to <a href="https:&#x2F;&#x2F;github.com&#x2F;mrc-ide&#x2F;covid-sim&#x2F;issues&#x2F;165" rel="nofollow">https:&#x2F;&#x2F;github.com&#x2F;mrc-ide&#x2F;covid-sim&#x2F;issues&#x2F;165</a> which is at least non-partisan unlike the very domain name of this submission.
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aphextron大约 5 年前
&gt;&quot;lockdownsceptics.org&quot;<p>It seems their conclusion is foredrawn, so I wouldn&#x27;t expect much scientific rigor here. This article reeks of the kind of cherry-picking and straw man arguments you see in climate change denial.
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avs733大约 5 年前
Well at least they are upfront about their bias...and I must tell you, as an academic, I&#x27;m SHOCKED, SHOCKED I tell you to find ugly code in a research paper. And from my prior experience working as a defense contractor, I&#x27;m SHOCKED SHOCKED I tell you to that its possible for governments to possibly use messy code for decisions making. But what I&#x27;m most shocked by is that a software engineer thinks them not understanding a model from another field is a valid critique of it (so shocked I laughed).<p>If you are curious about the reliability of this particular source you can start at the end and read backwards:<p>&quot;On a personal level, I’d go further and suggest that all academic epidemiology be defunded. This sort of work is best done by the insurance sector. Insurers employ modellers and data scientists, but also employ managers whose job is to decide whether a model is accurate enough for real world usage and professional software engineers to ensure model software is properly tested, understandable and so on. Academic efforts don’t have these people, and the results speak for themselves.&quot;<p>Sue may be a great programmer but she regularly steps out of commenting on the code to comment on the model...which is like the guy who designed the tractor wheels telling the farmer what to plant. While readability of code may be nice, not a single comment she makes actually disputes the findings of the model. Some things in nature are actually stochastic (I&#x27;m sorry...RANDOM ::clutches pearls::). If you think the entire world is deterministic great...show me the computing power and societal knowledge that can account for those variables. And if your solution to global health is capitalism, look at the gates foundation, if you wanna look at what other approaches have gotten us, look at the Carter Center and Jonas Salk. Epidemiologists didn&#x27;t build the ObamaCare website...<p>In the past 100 years, epidemiology has:<p>* Brought us a world where infectitious diseases are no longer the SINGLE LARGEST CAUSE OF DEATH to the human species<p>* Made workplaces safer, and the food chain safer<p>* Reduced the maternal death rate by 90%<p>* Eliminated small pox entirely and eliminated multiple other diseases practically<p>I don&#x27;t know Sue, but I&#x27;m team Salk not team Sue here...what a loon.
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alanfranz大约 5 年前
The article is partisan, and yet it DOES make some valid points.
DiogenesKynikos大约 5 年前
Rather than defunding epidemiology, how about giving them enough money to hire professional programmers?<p>It&#x27;s a good investment, given how much is at stake.
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TechBro8615大约 5 年前
It’s very disappointing to see this submission flagged. Further, the general trend of politicization of the scientific process is highly worrying. I fear the response to the pandemic is being driven by an emotionally political monoculture rather than data, facts and critical reasoning.<p>Gailileo would not be happy to see this.
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s9w大约 5 年前
The code is a dumpster fire. I wouldn&#x27;t trust it to manage my shopping list and would get in deep shit at work for something like that. Not sure if that article itself makes good points, but the code alone should anyone nope out. Publishing any results from this feels criminal, let alone something world-changing as their reports.