6 ms·

Covid-19 Sanity – Covid-19 papers from bioRxiv/medRxiv searchable and sortable

140 points by hardmaru 7y ago

datnoblesavage 7y ago
https://www.frontiersin.org/articles/10.3389/fvets.2018.00084/full https://www.frontiersin.org/articles/10.3389/fvets.2018.0008...
- cowsandmilk 7y ago
  Any context here? The only apparent relation is that this paper is also about viruses.
mkolodny 7y ago
Nice! I think adding upvoting HN-style would help with the sorting. Edit: And HN-style comments might make it easier to discuss the papers.
- fsh 7y ago
  I think that a reddit/hn-style voting system is the absolute opposite of what you want to have for scientific publications. These systems tend to enforce a strong hive-mind, where only the most popular posts and opinions are visible and anything else gets downvoted into oblivion.
  - tandav 7y ago
    I see no reason why comments can be bad
  - leetcrew 7y ago
    don't citations already function like a voting system (albeit with no downvotes)? a paper with zero citations will be ignored just as surely as a comment in a large thread with zero votes.
- AshamedCaptain 7y ago
  Because democratic research is certainly going to do wonders in an era where the equipment and/or resources to reproduce any of the claims of these papers is way inaccessible to the average voter. I'd put my finger that even random sorting would bring more value.
- Vinnl 7y ago
  It's not exactly that, but with Plaudit [1] you're able to see which academics have read it and considered it worthwhile enough to endorse. Ideally bioRxiv/medRxiv would integrate it natively like several other preprint servers have done (e.g. [2]), but for now you'll need an extension though. (Disclosure: I'm a volunteer working on Plaudit.) [1] https://plaudit.pub/extension/ https://plaudit.pub/extension/ [2] https://psyarxiv.com/y38m9/ https://psyarxiv.com/y38m9/
- MaxBarraclough 7y ago
  How would that work? Would random people be able to vote on which research papers have the most merit? Only people with relevant doctorates? Another commenter mentioned a projected call Plaudit, which seems to use the 'ORCiD' system to decide who is worth taking seriously. [0] Can anyone explain how that really works? [0] https://plaudit.pub/#concept https://plaudit.pub/#concept
rubidium 7y ago
Ask HN: Has any study been done doing a random sampling of a population using an antibody immunity test? It seems the natural next step given we have such a test. Until we do that, I feel like we have no idea of the actual infection rate and population immunity.
- phaemon 7y ago
  As an alternative point of view: who cares? We know for a fact that ICUs are being overloaded with cases and morgues are overwhelmed with the dead. Arguing over exact figures is like quibbling over your exact velocity as you're falling off a cliff. Finding some prettier numbers won't change the reality of the situation, no matter how convincingly you argue your case.
  - nothrabannosir 7y ago
    People are talking doomsday scenarios, on this very forum. Getting some hard facts would really help temper the hysteria, or allow people to prep further appropriately. We’re planning for more than the next three days here.
  - rubidium 7y ago
    An alternative to your alternative: science and medicine still work. Let's try and make it better. The better we understand our situation the better we can react appropriately. Yes, it's really bad in a few places right now. It looks like it's going to be really bad in a lot more places in the next 15-20 days. How _long_ will it be really bad for and for how _many_ people will it be really bad are important questions to understand. Don't let the dire situation make you irrational.
    - phaemon 7y ago
      I'm not being irrational; you are. I accept what I'm seeing as the reality of the situation. You appear to be looking for numbers that will tell you things are different to the observed reality. That's my point.
mandy12xx 7y ago
any good source on the tfidf exemplar svm model that was used for this?
AshamedCaptain 7y ago
Why would you even do this? On the days where I was still energetic enough to try and debunk some of the pseudosciences, I quickly discovered that one of the primary rules is absolutely never to trust one single article, however "scientific", and however reputable the publisher of the journal/conference is. Otherwise one quickly becomes overwhelmed by the amount of crap published by otherwise "respectable" publishers (e.g. Elsevier's Journal of Homeopathy). Let's not even get into non-reviewed articles... The only things that _may_ have any value whatsoever are the ones published in utmost respectable _journals_ themselves (e.g. Nature, but absolutely not on any of their spinoffs), and/or when there are very big labs/organizations in the authors list. Very big. I mean usually national pharmaceutical associations (obviously not from all states) or huge corporations (who will generally avoid putting their name on the line either way). Meta-analyses most importantly do NOT have any intrinsinc value either _just because_ they are meta-analyses. By reading bioXiv directly, you are most likely doing yourself a disservice. Unless you are a state agency or huge corporation having huge resources backing your which allows you to internally replicate whatever they claim.
- whatshisface 7y ago
  You're going too far in dismissing the value of individual scientific papers. If you read the methods and analysis yourself you can figure out how good their results are. If you read a lot of papers or read several meta-analyses you can form a opinion about what the consensus is. All of these options are more work than reading one abstract and calling it a day but that doesn't mean scientific papers are worthless. If scientific papers did not contain any information then scientists would not read them.
  - AshamedCaptain 7y ago
    No, you cannot figure out by yourself "how good the results are". That is the one of the critical points. The paper might even pass peer review and get accepted -- which, assuming a reasonable quality journal, means that the methods and analysis they claim make sense. But that is just the _very minimum_ you can expect in an article. Incredibly enough, by itself, that is already a huge filter. But sadly that is nowhere near enough to give any value whatsoever to the article. i.e. the article can be perfect and still just wrong. Even assuming good faith from the authors, they could just be the lucky 5% who got a positive out of an impossible thing and decided to publish. In a world with a general pressure to publish positive results and specially in a highly-hyped topic such as this one, you have a very high chance of seeing such a result. At the end of the day this is the only argument I have left to debunk some homeopathy papers. Scientists who are in a position where they have the resources to _reproduce_ the articles should and do read them. "Mortals" are not and reading these articles is a waste of time and potentially a disservice. There are tens of journals claiming _utter non-sense_ being published every single month. Using un-reviewed papers to estimate "consensus" is also pointless. Using publication numbers / citations / impact factors is slightly better but also extremely dangerous. If anything pseudo-science chaps are good at is at publishing large numbers of astonishing crap. The sad truth is that filtering good science vs not is out of reach for the average layman, which leaves you with unscientific stuff such as "reputation" as your only tool.
omgJustTest 7y ago
THanks for these. I am interested in modeling this effort, and it is difficult to find papers that outright call R00, population logistic saturation parameters, case resolution timescale, detection probabilities (ie if you have x tests per million ppl, what is the actual number of cases), etc. R00 that I typically use is about 2.1-2.6, however relating this to the 30-60% case increase per day is a difficult task. If you know more information about where I could find these I would appreciate it.
gregwebs 7y ago
There's some useful paper discussion on https://www.reddit.com/r/COVID19/ https://www.reddit.com/r/COVID19/
Jovensa 7y ago
https://projecteve.com/organizing-tech-tools-for-work/#comment-586225 https://projecteve.com/organizing-tech-tools-for-work/#comme...
Jovensa555 7y ago
https://projecteve.com/organizing-tech-tools-for-work/#comment-586225 https://projecteve.com/organizing-tech-tools-for-work/#comme...

140 points by hardmaru 7y ago

https://www.frontiersin.org/articles/10.3389/fvets.2018.00084/full https://www.frontiersin.org/articles/10.3389/fvets.2018.0008...

cowsandmilk 7y ago
Any context here? The only apparent relation is that this paper is also about viruses.

mkolodny 7y ago

Nice! I think adding upvoting HN-style would help with the sorting. Edit: And HN-style comments might make it easier to discuss the papers.

fsh 7y ago
I think that a reddit/hn-style voting system is the absolute opposite of what you want to have for scientific publications. These systems tend to enforce a strong hive-mind, where only the most popular posts and opinions are visible and anything else gets downvoted into oblivion.
- tandav 7y ago
  I see no reason why comments can be bad
- leetcrew 7y ago
  don't citations already function like a voting system (albeit with no downvotes)? a paper with zero citations will be ignored just as surely as a comment in a large thread with zero votes.
AshamedCaptain 7y ago
Because democratic research is certainly going to do wonders in an era where the equipment and/or resources to reproduce any of the claims of these papers is way inaccessible to the average voter. I'd put my finger that even random sorting would bring more value.
Vinnl 7y ago
It's not exactly that, but with Plaudit [1] you're able to see which academics have read it and considered it worthwhile enough to endorse. Ideally bioRxiv/medRxiv would integrate it natively like several other preprint servers have done (e.g. [2]), but for now you'll need an extension though. (Disclosure: I'm a volunteer working on Plaudit.) [1] https://plaudit.pub/extension/ https://plaudit.pub/extension/ [2] https://psyarxiv.com/y38m9/ https://psyarxiv.com/y38m9/
MaxBarraclough 7y ago
How would that work? Would random people be able to vote on which research papers have the most merit? Only people with relevant doctorates? Another commenter mentioned a projected call Plaudit, which seems to use the 'ORCiD' system to decide who is worth taking seriously. [0] Can anyone explain how that really works? [0] https://plaudit.pub/#concept https://plaudit.pub/#concept

rubidium 7y ago

Ask HN: Has any study been done doing a random sampling of a population using an antibody immunity test? It seems the natural next step given we have such a test. Until we do that, I feel like we have no idea of the actual infection rate and population immunity.

phaemon 7y ago
As an alternative point of view: who cares? We know for a fact that ICUs are being overloaded with cases and morgues are overwhelmed with the dead. Arguing over exact figures is like quibbling over your exact velocity as you're falling off a cliff. Finding some prettier numbers won't change the reality of the situation, no matter how convincingly you argue your case.
- nothrabannosir 7y ago
  People are talking doomsday scenarios, on this very forum. Getting some hard facts would really help temper the hysteria, or allow people to prep further appropriately. We’re planning for more than the next three days here.
- rubidium 7y ago
  An alternative to your alternative: science and medicine still work. Let's try and make it better. The better we understand our situation the better we can react appropriately. Yes, it's really bad in a few places right now. It looks like it's going to be really bad in a lot more places in the next 15-20 days. How _long_ will it be really bad for and for how _many_ people will it be really bad are important questions to understand. Don't let the dire situation make you irrational.
  - phaemon 7y ago
    I'm not being irrational; you are. I accept what I'm seeing as the reality of the situation. You appear to be looking for numbers that will tell you things are different to the observed reality. That's my point.

mandy12xx 7y ago

any good source on the tfidf exemplar svm model that was used for this?

AshamedCaptain 7y ago

Why would you even do this? On the days where I was still energetic enough to try and debunk some of the pseudosciences, I quickly discovered that one of the primary rules is absolutely never to trust one single article, however "scientific", and however reputable the publisher of the journal/conference is. Otherwise one quickly becomes overwhelmed by the amount of crap published by otherwise "respectable" publishers (e.g. Elsevier's Journal of Homeopathy). Let's not even get into non-reviewed articles... The only things that _may_ have any value whatsoever are the ones published in utmost respectable _journals_ themselves (e.g. Nature, but absolutely not on any of their spinoffs), and/or when there are very big labs/organizations in the authors list. Very big. I mean usually national pharmaceutical associations (obviously not from all states) or huge corporations (who will generally avoid putting their name on the line either way). Meta-analyses most importantly do NOT have any intrinsinc value either _just because_ they are meta-analyses. By reading bioXiv directly, you are most likely doing yourself a disservice. Unless you are a state agency or huge corporation having huge resources backing your which allows you to internally replicate whatever they claim.

whatshisface 7y ago
You're going too far in dismissing the value of individual scientific papers. If you read the methods and analysis yourself you can figure out how good their results are. If you read a lot of papers or read several meta-analyses you can form a opinion about what the consensus is. All of these options are more work than reading one abstract and calling it a day but that doesn't mean scientific papers are worthless. If scientific papers did not contain any information then scientists would not read them.
- AshamedCaptain 7y ago
  No, you cannot figure out by yourself "how good the results are". That is the one of the critical points. The paper might even pass peer review and get accepted -- which, assuming a reasonable quality journal, means that the methods and analysis they claim make sense. But that is just the _very minimum_ you can expect in an article. Incredibly enough, by itself, that is already a huge filter. But sadly that is nowhere near enough to give any value whatsoever to the article. i.e. the article can be perfect and still just wrong. Even assuming good faith from the authors, they could just be the lucky 5% who got a positive out of an impossible thing and decided to publish. In a world with a general pressure to publish positive results and specially in a highly-hyped topic such as this one, you have a very high chance of seeing such a result. At the end of the day this is the only argument I have left to debunk some homeopathy papers. Scientists who are in a position where they have the resources to _reproduce_ the articles should and do read them. "Mortals" are not and reading these articles is a waste of time and potentially a disservice. There are tens of journals claiming _utter non-sense_ being published every single month. Using un-reviewed papers to estimate "consensus" is also pointless. Using publication numbers / citations / impact factors is slightly better but also extremely dangerous. If anything pseudo-science chaps are good at is at publishing large numbers of astonishing crap. The sad truth is that filtering good science vs not is out of reach for the average layman, which leaves you with unscientific stuff such as "reputation" as your only tool.

omgJustTest 7y ago

THanks for these. I am interested in modeling this effort, and it is difficult to find papers that outright call R00, population logistic saturation parameters, case resolution timescale, detection probabilities (ie if you have x tests per million ppl, what is the actual number of cases), etc. R00 that I typically use is about 2.1-2.6, however relating this to the 30-60% case increase per day is a difficult task. If you know more information about where I could find these I would appreciate it.

gregwebs 7y ago

There's some useful paper discussion on https://www.reddit.com/r/COVID19/ https://www.reddit.com/r/COVID19/

Jovensa 7y ago

https://projecteve.com/organizing-tech-tools-for-work/#comment-586225 https://projecteve.com/organizing-tech-tools-for-work/#comme...

Jovensa555 7y ago

https://projecteve.com/organizing-tech-tools-for-work/#comment-586225 https://projecteve.com/organizing-tech-tools-for-work/#comme...