Kinshasa, the capital of the Democratic Republic of Congo.
We know the city where HIV first emerged
41–48 of 48 posts
Re: We know the city where HIV first emerged
#42tl;dr, Kinshasa, Democratic Republic of the Congo (then known as Leopoldville)
There's actually more content in the article. It's far from click-bait.
After reading it I think that the exact city is the least interesting fact they have to offer.
Re: We know the city where HIV first emerged
#43tl;dr, Kinshasa, Democratic Republic of the Congo (then known as Leopoldville)
There's actually more content in the article. It's far from click-bait. After reading it I think that the exact city is the least interesting fact they have to offer.
I don't disagree. The story is interesting. I just realized that anyone who read the headline would want to know what city. I probably came across snarkier than intended.
Re: We know the city where HIV first emerged
#44Earlier quoted context omitted.
>"making MCMC quite difficult" They thinned 250 million steps to 500, then it sounds like they dropped the first 50-100 on top of that post-hoc (the 10-30% burn in gives an impression of manual tinkering). Obviously this is going to bring up questions regarding convergence, so reviewers should have asked for the diagnostic charts. This would probably have been better suited to ABC: https://en.wikipedia.org/wiki/Appro…
BEAST (which I assumed they used) is not very fast. 250 million generations on BEAST with the number of parameters they estimated and the size of their dataset would likely take about 2-4 weeks to run. Assuming they ran all 3 chains in parallel this is still a really long time to wait for an analysis. (edit: just checked, looks like they used 700+ sequences, so this is closer to 1-3 months of compute time) The standa…
It is not that 500 steps is too low that concerns me, it is not showing the posteriors for the parameters used (which it sounds like may simply be the custom in this area). I would think if people had such trouble using mcmc that common practice would be publishing diagnostic charts to reassure each other.
Re: We know the city where HIV first emerged
#45Is HN becoming "spammy"? In this case, would it hurt to include the name of the city in the title?
Re: We know the city where HIV first emerged
#46Earlier quoted context omitted.
BEAST (which I assumed they used) is not very fast. 250 million generations on BEAST with the number of parameters they estimated and the size of their dataset would likely take about 2-4 weeks to run. Assuming they ran all 3 chains in parallel this is still a really long time to wait for an analysis. (edit: just checked, looks like they used 700+ sequences, so this is closer to 1-3 months of compute time) The standa…
Disclaimer: I don't know anything about this stuff. Would they be able to run these MCMC chains in a way that perhaps progressively renders results at greater and greater accuracy? Then they could get some initial "low resolution" results and they wouldn't necessarily have to wait for weeks, but the full data will eventually be available.
In principle, there would be nothing stopping them from looking at the output every step, or every n steps. I don't know if the software they used supports this though.
Re: We know the city where HIV first emerged
#47tl;dr, Kinshasa, Democratic Republic of the Congo (then known as Leopoldville)
There's actually more content in the article. It's far from click-bait. After reading it I think that the exact city is the least interesting fact they have to offer.
Click-bait titles dont' mean the article is crap. It's a good article with a clickbait title, plain as that. Clickbait is when some information is left out of the title in an obvious way such that readers will click in pursuit of that piece of information, rather than clicking it in pursuit of expanding on the headline.
Re: We know the city where HIV first emerged
#48tl;dr, Kinshasa, Democratic Republic of the Congo (then known as Leopoldville)
There's actually more content in the article. It's far from click-bait. After reading it I think that the exact city is the least interesting fact they have to offer.
I believe you, but the name of the city could still be included in the title, at least.