6 ms·

Can I just make a general plea? You should upload your paper to arXiv. When you do, please upload your source (tex, or word I imagine), as well as a PDF. For

Can I just make a general plea? You should upload your paper to arXiv. When you do, please upload your source (tex, or word I imagine), as well as a PDF. For the blind, PDF is the worst possible format, and tex and word are the best formats. Don't hide, or lose, the blind-accessible version of your paper.

chime 10y ago
It would be great if arXiv upload screen said this. Not sure if it does or not.
- sibrahim 10y ago
  That's certainly been my experience. I've had arXiv automatically block bare uploads of TeX-derived PDFs (presumably identified through PDF metadata). For these, it required that the source be uploaded and compiled on their server. On balance, it's probably best to require source as arXiv does, but this can create interesting issues from time to time. Since the source is downloadable, researchers can inadvertently end up sharing partial results or snark that was commented out in the TeX source.
- kkylin 10y ago
  I haven't uploaded a paper in a while (coauthors have been doing it more recently), but I'm pretty sure it encourages uploading document sources somewhere during the process. The issue that sibrahim mentions, about stuff in comments, is real: on a multi-author tex the file tends to end up being pretty messy, with lots of informal remarks and old versions in the comments. I always strip out all the comments before submitting.
apathy 10y ago
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 degree strogatz and the law scholars) pushed forward what the Web was supposed to be. Not a place to buy stuff, but a place to learn stuff, without waiting for it to make its way through a hyper politicized review process so that it could be printed in a 17th century fashion and mailed to some corners of the world, eventually perhaps reaching a fraction of the people who could use it. Rather, everyone everywhere with a connection. Anyone who doesn't deposit preprints (arXiv, biorxiv, or wherever) or who doesn't agitate for their coauthors to do so is not really in it for the science. It's fine to be competitive -- deposit yours first. Make the fucking discovery instead of parasitically piggybacking on those who do the work. But that last part, that's hard. Very hard. As long as there is enough money left in academia to encourage lazy shits, those of us who care about scholarship will have to push, hard, to remove the last refuge of these scoundrels. You're either on the side of justice -- open data, open formats, open scholarship -- or you are tacitly endorsing Elsevier & Springer, who haven't the slightest problem using crap like incremental JavaScript & mangled PDFs to deny access to scholarship even to those who have paid. David (blocking on his last name) at CTC made that choice for me. He set an example that forced me to admit what was right. I hope others will do the same. It's the right thing to do.
- frozenport 10y ago
  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.
  - apathy 10y ago
    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 problem what led to machine learning falling into irrelevance? Because we wouldn't want that to happen to other fields. Can you imagine if raw clinical trial data was out there, for example? (The Horror! Best keep these appallingly expensive results locked up!)
    - frozenport 10y ago
      >>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.
agumonkey 10y ago
PDF readers manage to parse text back somehow effectively, maybe not on formula / formatting heavy PDFs. Anyway good call, accessibility is not only for mainstream websites. I'm sure the blind dude that aced math classes in college would agree.
- CJefferson 10y ago
  Formulas and many tables do very badly. Would be nice if latex embedded the source of equations into pdfs. Wonder how hard that would be to add?
  - agumonkey 10y ago
    Embedding anything in PDF doesn't seem hard (considering what a few security talks said). How large are latex files ? probably not much a few 100KBs. It's easy to add a compressed stream in a PDF. It's a great idea.
hackuser 10y ago
> 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?
- cygx 10y ago
  They probably can get at the text, but I have doubts about any formulae...
- robin-berjon 10y ago
  PDF is only accessible if it is specifically crafted to be so (and then again, I don't think that goes very far). To the best of my knowledge only Adobe's tools and Word actually output that (and at least in the latter they tend to look like train-wrecks, which may or may not be PDF's fault more than Word's).
- contravariant 10y ago
  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 selectfont % choose the size in points and establish % the font as the current one 72 500 moveto % position the current point at % coordinates 72, 500 (the origin is at the % lower-left corner of the page) (Hello world!) show % stroke the text in parentheses showpage % print all on the page Now if you're lucky you can just extract all quoted text and read those in order, but that's unlikely to work for all documents.
  - hackuser 10y ago
    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 all applications including all their versions, features, quirks, and platform integration issues - such a daunting and difficult task that it seems unlikely. But where do screen readers hook into the content? After it's output from the application but before it's an image for the screen (which could require OCR)? Ironically, I suppose PostScript or PDF could provide common interfaces.
mixedmath 10y ago
I'm a (PhD student) mathematician and every paper I've uploaded has included the TeX. I looked at about 10 papers in math at random, and 9/10 of them also included the TeX. But this isn't something I've looked for in the past. So I wonder: in your experience, about what percentage of papers on the arXiv have included the source?
- johncolanduoni 10y ago
  It's far less common in physics :/
- frozenport 10y ago
  Almost nobody in experimental life sciences uses Tex. My advisor refused to read anything that wasn't in MS Word.
  - jmnicholson 10y ago
    We're working to provide a Word-like interface on git repositories for researchers to write their manuscripts in at authorea.com. Our editor allows researchers to write in markdown, LaTeX, or rich text all within one article.
ASipos 10y ago
For the record, if you upload the TEX, arXiv autogenerates the PDF.
- ctchocula 10y ago
  The problem I face is that my papers is in multiple tex files in several folders connected to a main.tex using \includes. Is there a convenient option that will take care of this issue?
  - rhaps0dy 10y ago
    The latexpand perl script, the flatten and flatex programs. Please upload your papers in the future! :) https://tex.stackexchange.com/questions/21838/replace-inputfilex-by-the-content-of-filex-automatically https://tex.stackexchange.com/questions/21838/replace-inputf...
  - sibrahim 10y ago
    I've had success using \import{subdir/}{BasenameInSubdir} from the import package. The basic (and unfortunate in a xkcd/1479 way) issue appears to be that the arXiv compile server doesn't allow writing to subdirectories. A subdir \include implicitly requires write access for the aux file.
  - xvilka 10y ago
    Setting up something like webui for storing those files for every paper, something like gitlab or gogs, could really help. It could add more transparency, ability to add some feedback in the issues, and so on.
robin-berjon 10y ago
I know that Word has decent accessibility built in (because Microsoft actually cares about this) but I'm surprised that you're getting mileage out of TeX which is a very visual format. Do you basically screen-read the source? Or is there a non-visual output for it that works?
- CJefferson 10y ago
  Yes, you do have to learn Tex to read it, but I don't know of any other format any blind mathematician uses. It is common to teach maths with latex -- while it isn't perfect by any means, it is better than any alternative.

chime 10y ago

It would be great if arXiv upload screen said this. Not sure if it does or not.

sibrahim 10y ago
That's certainly been my experience. I've had arXiv automatically block bare uploads of TeX-derived PDFs (presumably identified through PDF metadata). For these, it required that the source be uploaded and compiled on their server. On balance, it's probably best to require source as arXiv does, but this can create interesting issues from time to time. Since the source is downloadable, researchers can inadvertently end up sharing partial results or snark that was commented out in the TeX source.
kkylin 10y ago
I haven't uploaded a paper in a while (coauthors have been doing it more recently), but I'm pretty sure it encourages uploading document sources somewhere during the process. The issue that sibrahim mentions, about stuff in comments, is real: on a multi-author tex the file tends to end up being pretty messy, with lots of informal remarks and old versions in the comments. I always strip out all the comments before submitting.

apathy 10y ago

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 degree strogatz and the law scholars) pushed forward what the Web was supposed to be. Not a place to buy stuff, but a place to learn stuff, without waiting for it to make its way through a hyper politicized review process so that it could be printed in a 17th century fashion and mailed to some corners of the world, eventually perhaps reaching a fraction of the people who could use it. Rather, everyone everywhere with a connection. Anyone who doesn't deposit preprints (arXiv, biorxiv, or wherever) or who doesn't agitate for their coauthors to do so is not really in it for the science. It's fine to be competitive -- deposit yours first. Make the fucking discovery instead of parasitically piggybacking on those who do the work. But that last part, that's hard. Very hard. As long as there is enough money left in academia to encourage lazy shits, those of us who care about scholarship will have to push, hard, to remove the last refuge of these scoundrels. You're either on the side of justice -- open data, open formats, open scholarship -- or you are tacitly endorsing Elsevier & Springer, who haven't the slightest problem using crap like incremental JavaScript & mangled PDFs to deny access to scholarship even to those who have paid. David (blocking on his last name) at CTC made that choice for me. He set an example that forced me to admit what was right. I hope others will do the same. It's the right thing to do.

frozenport 10y ago
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.
- apathy 10y ago
  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 problem what led to machine learning falling into irrelevance? Because we wouldn't want that to happen to other fields. Can you imagine if raw clinical trial data was out there, for example? (The Horror! Best keep these appallingly expensive results locked up!)
  - frozenport 10y ago
    >>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.

agumonkey 10y ago

PDF readers manage to parse text back somehow effectively, maybe not on formula / formatting heavy PDFs. Anyway good call, accessibility is not only for mainstream websites. I'm sure the blind dude that aced math classes in college would agree.

CJefferson 10y ago
Formulas and many tables do very badly. Would be nice if latex embedded the source of equations into pdfs. Wonder how hard that would be to add?
- agumonkey 10y ago
  Embedding anything in PDF doesn't seem hard (considering what a few security talks said). How large are latex files ? probably not much a few 100KBs. It's easy to add a compressed stream in a PDF. It's a great idea.

hackuser 10y ago

> 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?

cygx 10y ago
They probably can get at the text, but I have doubts about any formulae...
robin-berjon 10y ago
PDF is only accessible if it is specifically crafted to be so (and then again, I don't think that goes very far). To the best of my knowledge only Adobe's tools and Word actually output that (and at least in the latter they tend to look like train-wrecks, which may or may not be PDF's fault more than Word's).
contravariant 10y ago
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 selectfont % choose the size in points and establish % the font as the current one 72 500 moveto % position the current point at % coordinates 72, 500 (the origin is at the % lower-left corner of the page) (Hello world!) show % stroke the text in parentheses showpage % print all on the page Now if you're lucky you can just extract all quoted text and read those in order, but that's unlikely to work for all documents.
- hackuser 10y ago
  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 all applications including all their versions, features, quirks, and platform integration issues - such a daunting and difficult task that it seems unlikely. But where do screen readers hook into the content? After it's output from the application but before it's an image for the screen (which could require OCR)? Ironically, I suppose PostScript or PDF could provide common interfaces.

mixedmath 10y ago

I'm a (PhD student) mathematician and every paper I've uploaded has included the TeX. I looked at about 10 papers in math at random, and 9/10 of them also included the TeX. But this isn't something I've looked for in the past. So I wonder: in your experience, about what percentage of papers on the arXiv have included the source?

johncolanduoni 10y ago
It's far less common in physics :/
frozenport 10y ago
Almost nobody in experimental life sciences uses Tex. My advisor refused to read anything that wasn't in MS Word.
- jmnicholson 10y ago
  We're working to provide a Word-like interface on git repositories for researchers to write their manuscripts in at authorea.com. Our editor allows researchers to write in markdown, LaTeX, or rich text all within one article.

ASipos 10y ago

For the record, if you upload the TEX, arXiv autogenerates the PDF.

ctchocula 10y ago
The problem I face is that my papers is in multiple tex files in several folders connected to a main.tex using \includes. Is there a convenient option that will take care of this issue?
- rhaps0dy 10y ago
  The latexpand perl script, the flatten and flatex programs. Please upload your papers in the future! :) https://tex.stackexchange.com/questions/21838/replace-inputfilex-by-the-content-of-filex-automatically https://tex.stackexchange.com/questions/21838/replace-inputf...
- sibrahim 10y ago
  I've had success using \import{subdir/}{BasenameInSubdir} from the import package. The basic (and unfortunate in a xkcd/1479 way) issue appears to be that the arXiv compile server doesn't allow writing to subdirectories. A subdir \include implicitly requires write access for the aux file.
- xvilka 10y ago
  Setting up something like webui for storing those files for every paper, something like gitlab or gogs, could really help. It could add more transparency, ability to add some feedback in the issues, and so on.

robin-berjon 10y ago

I know that Word has decent accessibility built in (because Microsoft actually cares about this) but I'm surprised that you're getting mileage out of TeX which is a very visual format. Do you basically screen-read the source? Or is there a non-visual output for it that works?

CJefferson 10y ago
Yes, you do have to learn Tex to read it, but I don't know of any other format any blind mathematician uses. It is common to teach maths with latex -- while it isn't perfect by any means, it is better than any alternative.