Library-managed 'arXiv' spreads scientific advances rapidly and worldwide • Hacker News Board

Re: Library-managed 'arXiv' spreads scientific advances rapidly and worldwide

#131

Post by tripzilch » Wed, Dec 28, 2016, 3:03 PM UTC

frozenport wrote: post #107

apathy wrote: post #62

Earlier quoted context omitted.

When I worked at the Cornell Theory Center in the late 90s, I didn't know about the arXiv, but I sure as hell knew about screen readers. One of the best FORTRAN programmers (numerical analysis/applied math research faculty I think) was blind as a bat. I learned a lot about not underestimating people there. It's a strange university but it always makes me happy to think that it (specifically Ginsparg, and to some degr…

The OpenAcess and self-publication has removed an important check on research papers. If nobody cared about your subject, or if a journal's peer review process resulted in boring articles, it would not be financially viable. I think advocates of sharing science should also understand that, at present, the majority of the content is asinine or incorrect. Removing checks and balances is not helping.

Could you try and make that argument without the term "financially viable"? We're talking about science here. Capitalism is a tiny thing that really isn't required to rule everything, and particularly in this case I don't think it has any authority based on which to implement that "check".

If I just leave that out you seem to imply science publications should be selected by whether enough people care about, or whether they are boring or not. Both (especially the latter) are rather bad measuring sticks for the quality and importance of research.

Adding "financially viable" to "less boring" produces "EXCITING!", adding it to "enough people care" yields "POPULAR!". These are definitely not forces that should be pulling scientific research.

Not saying there shouldn't be checks. Just that market forces are probably too stupid for it.

Re: Library-managed 'arXiv' spreads scientific advances rapidly and worldwide

#132

Post by grigjd3 » Wed, Dec 28, 2016, 3:05 PM UTC

frozenport wrote: post #107

apathy wrote: post #62

Earlier quoted context omitted.

When I worked at the Cornell Theory Center in the late 90s, I didn't know about the arXiv, but I sure as hell knew about screen readers. One of the best FORTRAN programmers (numerical analysis/applied math research faculty I think) was blind as a bat. I learned a lot about not underestimating people there. It's a strange university but it always makes me happy to think that it (specifically Ginsparg, and to some degr…

The OpenAcess and self-publication has removed an important check on research papers. If nobody cared about your subject, or if a journal's peer review process resulted in boring articles, it would not be financially viable. I think advocates of sharing science should also understand that, at present, the majority of the content is asinine or incorrect. Removing checks and balances is not helping.

arXiv isn't meant to replace peer review. When I submitted to phys. rev. d, a submission to arXiv to allow people to see the work ahead of review was expected.

Re: Library-managed 'arXiv' spreads scientific advances rapidly and worldwide

#133

Post by tripzilch » Wed, Dec 28, 2016, 3:10 PM UTC

noamyoungerm wrote: post #123

hackuser wrote: post #71

Earlier quoted context omitted.

> For the blind, PDF is the worst possible format I'm surprised. Nobody has created an accessibility solution for PDFs after all these years of ubiquity? What's the story?

It's totally possible (and a relatively frequent occurrence) to have pdfs where the order of characters in the code has no relationship at all to how those same characters are laid out visually on the page. Anything marginally more complex than a series of paragraphs with no formatting at all basically requires you to render out the whole pdf and figure out the order that you are actually supposed to read the charact…

Yup. For instance, Word's PDF output, has an absolutely positioned textbox for every word (and sometimes sub-word). This is for kerning purposes. If you want your original text back, you're going to need some OCR-like preprocessing and heuristics to guess what textboxes belong to the same line. If you have multiple columns, good luck distinguishing them from accidental rivers.

It's not impossible, but I wouldn't know immediately what tools get this most right. And it's always a lossy operation going back and forth.

Re: Library-managed 'arXiv' spreads scientific advances rapidly and worldwide

#134

Post by [deleted] » Wed, Dec 28, 2016, 3:23 PM UTC

hackuser wrote: post #96

contravariant wrote: post #95

Earlier quoted context omitted.

Well, I don't know about PDF, but PostScript, which it's based on is basically just a programming language for drawing symbols in specific positions on a page. Depending on how it was written (or more likely, generated) this could be readable, or incredibly unreadable. As an example, in post script the following example from Wikipedia would simply show the text Hello World: %!PS /Courier % name the desired font 20 se…

Almost all formats would similarly require content to be parsed from code; for example, consider HTML, Word, or Excel. It makes me wonder how screen readers work. Thinking out loud, it seems that the screen readers should let the applications (e.g., Word) handle their own parsing and presentation and obtain the data after that. Otherwise, the screen reader would have to reinvent many wheels, interpreting the code for…

[deleted]

Re: Library-managed 'arXiv' spreads scientific advances rapidly and worldwide

#135

Post by lorenzhs » Wed, Dec 28, 2016, 3:36 PM UTC

greeneggs wrote: post #102

GFK_of_xmaspast wrote: post #88

Earlier quoted context omitted.

Can you link three examples.

Here's an example: https://arxiv.org/abs/1611.06999 I believe the PDF link is only removed after a paper has been withdrawn. But if you click on v1, you can still access the original paper (incorrect, in this case).

v2 is a 0kB file. As you note, v1 is still available, just as with any other paper that was updated.

In any case I don't think that withdrawn papers support the OP's claim that PDF links are hard to find for normal papers.

Re: Library-managed 'arXiv' spreads scientific advances rapidly and worldwide

#136

Post by nileshtrivedi » Wed, Dec 28, 2016, 3:37 PM UTC

frozenport wrote: post #107

apathy wrote: post #62

Earlier quoted context omitted.

When I worked at the Cornell Theory Center in the late 90s, I didn't know about the arXiv, but I sure as hell knew about screen readers. One of the best FORTRAN programmers (numerical analysis/applied math research faculty I think) was blind as a bat. I learned a lot about not underestimating people there. It's a strange university but it always makes me happy to think that it (specifically Ginsparg, and to some degr…

The OpenAcess and self-publication has removed an important check on research papers. If nobody cared about your subject, or if a journal's peer review process resulted in boring articles, it would not be financially viable. I think advocates of sharing science should also understand that, at present, the majority of the content is asinine or incorrect. Removing checks and balances is not helping.

This argument applies to all speech that has now become easier and cheaper:

"If nobody cared about your opinion, it would not be financially viable to publish it. But now we have blogs/tweets."

Effectively, cost of publishing was working as a quality filter. Now, we need to actually implement proper filters instead of bad proxies for quality.

Re: Library-managed 'arXiv' spreads scientific advances rapidly and worldwide

#137

Post by science404 » Wed, Dec 28, 2016, 4:37 PM UTC

There's something I've always wondered about.. what do you do if you upload your journal submission to arxiv but it's later rejected? That possibility has always been a deterrent to submitting to arxiv for me. Seems to me this discussion assumes arxiv uploads will be accepted to some journal eventually..

Re: Library-managed 'arXiv' spreads scientific advances rapidly and worldwide

#138

Post by apathy » Wed, Dec 28, 2016, 7:26 PM UTC

tripzilch wrote: post #131

frozenport wrote: post #107

Earlier quoted context omitted.

The OpenAcess and self-publication has removed an important check on research papers. If nobody cared about your subject, or if a journal's peer review process resulted in boring articles, it would not be financially viable. I think advocates of sharing science should also understand that, at present, the majority of the content is asinine or incorrect. Removing checks and balances is not helping.

Could you try and make that argument without the term "financially viable"? We're talking about science here. Capitalism is a tiny thing that really isn't required to rule everything, and particularly in this case I don't think it has any authority based on which to implement that "check". If I just leave that out you seem to imply science publications should be selected by whether enough people care about, or whethe…

CNS (Cell, Nature, Science) == Buzzfeed science

Although that's not giving BuzzFeed enough credit, they tend to check their sources & verify results/reports. Also if a piece of fake news is simply resubmitted, they don't pretend like they never checked on it before.

There are plenty of checks (mostly from NIH, mostly for incremental garbage work on dead models like cell lines) and very few balances against the tyranny of CNS...

Re: Library-managed 'arXiv' spreads scientific advances rapidly and worldwide

#139

Post by frozenport » Thu, Dec 29, 2016, 4:44 AM UTC

apathy wrote: post #111

frozenport wrote: post #107

Earlier quoted context omitted.

The OpenAcess and self-publication has removed an important check on research papers. If nobody cared about your subject, or if a journal's peer review process resulted in boring articles, it would not be financially viable. I think advocates of sharing science should also understand that, at present, the majority of the content is asinine or incorrect. Removing checks and balances is not helping.

The majority of content in most journals is asinine or incorrect. About the only thing that can fix this is quicker turnaround (cf STAP, NgAgo, the godawful GWAS paper in Neuron recently, etc). It's not at all clear to me that the checks or balances were helping beforehand. Hiring a shit ton of MBA types to administer research probably didn't help much either. Also, out of curiosity, is this open access / fast review…

>>fix this is quicker turnaround

Why? As the first author of several publications, more than half the reviews I received were not well thought out. This part of the process doesn't happen, Open Acess and self publishing websites exploited this fact for greater throughput.

>>machine learning

I would argue that the machine learning bloom in recent years is because of an availability of new technology from industry, supported by industry. This is also why they were able to tolerate less conventional venues for publication - as these were not viewed as mile markers for progress. Yet, when I look at more "settled" machine learning fields like speech, I see the same plethora of academic papers filled with useless crap.

Perhaps the growth of ML has nothing to do with Open Acess. There is although certainly there is an underlying profit motive for successful technologies, Google ain't going to use a technique that doesn't work.

>>raw clinical trial data

It would be great if it were published, and indeed many people would pay for quality trial data. I see OA and self-publishing of research results having no relation to authors withholding clinical data.

Re: Library-managed 'arXiv' spreads scientific advances rapidly and worldwide

#140

Post by apathy » Thu, Dec 29, 2016, 6:33 AM UTC

frozenport wrote: post #139

apathy wrote: post #111

Earlier quoted context omitted.

The majority of content in most journals is asinine or incorrect. About the only thing that can fix this is quicker turnaround (cf STAP, NgAgo, the godawful GWAS paper in Neuron recently, etc). It's not at all clear to me that the checks or balances were helping beforehand. Hiring a shit ton of MBA types to administer research probably didn't help much either. Also, out of curiosity, is this open access / fast review…

>>fix this is quicker turnaround Why? As the first author of several publications, more than half the reviews I received were not well thought out. This part of the process doesn't happen, Open Acess and self publishing websites exploited this fact for greater throughput. >>machine learning I would argue that the machine learning bloom in recent years is because of an availability of new technology from industry, sup…

Re: 1: no shit. The turnaround is for rebuttals. I try to do thorough reviews (I have published plenty as well) but realistically I recognize that no one has the sort of free cycles required to catch everything in advance. What's worse is that an awful lot of reviews are pure political bullshit.

In the end it's the people who may or may not try to build on your work (or mine!) that are the best judges of whether it's BS.

Re: 2: probably, but diffusion of ideas benefits massively from readily accessible documentation. One of the things that will cause me to immediately reject a paper is if its method implementation does not work as described. I will always reject in such cases. They are alarmingly common and this is one of the few easy cases in reviewing. Lack of an implementation is also cause to reject.

Re: 3: it has everything to do with it. Unless you're running and publishing trials please don't lecture me on this. See opentrials for a particularly frightening take on why published trials so poorly represent those submitted to the FDA or registered with CTEP. Meanwhile actual RCTs get buried by shitbags demanding more subjects than there are recorded cases in the past 40 years (no joke).

If you're not doing trials, you may have to take my word for it (or get involved in RCTs and find out for yourself). A lot of the enterprise is actively harmful to science by omission.