6 ms·

The one piece of advice I give new PhD students is to maintain a list of your references for a bibliography ahead of time. For every paper you read, copy the ci

The one piece of advice I give new PhD students is to maintain a list of your references for a bibliography ahead of time. For every paper you read, copy the citation in BibTeX format and write a couple of sentences to remind yourself what the paper was about. Do this for every source, even if it doesn't seem important at the time.

ifh-hn 7mo ago
Zotero and AI have this covered now. If there's one thing AI is good at it's summarising crappy formatted papers. Never understood the 2 and 3 column thing. Horrendous way to format something.
- setopt 7mo ago
  2-column format has narrower columns, which means that your eyes move more vertically than horizontally while reading it. That is considered conducive to “skimming” long texts if you’re a “speed reader”. Do you mean that you’re using AI as a search engine for your local bibliography? I haven’t seen any AI plugins for Zotero.
  - ifh-hn 7mo ago
    I'm severely dyslexic and the columns are a massive hindrance for me, and I also cannot skim read due to this and meares irlen. So my dislike is not universal applicable, just personal experience. On the zotero front there a bunch of AI plugins. But I've not used them. But yes the premise is that your can speak and ask your library questions. Some are set up differently though. Personally I can fire a paper into an llm and get a good idea of the content immediately and then ask questions about it. It's more interactive and allows me to get a better idea of it prior to reading it.
    - somethingsome 7mo ago
      LLMs make too many mistakes when summarizing papers in their current state, I would never trust it to summarize a whole paper at the moment. I only use it on a sentence or paragraph basis, otherwise it misses the point 90% of the time. I would strongly advise against this use for the moment. The important part of reading a paper is not only to extract general rules, but to build your own internal model. Without it you cannot effectively do research. The main interesting points are often in the subtleties of the details deep in the paper. Internal tought that come easily to mind when I read : - 'oh they used that equation, but that could be also be interpreted totally differently, what happens if we change point of view, does it makes sense from this other perspective' - 'I see they claim to achieve better results than sota, but actually, they compared with other methods that are not solving exactly the same problem, what shortcut or changes did they had to do to obtain a fair comparison, is it a fair comparison, can I trust those numbers? ' - 'oh, the authors didn't realize that they solved this other problem, or did they realize but there was a block somewhere preventing it?' - 'I like this trick to achieve that result, but at the same time, it will prevent to solve a whole class of other problems, so their method will not work on those cases' ... Also, notice that a paper IS a summary of multiple months/years of work, and researchers summarize it already to the maximum to stay within the page limit, by summarizing a summary you will always miss many things.
      - ifh-hn 7mo ago
        Fair points. And likely why I'm not suited to academia too. I've just never really groked the practice. I've obviously only experience from bachelor's and masters but it always seems that you have an idea and the research is finding papers to back it up, and then some that might not. The work you do doesn't really matter as it seems secondary to the nonsense around "the literature".
        aragilar 7mo ago
        In what, that does not align at all with my experience in the sciences (where the point is the novelty, not summarise the literature)?
        ifh-hn 7mo ago
        I've a bachelors of science (first) in computer science, and currently doing a dissertation for a master's in cyber security, on route for a first but that might change depending on the mark for this dissertation. My experience with the bachelors was that despite my project being derailed by the bullshit around formatting the document, doing "research" by searching the library for peer reviewed papers that backed up my claims, etc, etc; I got a excellent mark. In short I set out to make something and due to the academic processes failed in making anything, but because I was able to critically reflect on it, I got a good mark. Waste of time, unless you were just are a good mark. For my masters I know the project doesn't matter, I'm concentrating on the academic nonsense because that's where the marks are.
        ModernMech 7mo ago
        The work you were given in your undergraduate and master’s was not research, it was homework. The task was critical reflection, which is repeatable and achievable for students; whereas research is expensive, one off, and generally out of reach for undergrads, and requires intensive oversight by an experienced researcher. The waste of time would be for a professor to train you up to be a researcher before you’ve proven you are ready, hence the homework assignments.
  - bobmarleybiceps 7mo ago
    I feel like that's true when the font is insanely small, which I guess was good when people would print entire proceedings. Reading two column super small font on a computer is super annoying though tbh.
    - setopt 7mo ago
      If you have a hiDPI monitor, then reading even small fonts is IMO less annoying. But no monitor can still beat the DPI of a good printer.
  - pks016 7mo ago
    There are few. I use zoteroGPT to extract things(e.g. methods, sample size, species etc.) from a bunch of papers/collection. I don't use it for summary.
- SirHumphrey 7mo ago
  The comments you write in to Zotero are not what paper is about - abstract covers this well enough - it’s about what you found interesting or useful about the paper.
ccppurcell 7mo ago
Use zotero and betterbibtex. By all means type a comment so you know which ideas came from where but I'm a big advocate of taking notes by hand when you really want to understand something, as opposed to reminding your future self about something you already understand.
- ifh-hn 7mo ago
  There's also better notes too for this.
whateverboat 7mo ago
The lack of good tools to have good research notes with good search is kind of mind-boggling. I have reverted to having a website for myself, a private one that I run on my machine, using mkdocs which comes close to what I would want.
psychoslave 7mo ago
Not within a PhD, but as a side project I work on a research project on wikiversity about grammatical gender in French. It does reference a bunch of books and academic works, like probably a hundred I guess. The most tedious work though is to check which nouns are used only in a single gender of do have some epicenic or specific inflection used in the wild and giving a reference that attest that when it's not already so consensual that most general public dictionary would already document the fact. For that the research refers to thousand of webpages. I'm glad that most of the time I just need to drop the DOI, ISBN, or page URL and MediaWiki will handle the filing of the most relevant fields. That's not perfect, it generates the output with many different models currently (some don't have an excerpt field), and some required fields might be left blank, url to pdf won't work, and so on. But all in all it make the process of taking note of the reference quick and not going too much in my way. Creating a structured database out of it can certainly be done later.
DamonHD 7mo ago
I have had some fun exhuming my old LaTeX skills and assembling a BibTeX bibliography from which I automatically extract the right entries presented in whichever style is needed for a given paper and for my own (HTML) site. I even publish the collection in Zenodo in case useful to others. I use the 'annote' field for the reminder you suggest.
geokon 7mo ago
why? like what are you doing with this mega list later? Ive never felt the need for something like this in my research but maybe im missing something
- gnfargbl 7mo ago
  Presumably the idea is that you put the relevant parts of the list in your thesis. You need to convince your examiner that you understand the background to the original research you did, and a solid reference list (with supporting text in the introductory/background section of your thesis) is part of doing that. Personally I did the references at the end and didn't feel like I suffered from that decision, but the key references in my particular area were a relatively small and well-known set.
  - geokon 7mo ago
    Hmm, yeah. I mean you often see huge reference lists which always just makes me feel like the person can't possible be actually well acquainted with the stuff that's being referenced. So who are you really fooling? Seems all very performative, though I guess I understand the motivation
RhysU 7mo ago
Citeulike [1] was great but is sadly no more. Add any paper you pick up to your tracking system before you read it. Make that part of your reading ritual. Save the PDF right away, too. You may later lose access to the journal. Or, CiteULike (where I^Hyou uploaded all those articles) may go away. [1] https://en.wikipedia.org/wiki/Citeulike https://en.wikipedia.org/wiki/Citeulike
whiplash451 7mo ago
This is very good advice for a few reasons: 1. It reduces the odds of missing a key reference in your papers and accelerates the write-up of the (often mandatory) Related Work section 2. It helps you maintain a mental map of the field as your research progresses
xtracto 7mo ago
Ha! You just made me remember how much I used JabRef (open source bibtex reference app) back in 2004 when I did my PhD. It was the best/worst 4 years of my life. I studied overseas (uk), met my future wife and got a PhD that really wasn't useful for much to me. Fortunately it was under a scholarship.

ifh-hn 7mo ago

Zotero and AI have this covered now. If there's one thing AI is good at it's summarising crappy formatted papers. Never understood the 2 and 3 column thing. Horrendous way to format something.

setopt 7mo ago
2-column format has narrower columns, which means that your eyes move more vertically than horizontally while reading it. That is considered conducive to “skimming” long texts if you’re a “speed reader”. Do you mean that you’re using AI as a search engine for your local bibliography? I haven’t seen any AI plugins for Zotero.
- ifh-hn 7mo ago
  I'm severely dyslexic and the columns are a massive hindrance for me, and I also cannot skim read due to this and meares irlen. So my dislike is not universal applicable, just personal experience. On the zotero front there a bunch of AI plugins. But I've not used them. But yes the premise is that your can speak and ask your library questions. Some are set up differently though. Personally I can fire a paper into an llm and get a good idea of the content immediately and then ask questions about it. It's more interactive and allows me to get a better idea of it prior to reading it.
  - somethingsome 7mo ago
    LLMs make too many mistakes when summarizing papers in their current state, I would never trust it to summarize a whole paper at the moment. I only use it on a sentence or paragraph basis, otherwise it misses the point 90% of the time. I would strongly advise against this use for the moment. The important part of reading a paper is not only to extract general rules, but to build your own internal model. Without it you cannot effectively do research. The main interesting points are often in the subtleties of the details deep in the paper. Internal tought that come easily to mind when I read : - 'oh they used that equation, but that could be also be interpreted totally differently, what happens if we change point of view, does it makes sense from this other perspective' - 'I see they claim to achieve better results than sota, but actually, they compared with other methods that are not solving exactly the same problem, what shortcut or changes did they had to do to obtain a fair comparison, is it a fair comparison, can I trust those numbers? ' - 'oh, the authors didn't realize that they solved this other problem, or did they realize but there was a block somewhere preventing it?' - 'I like this trick to achieve that result, but at the same time, it will prevent to solve a whole class of other problems, so their method will not work on those cases' ... Also, notice that a paper IS a summary of multiple months/years of work, and researchers summarize it already to the maximum to stay within the page limit, by summarizing a summary you will always miss many things.
    - ifh-hn 7mo ago
      Fair points. And likely why I'm not suited to academia too. I've just never really groked the practice. I've obviously only experience from bachelor's and masters but it always seems that you have an idea and the research is finding papers to back it up, and then some that might not. The work you do doesn't really matter as it seems secondary to the nonsense around "the literature".
      - aragilar 7mo ago
        In what, that does not align at all with my experience in the sciences (where the point is the novelty, not summarise the literature)?
        ifh-hn 7mo ago
        I've a bachelors of science (first) in computer science, and currently doing a dissertation for a master's in cyber security, on route for a first but that might change depending on the mark for this dissertation. My experience with the bachelors was that despite my project being derailed by the bullshit around formatting the document, doing "research" by searching the library for peer reviewed papers that backed up my claims, etc, etc; I got a excellent mark. In short I set out to make something and due to the academic processes failed in making anything, but because I was able to critically reflect on it, I got a good mark. Waste of time, unless you were just are a good mark. For my masters I know the project doesn't matter, I'm concentrating on the academic nonsense because that's where the marks are.
        ModernMech 7mo ago
        The work you were given in your undergraduate and master’s was not research, it was homework. The task was critical reflection, which is repeatable and achievable for students; whereas research is expensive, one off, and generally out of reach for undergrads, and requires intensive oversight by an experienced researcher. The waste of time would be for a professor to train you up to be a researcher before you’ve proven you are ready, hence the homework assignments.
- bobmarleybiceps 7mo ago
  I feel like that's true when the font is insanely small, which I guess was good when people would print entire proceedings. Reading two column super small font on a computer is super annoying though tbh.
  - setopt 7mo ago
    If you have a hiDPI monitor, then reading even small fonts is IMO less annoying. But no monitor can still beat the DPI of a good printer.
- pks016 7mo ago
  There are few. I use zoteroGPT to extract things(e.g. methods, sample size, species etc.) from a bunch of papers/collection. I don't use it for summary.
SirHumphrey 7mo ago
The comments you write in to Zotero are not what paper is about - abstract covers this well enough - it’s about what you found interesting or useful about the paper.

ccppurcell 7mo ago

Use zotero and betterbibtex. By all means type a comment so you know which ideas came from where but I'm a big advocate of taking notes by hand when you really want to understand something, as opposed to reminding your future self about something you already understand.

ifh-hn 7mo ago
There's also better notes too for this.

whateverboat 7mo ago

The lack of good tools to have good research notes with good search is kind of mind-boggling. I have reverted to having a website for myself, a private one that I run on my machine, using mkdocs which comes close to what I would want.

psychoslave 7mo ago

Not within a PhD, but as a side project I work on a research project on wikiversity about grammatical gender in French. It does reference a bunch of books and academic works, like probably a hundred I guess. The most tedious work though is to check which nouns are used only in a single gender of do have some epicenic or specific inflection used in the wild and giving a reference that attest that when it's not already so consensual that most general public dictionary would already document the fact. For that the research refers to thousand of webpages. I'm glad that most of the time I just need to drop the DOI, ISBN, or page URL and MediaWiki will handle the filing of the most relevant fields. That's not perfect, it generates the output with many different models currently (some don't have an excerpt field), and some required fields might be left blank, url to pdf won't work, and so on. But all in all it make the process of taking note of the reference quick and not going too much in my way. Creating a structured database out of it can certainly be done later.

DamonHD 7mo ago

I have had some fun exhuming my old LaTeX skills and assembling a BibTeX bibliography from which I automatically extract the right entries presented in whichever style is needed for a given paper and for my own (HTML) site. I even publish the collection in Zenodo in case useful to others. I use the 'annote' field for the reminder you suggest.

geokon 7mo ago

why? like what are you doing with this mega list later? Ive never felt the need for something like this in my research but maybe im missing something

gnfargbl 7mo ago
Presumably the idea is that you put the relevant parts of the list in your thesis. You need to convince your examiner that you understand the background to the original research you did, and a solid reference list (with supporting text in the introductory/background section of your thesis) is part of doing that. Personally I did the references at the end and didn't feel like I suffered from that decision, but the key references in my particular area were a relatively small and well-known set.
- geokon 7mo ago
  Hmm, yeah. I mean you often see huge reference lists which always just makes me feel like the person can't possible be actually well acquainted with the stuff that's being referenced. So who are you really fooling? Seems all very performative, though I guess I understand the motivation

RhysU 7mo ago

Citeulike [1] was great but is sadly no more. Add any paper you pick up to your tracking system before you read it. Make that part of your reading ritual. Save the PDF right away, too. You may later lose access to the journal. Or, CiteULike (where I^Hyou uploaded all those articles) may go away. [1] https://en.wikipedia.org/wiki/Citeulike https://en.wikipedia.org/wiki/Citeulike

whiplash451 7mo ago

This is very good advice for a few reasons: 1. It reduces the odds of missing a key reference in your papers and accelerates the write-up of the (often mandatory) Related Work section 2. It helps you maintain a mental map of the field as your research progresses

xtracto 7mo ago

Ha! You just made me remember how much I used JabRef (open source bibtex reference app) back in 2004 when I did my PhD. It was the best/worst 4 years of my life. I studied overseas (uk), met my future wife and got a PhD that really wasn't useful for much to me. Fortunately it was under a scholarship.