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Nonacademic Letter of Recommendation for Masters
I've been working as a TA for an on campus program for the last year and a half. The director really likes me; she has a Masters in Mathematics and runs the learning services program for the STEM programs but she doesn't teach or do research.
I'm planning on applying to Master's in Computer Science programs and want to eventually do work in mass education programs (like Khan Academy or Coursera). Would it be acceptable to ask for a letter of recommendation from her?
I figured it would be "different" in a good way; also, any other letters would be "average" at best. I was a good student but not much more in my classes.

"She likes me" doesn't say much.  Has her experience with you given her confidence that you would succeed in a masters program in computer science?  Can she give specifics that computer scientists would find convincing?  That's what an admission committee wants to see.

@NateEldredge I believe that she has confidence that I will definitely succeed in the masters program but will probably put emphasis on my affinity to better education.

Master's in Computer Science — Which kind? Professional / course-based / terminal masters, or research / thesis masters?

@JeffE Terminal Course-based masters looking to go into mass education/industry. Looking to work for a company similar to edx.

it depends on the university, for instance on my university the hierarchy of letter of recommendations goes like this:

Top priority: Faculty (same/different institution)
Mid: Staff (on same institution)
Low: High-school Instructors

Of course having faculty give you letters of recommendation is better.
Just remember that "usually" you need 2-3 letters of recommendation.
I would suggest to use the letter of recommendation from this director that you mention, If and only if you cant get letters of recommendations from faculty.

The stakes are usually a little lower for masters programs, so this might be okay. If the primary funding source at your new program is a TA-ship, then your experience teaching could count in your favor. Its better if the teaching experience is directly in your new research area. Your reader wants to know that you are ready to start developing more specialized skills in your research area. If you're teaching in that area, then it shows that you understand the basic issues well enough to break them down for a less sophisticated audience. That's good. Make sure the writer really focuses on your engagement with CS more that your engagement with the students. Ask your writer to describe the areas that you were teaching on, and how you handled the material or broke it down, how you dealt with answering questions when you didn't know the answer (did you do research? That's grad level thinking). Have her give examples. Also ask to avoid using feeling language (e.g., she is a caring an compassionate teacher) or personality characteristics (e.g., she is very enthusiastic). If she hasn't written many letters, then she might not know to avoid this.
I will also note, as someone with somewhat eclectic credentials, "different" is rarely a good thing in academic. The goal is to have her tailor the letter to align you as closely as possible with your discipline.

This sounds like a good way to strengthen your application.
Also, there is something you can do to strengthen the other potential letters.  If you get to know a professor from a class you have taken, by going to office hours at least once, to show interest in the professor's research, and share something about yourself, the professor will be able to write a slightly less cookie-cutter letter.


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Do you include papers that you contributed to but weren't cited as an author in on your CV?
I'm an undergraduate and about to apply to graduate school. I did summer research that contributed to a paper and was asked to extend my time there to write the publication but could not stay due to academic reasons. Because I contributed to it, is it appropriate to include it on my CV?

Why isn't your name on this paper?

They said that the if I wanted my name on it, I'd have to stay back to help write it.

Significant data collection, preparation, and analysis crosses my threshold for authorship easily. The Internet is also a great mechanism for exchanging drafts and collaborating on writing. I find cutting a student out for not being physically present and not finding ways to work them into authorship pretty sad.

@BillBarth - I would recommend not turning this question into a discussion on whether the OP should have been included as an author, because that really won't lead to anywhere useful. It's entirely possible you're right, but at this point, it's water under the keel.

Related: http://academia.stackexchange.com/questions/1112/should-i-include-a-publication-where-im-only-acknowledged-and-not-one-of-the-a

I had a similar situation, there were a few papers I assisted with as an undergraduate where I was listed in the acknowledgements but wasn't listed as an author. Generally, people don't list those on their CV, simply because it will look odd... you'll get a lot of people asking, "why are you listing this if your name isn't on it?"
That said, since it's your CV, you can list anything you want with the proper commentary. You may consider listing it as:

<Citation goes here>
Note: I am listed in the acknowledgements section for this paper, as I assisted extensively with data preparation and analysis.

Do realize that the fact that your name isn't on the paper will significantly decrease it's value in your promoting yourself. The more I think about it, it's probably a bad idea to list it... I would recommend just listing the work you did in the appropriate section on your CV and leave the paper out.

When describing the work, you could add a note like "This work contributed to the following publication: ...".

source: Stack Exchange

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How to proceed after reject & resubmit
I recently got a reject & resubmit which usually would not bother me too much, however, this case is a bit special:
The specific journal runs a single-blind peer review process. One review was very positive and the other one was extremely negative (if not to say rude). The AE and SE also provided their own comments and decided "reject with merit". Which is ok, however, there is scant evidence that the negative review has been done by my former phd supervisor. As indicated by the rude review we did not separate after my graduation in a good way.
The problem is: I do not know how to proceed from this point. How do i make sure that i will get a fair and (more important) ethical review process after re-submission? I'm also not sure how common it is to ask the authors for a decision about the resubmission (incl. a concrete time horizon) after rejection (note it is a top trier journal).
According to the peer-review process i should have no idea about the reviewers. However, it is not always too difficult to figure out (in particular if the particular research area is small and you have worked for years for a specific memeber).
Many thanks in advance!

You can always ask in the cover letter that specific researchers be excluded as reviewers due to conflict. If the editor respects your wish, that is another question, but they potentially might.

Let me suggest two things. First is that you ignore the rudeness and take what is in the reviews you got to improve the paper as best you can. In other words, standard practice.
But, when you resubmit, let the editor know that you have conflicts, beyond the paper, with individual A (by name) and that you don't believe they can give you a fair reading. Ask that the editor not assign them as your reviewer. I suspect that this is an unusual request (in some fields), but that it would be honored. The editor needs honest appraisals, unclouded by personal issues.

In my field it's pretty common on submission for journals to ask for a "list of reviewers" and "list of not reviewers". Editors are free to choose who they want to actually ask, and will typically find some of their own outside the first list, but I haven't seen one ignore the second list. Might be unusual that a former supervisor makes that list, or maybe not, but having the list/making the request itself doesn't seem unusual.

Many thanks for the suggestions! I was not sure about the appropriateness of such a request (as it may appear a bit infantile). Luckily, the editor said that we do not need to directly address all comments in the reviewer letters. For some statements it would have been hard without embarrassing the specific reviewer and this would not necessarily have contributed to the situation.

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Is there a simple way to bulk download a large number of papers from a list of references
I've got a library of 1200 references I'm using for a systematic review. Now I need to download the PDFs of all these references, which will take days if I do it manually. Is there a simple way to automatically download as many as possible from pubmed / Google Scholar / (maybe Scihub)? I have institutional access.
Edit: My solution was to load the reference list into multiple reference managers and run the PDF import function in all of them. Some managers succeeded where others failed. I had to do the rest manually.

Did you try to ask your librarian?

If you want to do a systematic review of these 1200 works I suspect you would need to read at the very least the abstract but presumably significant parts of the text in each of them. Relative to that effort, the downloading is completely trivial.

For systematic review, if you're following PRISMA, you'll typically do some preliminary 'checks' before getting to the lists for full text review.
I'm assuming the 1200 odd references are your final list after the duplicate removal and screening, and perhaps your forward-and-reverse literature chaining.
In Zotero, you can enable automatic PDF download in preference. For your purpose, you then bulk import reference using doi or bibtex or ris.

Someone recently developed a working script for bulk adding doi and updating metadata

The trick with Zotero is that Zotero is able to download pdf link to an entry from multiple sources. There are limitations though.
Beware that most academic database would lock you out if performing large bulk downloads at fast rate. Always a good idea to use proxy. In your case, you already having institutional access which might assist.
With Endnote, you can bulk import PDF files or like you have in Mendeley, you can set a 'watch' on a folder from which Endnote will automatically import entries for PDF files added to the folder. Unfortunately, that does not address your challenge.
With Endnote, similar to Zotero, you can import reference list to populate tour Endnote database.

simply export reference list from your search (Google, Scopus ...) to a RIS file.

[Technical approach beyond the scope of Academia forum]
For other technical solutions beyond the scope of Academia, you can work directly with API of academic database.

Science direct and Scopus provide API access, which you register for for free. You'll still need access to perform low-level tasks and download.
you can leverage Python to work with academic database API
for Google Scholar, use Scholarly: Scholarly pypi, GitHub
for Scopus, pybliometrics is well used.
Pyscopus claims to be more friendly. I'm yet to use Pyscopus unlike others. More so, it's inactive since 2019!

There's one I've used recently, just can't recall the name offhand. It allows robust analysis and topic search. I'll update in due course.
[Scientific PDF download]

RESP: Research Papers Search claims to search and download scientific papers. Yet to try it out.
Articledownloader is worth exploring
PyPaperBot is well used for downloading scientific articles from DOI or academic database.

I'm busy with a fork of Automated Search Helper. A research project by Lech Madeyski team at Wroclaw University of Science and Technology, Poland. I'm yet to upload latest revision which has the

pdf downloader working with JSGlue, Jinja2
I have it working locally but need some code clean-up and documentation.

NB: with automatic downloaders, beware of captcha and blocking/ban by academic database
SciPDFParser comes across as a good parser of downloaded articles PDF.

I don't know of any tool to specifically scrape academic databases for pdf's. There may be some obscure program out there on GitHub or a web-crawler that could be repurposed. This question is a bit dated but addresses your problem in more detail and proposes some interesting solutions in that vein.
The easiest off the shelf solution is Endnote. It has a feature that allows for automatic search and retrieval of pdf's. If you have access, it works fairly well. Though it doesn't capture everything. I suspect that there are other reference managers with a similar feature. I don't know of free ones specifically, if that is a concern.
If none of those options are workable for you, consider if it is necessary to download all those pdf's. I'm assuming that you are just beginning to conduct your screening and so you likely don't need the full texts right away. I have conducted a handful of systematic reviews and I have always relied on title and abstract for the initial screen. If I could not make a decision from that info, simply navigating to the original online version was sufficient. Since you already have institutional access, why store them on your local device from the get-go? It would be significantly easier to download and store the papers you flag for further review or inclusion. This may not be right in your case, but it's something to consider if all else fails.

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Should I Change my Research Focus?
I just finished my first semester in a PhD program in Pure and Applied mathematics. My initial focus was on probability, statistics, modeling, and machine learning. To this end I took a course in (Modern) Probability, Nonlinear Optimization, and the mandatory Functional Analysis. Based on my performance in these courses my advisor suggested that I should consider maybe switching to a different focus, as he thinks I will struggle to pass the qualifying exam (specifically in the two elective courses Probability and Nonlinear Optimization).
However, I do not believe my scores reflect my real capability or interest in the subjects, but rather reflect a gap in what was taught and what was tested. I am sure I could study really hard and succeed.
I am posting here to get a second opinion on whether or not I should change my focus, or if I should stick with it and double down and study really hard. I posted on math.stackexchange and was advised to post here for a second opinion. (https://math.stackexchange.com/questions/3984219/what-are-some-possible-phd-research-areas-based-on-these-course-pairs?noredirect=1#comment8221305_3984219)
What would you advise? Should I change my focus to another one that I might have a better synergy with? Thank you!

Listen to your advisor. I have found that going through the doors that open for me, even if those doors are different from the ones that I initially had in mind, has never served me wrong. Don't be the person who won't walk through the door because they insist a different one should be opening.

Thank you for your advice. I will try my best to follow their advice. The only problem is figuring out a new area to focus on. I will try to overcome any issues I encounter and find a path to success. Thank you for your help.

This requires self-evaluation and introspection. That being said, don't let a bad grade in a course deter you from pursuing your interest(s) in mathematics. In my experience, the first semester in a PhD program is usually the worst in terms of grades. This is because you are still trying to adjust from undergraduate math to graduate. You may also have grading/TA duties, so time management skills are essential.

@LordVader007 thank you for your advice. It was my first semester working as a TA too, and I definitely felt overwhelmed. I will do some introspection and will see if the probability / statistics courses are what I am really passionate about. I will also see if I can optimize my time-management to really do well next semester. Thank you for your help.

Your advisor's advice is probably worth taking. They know you better than we do.
But your current goal is to get a doctorate. The specific sub field is less important than that goal. You can always take up a different specialty later if it isn't too different.
Find a path to success. Examine the obstacles (exams, ...) and find a way through them. You may have made some judgmental errors, but don't make any more.
But to find that path, in mathematics, find a field in which you have true insight into how things work. Math insight isn't general. You can have deep insight into one field (analysis) and little in another (algebra).

Thank you for your advice. I will not give up.


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What should I do if my PhD supervisor is not proficient in my field?
I am a first-year PhD student in machine learning at a reputable university in the UK. Over the past six months, my work has consisted of reading papers that I find interesting, studying textbooks, and experimenting with code. Although this may seem like a typical first-year experience, I have come to realize that my supervisor lacks proficiency in my field (I have had to explain fundamental concepts), which has made our meetings and my work less productive than anticipated.
Our meetings go something like this: I attempt to explain a paper I have read and then discuss possible incremental improvements, and the meeting would end with my supervisor telling me to go test my ideas. Although experimentation can be an essential part of research, coding every idea that I have is time-consuming. If my supervisor was more proficient in the field, I believe I would receive better direction and save a lot of time. They could immediately identify issues with my ideas or suggest other works that address the same problem.
While I understand that the PhD process should be student-led, I feel as though I don't have anyone to discuss ideas with.
I don't have experience with other PhD supervisors, so what is the role of a PhD supervisor? And what should I do about my situation?

Sounds pretty normal. "Coding every idea that I have is time-consuming" maybe, but that's what you're there for. You'll get faster (and more knowledgeable regarding which ideas are worth pursuing) over time.

Can you explain what evidence you have that your supervisor lacks proficiency? You did not include any information that suggests that this is the case in your question.

In any case, shouldn't you somehow arrange to switch advisors to one who is expert in the area of your desired projects?

Unfortunately,  be prepared to take longer to complete your tasks/degree.   This is the main reason why I am always a few steps ahead of my students.  Otherwise, they will not finished.  The only think you can do is find someone with more experience.

@user572780, based on some of your comments, is your project about applying machine learning in a particle physics context?

But your project is offered by someone from the physics department?

mathematical physics, or computer science, or something else?

Let us continue this discussion in chat.

I don't see that there are other options than one of the following: 1. Find a new advisor. 2. Find a co-advisor or an active collaborator whose expertise is closer to what you want to work on. 3. Learn to work with the current advisor.

@AdamPřenosil How do I go about finding a co-supervisor? Is it appropriate to cold-email other researchers and just ask to work with them?

That would really be a topic for a new question. (But in case you decide to post a new question, please check whether it has already been answered at Academia SE before.)

@NAMcMahon I never got your elaboration.

If all the experts in a field know what the "result" will be, then there is absolutely no value in the research. Research is about finding the answers to questions we (we being all humanity) do not know the answers to.
If you read papers and have ideas about how to improve them, those ideas are only interesting and useful if they would require some sort of test. If your advisor recommends that you test your ideas, that's because that's how research works.
If you don't understand how to test your idea, that's something you should discuss with your supervisor. If you've tested your idea but aren't sure your test actually shows what you think it does, that's something you should discuss with your supervisor. If you have lots of different ideas to test, you might ask for advice on prioritizing them. Ultimately, though, you're going to have to test some ideas.
In other fields, there may be much higher barriers to testing a theory than writing some code: you may need to do weeks or months of experiments, or go through time-consuming regulatory steps for research in animals or with humans. In that case, you likely want to do a bit more refining before doing any single test.

@Bryan_Krause, I don't expect my supervisor to be to able to tell me which ideas are good. However, based on my experience, I believe someone with more experience would be able to immediately rule out some ideas.

@user572780 Maybe, maybe not. Presumably you've not presented every possible idea, you've presented some ideas that seem reasonable to you. If you've read the work and "done your homework", you've already narrowed it down quite a bit. Your advisor may also see some learning value in doing the trial and error steps, even if they suspect some of your ideas are not likely to turn out. There's also the game theory aspect where the most interesting results might be when you try something unlikely to work and yet it works anyways.

Maybe your advisor is incompetent, but your post hasn't convinced me of that, and I have some prior that they are not entirely incompetent in that they've been successfully hired to their current position.

@Bryan_Krause, I don't think my post is meant to convince you of anything. Also, I am not claiming that my supervisor is incompetent. They might be the best particle physicist in the world. I am saying that they aren't proficient in my specific field as I am having to explain undergraduate-level concepts.

@user572780 That's fine, but I'm going to write answers according to the information I have; I can't have information not in your post. Your mention of explaining undergraduate-level concepts didn't come until a comment written after I wrote my answer, though I'd wonder to what extent you're being asked to explain such concepts to demonstrate your understanding of them (perhaps in a specific context) versus educating your supervisor. If you're doing a PhD in machine learning, though, I can't say it makes any sense to me to choose a particle physicist as supervisor, how did that come about?

@BryanKrause a lot of high energy physics research is starting to move towards AI to analysis experimental data (easily petabytes of data that has to be searched through). Though I don't know if the OPs advisor is a particle physicist

@NAMcMahon There's a substantial difference between using a given analysis approach applied to a problem in some field, and getting a PhD in the areas of statistics or machine learning. Though the former is likely to involve some methods development and may include comparisons of different approaches, the nature and expectations of the thesis are going to be entirely different.

That's true, though its also possible that OP's project was titled something like "Unsupervised learning and deep neural networks for new particle discovery in the LHC run 3" which sounds like its a PhD focused on machine learning it that's not your background, though it would maybe closer to an applied ML PhD (focused on particle physics). I'm trying to be flexible in what OP has said in order to resolve explaining these undergraduate level concepts with their supervisor being a competent researcher.

(assuming the supervisor was not just testing OP, which I considered most likely before particle physics was mentioned).

@NAMcMahon Sure, in that case my advice would be "meet with your advisor ASAP and figure out what the bounds and expectations of your PhD thesis are", because there could be a substantial disconnect (I'd be a bit puzzled how that wasn't revealed earlier, though it's quite possible for people with different expectations to completely talk past each other and hear what they think they should hear instead of what is being actually said)

Let us continue this discussion in chat.

I had the same experience when I did my Ph.D. in the UK.
I worked on distributed computation and operating systems and neither my first nor second supervisor had a good understanding of what I was doing.
To be frank, it was frustrating as there was no good academic exchange, debate, or collaborative work.
A lot of my co-PhDs had the same feeling.
You will learn to live with it. You need to take the lead on your research earlier. You will decide what route you follow, and what ideas to try from the start (now). The supervisor's feedback will be mostly on the methodical and publishing side.
My supervisor's involvement improved when I had results. I guess, it will be similar on your end. As soon as you apply your machine learning research to the field of your supervisor, they'll get more involved.
My advice is to go to conferences and look for people who do something similar.
Stay in contact with them and collaborate. This is something I should have done earlier in my PhD.
Alternatively, you could look for an academic in your institute/uni that has more experience in machine learning / your area of interest and collaborate with them more.
Generally speaking: A supervisor should guide you a bit with your research, and help with how research is done. Ideally, you want one where the research group works in close alignment, but a lot of young supervisors get PhD students with very different focuses, which makes collaboration within the group very difficult. More seasoned supervisors tend to get PhD students that share a common focus. The second supervisor (in the UK) is often just a formality and is, in most cases, not involved in your research.

If you really want to be successful in academia, it is important that you have your own ideas and make progress on your own.
Your advisor seems to be open to letting you explore your own ideas and is not forcing you to do exactly what he wants, which is a fairly rare opportunity.
Also, unless your advisor is insecure about his lack of knowledge and prevents you from discussing ideas or learning from other groups, you can just try to collaborate or learn from others. Conferences, collaboration, whatever you like.
The impression that I get from reading your post is that your fear over your own ideas not working out makes you want to blame your advisor for not helping. If you're really so concerned that a specific idea is good, then go find a friend in the field and see what they think. (But show them in the form of a small written writeup of the idea so it's harder for them to steal it.)

My advisor doesn't prevent me from collaborating with others, it's the exact opposite, they encourage it. My biggest issue is that I don't have someone else to discuss ideas with. I tried to reach out to other researchers, but it seems that they were uninterested.


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Wrong publishing date
Hej  I´ve just got a new scientific paper published and have discovered that it is wrong publication year
Thies-Lagergren, L., Kvist, L. J., Gottvall, K., & Jangsten, E. (1920). A Swedish register-based study exploring primary postpartum hemorrhage in 405 936 full term vaginal births between 2005 and 2015. European Journal of Obstetrics & Gynecology and Reproductive Biology.
It should be Thies-Lagergren, L., Kvist, L. J., Gottvall, K., & Jangsten, E. (2021). A Swedish register-based study exploring primary postpartum hemorrhage in 405 936 full term vaginal births between 2005 and 2015. European Journal of Obstetrics & Gynecology and Reproductive Biology.
When searching on Google Scholar it will not show under publication year 2021 only when combing my name + PPH it will show and you see the date 1920 which means it is far back in the publication line if you understand...
How can this be amended?
Important as I want my results to be known!
Greetings Li

I downloaded the pdf and see that the year is 2021. Can you clarify where you got that 1920?

I "have discovered that it is wrong publication year" - Where did you discover this? In someone's citation? On google scholar? In your library catalogue?

When searching on Google Scholar it will not show under publication year 2021 only when combing my name + PPH  it will show and you see the date 1920 which means it is far back in the publication line if you understand.....

When searching on Google Scholar, it now shows 2021. Please try it yourself. Next time, if it happens, the first thing to do is to notify Google, let them correct it.

If you see any wrong metadata about your published article, the first persons you should address are the editors of the journal.
However, in your case, I do not see the wrong year you claim to see. Where is it that you encountered it?
The metadata to your paper are correctly documented (at CrossRef). See the date-field here:

In addition, both the website at Elsevier and the PDF-version seem to name the correct year as well:


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Meeting a big scientist
I'm going to meet a big scientist. What should I say in the first meeting? I want to impress him and become a friend of him so that I can do common projects with him.
Please help me. It is the most important meeting in my life.
Information about the meeting:
He is going to attend a conference in his country and I'm going to attend the conference, too. I want to go to him, say hello, and speak about his works. I'm a Ph.D. student in physics.

To be clear, you want to become a professional colleague, not a personal friend, right? One is expected, the other could be, well, creepy.

A good way to start could be drumming up a short list of concise, but interesting questions you might ask him about his work. Then try to connect it to your own work or tease out how your interests going forward actually build on this idea. You can try to ask if he/she'd be interested in collaborating, but big names are notoriously hard to get a hold of, even for their own students, let alone other students outside their wing. Don't know if this is the case for your field, but I'm fairly sure it's a common problem.
A more realistic expectation at this point would be for you to (1) pique his/her interest and ask if it's alright to keep them updated about your project or keep in touch with his/her work. (2) Begin the project on your own, and keep them updated when you've demonstrated a good amount of progress (and success!) in the project. (3) Then, down the road, they'd be more interested/motivated to collaborate on a paper.
Good luck!

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Can a faculty on a 12-month appointment apply for grants?
I'm wondering if a 12-month appointed faculty (mainly teaching but also research duty, R1 university in the US) is allowed to pay him/herself from grants (especially NSF or NIH). I heard that they may buy the time with grant money, but I haven't heard if they can be paid extra. Also a rumor says agencies sometimes don't like to trade course loads.
Does anyone have experiences with these? Thanks.

Not sure that there's a general rule across all funding agencies in all countries of the world, but if you can name one or two that you are interested in, someone may be able to help.

Good idea- thanks, I edited the question. Wondering about NSF or NIH.

Note that a grant can do more for you than pay a salary. Are you just looking for extra personal income from a grant?

Maybe the terminology is different in the US (UK here) but whether you can apply for grants and whether you can pay yourself from a grant would be two entirely different questions here.

I would strongly suspect that what happens is that you continue to get paid your regular salary, you work on the grant project instead of your normal teaching/research duties, and the university gets reimbursed by NSF for the amount of your salary.  I very much doubt there is a scenario in which you get paid twice.  It seems that the official rules are in OMB Circular A-21 but it's a bit dense.

Just a clarification - are you really appointed 12 months, or are you appointed 9 months with your salary paid over 12?

I believe the former. It makes sense that the grant will go to the department then.

This will entirely depend on the nature of the position, and "12 month position" isn't actually precise enough to answer it. There are several factors to consider:

There are 12-month faculty positions (including my own, and many positions at medical schools and other institutions) where not only can you bring in research funding, but you are expected to do so. The most extreme version of this is 12-month positions with 100% soft money. In my experience, this is actually the type of position the NIH is used to dealing with, in contrast to the NSF.
"I haven't heard if they can be paid extra" - this will again depend on the position. One institution I was considering a job at had incentives in place such that you could indeed pay yourself extra if you brought in grants (and one place actually automatically paid you more if you brought in more grants). My current institution only covers 75% of my salary, so covering the other 25% is technically "paying myself more", but it's capped.
Buying out coursework time is contingent on the department among other things.

Basically: Yes, but the nature of how falls under "It depends".


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How do you benchmark against another paper's result if their code is not released, and my replication of their method obtain different results?
I've developed an algorithm that I believe should theoretically improves upon a previous work. In the previous work, the authors have provided results for a baseline method and their own method. The authors however did not release any codes for the paper. As this work is in machine learning domain, I understand that it could be difficult to replicate their method's results due to a variety of reasons. However, the baseline method they've used is very simple and I am certain that I'm able to implement it correctly.
After running some experiments, it turns out that my method's result were not better than the numbers reported for their method. However my method was able to improve upon my own baseline numbers by a greater amount than their method against their baseline numbers. The problem lies in that my replication of the baseline results is different (worse) than their reported numbers for the baseline.
Now I am considering a few options for benchmarking my work:

Ignore their reported results and implement their method by myself. Compare my method against my own implementation of their method
Compare the difference-of-difference, i.e. how much my method improves upon my baseline numbers versus how much their method imporves upon their reported baseline numbers
Just mention that I am unable to replicate their results due to lack of code, and present my method's results only

What would be the best option for benchmarking my method?

Have you tried contacting the authors of the prior paper to ask if they can share their code / data with you?

I've emailed and hopefully they may share the code. However in the event that I don't get any reply, I would still want to seek advice on how to benchmark if possible

I think deciding among your options 1/2/3 fall into "content of research" and isn't really appropriate for this SE site. What does your advisor think?

In this scenario, if you don't compare your results to "their" results at all, then others will. If they they read yor paper and discover that, as you say, your results look no better than their results, then you will look bad. You should disclose this with the same common sense approach that you used in your question. I.e.

It goes without saying that you should make your code / data / model publicly available on github or some similar platform, so that at least your results can be reproduced by others.

Do cite their paper.

Provide all 5 results: from your base implementation, from their base implementation that you cite, from their implementation of their approach, from your re-implementation of their approach, and from your implementation of your approach.

Focus on the analysis of why your approach is better than (your understanding of) the base approach. Do explain briefly but clearly how your novel approach differs from their approach. It would also be nice, but not absolutely necessary, to analyze why your approach is better than their approach.

Thank you for the suggestions. That was very helpful advice!


text:
Letter of Recommendation for PhD application
I am applying for Ph.D. in the United States. During my undergrad, I had worked with a postdoc in the research lab I was working. Presently, the postdoc student has joined an esteemed university as an assistant professor, but has not yet started any research there. Can I approach him for a Letter of Recommendation for my Ph.D. application? How would that affect my application?

It would probably depend more on how well they know your work and can predict your future success than their actual career position at the moment. If you did good work with them it should work out. So, yes, ask them. Especially so if this was your only research experience.
You likely need three letters. If this is the one you think "weakest" then you are in good shape. It is good that they have moved beyond postdoc, which will add a bit to their credibility.

Can I approach him for a Letter of Recommendation for my Ph.D. application?

Yes. It seems a good idea. I would suggest that you at least reach out to him. Generally, a letter from an assistant professor at an esteemed university, who worked with you in the past, is a good idea.

How would that affect my application?

That depends on how the postdoc writes the letter of recommendation for you.
Specifically, it depends on how the postdoc thinks of your past performance in that research lab, and how he perceives your ability to learn and do research independently as well as in a team environment.
Do you feel that he really appreciates your work and contribution with him in the past ? If yes, that is a very good starting point.


text:
Can you describe profile of respondents in the result section?
I have read many articles where the description of respondents (their characteristics) are put at the beginning of results section. Is it ok? Will your manuscript be rejected if you did so, but reviewers require it to be in methodology section?

It depends: If you chose the respondents based on those characteristics, then it is part of your design and should thus be part of the methods section. If they weren't your choice, but instead an empirical finding, then it belongs in the results section.
Apparently, your reviewers thought those characteristics were part of your design. If that is not the case, then your text describing your design is not clear, and in that case that is what should be fixed, rather than moving text around.

Thank you for your explonation, sir. I haven't received feedback from reviewers yet. In my case, characteristics were something I found during research, not something I used for choosing respondents. What do you think would reviewers recommend moving this in mathodology section or just reject the manuscript?

Why would they recommend that?

I don't know. I was just interested if that is a reason for rejection or could they request some changes. Thanks.

Both are possible. It is such a hypothetical scenario, that I can't say more than that.

One can't predict what the editor will require. But the "expected" characteristics are probably best in the methodology. On the other hand, if the actual respondents didn't actually conform, then something in results might be essential. This would especially be true if there were no necessary characteristics in the target population. But the methodology should state that explicitly.
But normally, I'd think, that you describe the target population in the  methodology.
You can ask the editor for advice, of course.


text:
Forced to work as a postdoc without pay
I got an externally funded research grant as a lead researcher to carry out a project at a UK University, together with other senior co-PIs. The grant would pay my salary for the duration of the project as a postdoc, which would be 6 months. Due to several administrative and other issues, the project kept being delayed (outside of my control), by what the funding finished, but the project deliverables were not produced. I continued working on the project in the hope that we could finish it at some point, but other issues came up, preventing the project from being completed.
It has been now 4 months that I've been working as a postdoc in this project without any pay, and I can't continue living without any money to support myself. I got some legal advice from a lawyer about this where I was told I should just walk out since my contract finished and I have no obligation to work without a contract. However, being an ECR (early career researcher), it would be extremely damaging for my future career to abandon this project halfway and not get any publication from it.
After several meetings with the PIs discussing what to do with the project, and pointing out I need money to survive, their conclusion was that I must finish the project deliverables, without any further pay, as they are blaming me for the delays in the project (which is not the case, as I stated before). They are also threatening me (indirectly) with damaging my reputation as a scientist, blacklisting me for future grant applications (the senior PIs are in several grant committees in my area of research) and just in general destroying any chances of me having a future research career.
At this point, I have no idea what to do to get out of this problem... It seems my only options are either to quit academia entirely or accepting to being exploited and work without pay.
On top of all this, I discovered recently the grant has some small amount of leftover money from non needed consumables, which I requested to be redirected to my salary. The PIs refused this, as they are saying they will only pay me this amount if the project is finished.
I am looking for any advice on how to deal with this problem, particularly if someone else faced a similar situation before in a UK university.

You need to contact an employment attorney. If you cannot afford that, then I think you need to walk away. Work without pay is known by another name: Slavery.

Are they contending that you need to produce exactly what was stated in the proposal? Or just to have SOME tangible outcome?

Were you paid for the six months or not? What do you mean by 'the project kept being delayed' -- the beginning of the project, i.e.your first wage payment, or the finalizing of the project, i.e.you couldn't produce deliverables after the six months in which the project ran and while you were paid?

Related: https://academia.stackexchange.com/questions/104541/persistent-issues-with-salary-pay-as-a-postdoc-in-china-what-can-i-do

@Vladhagen work without pay is also known as volunteering. What you probably mean is that no-one can be forced to work without pay.

@Vladhagen that's a bit extreme and also is an example of trivializing slavery. The point here of course is that the poster is free to walk away.

@T_M I am using the term slavery very loosely here without regard to wokedness and intersectionality.

Ask the same on law.stackexchange.com. The odds are good, that you're lucky: If someone told you to work for him without a contract, you may have a verbal contract. Which usually is permanent. I do not know what's the pay, but I guess you will at least get the minimum wage. Ask on the law site for details, especially since I am not sure about the regulations in the UK. And then it is in the interest of the university to solve the problem with a real contract.

Is threatening and/or starting legal action against the university any less "damaging [to OP's] future career" than "abandon[ing] this project halfway and not get any publication from it" ?

Don‘t walk. Run. In particular, worrying about the effect on your career is misplaced. The PIs’ threats already show that they have no interest in supporting your career, and eating is not negotiable. I’m sorry you’ve found yourself in a subfield that tolerates this kind of abuse.

Thank you all for your comments! I tried to add more information to my question above, but it probably was not approved. I followed some of the advice given here and contacted the Union and the independent legal service for employees of the University. So thank you to all!

For some reason there is this belief in academia that people should work without pay. It's inappropriate. You need to walk away.
Even early career researchers are allowed to work for pay.
It would also seem that a 6-month grant would only be for a rather small project. Can the project be tied off quickly so that you can move on?
If the senior PIs are threatening to ruin your career, I would try to get some evidence of these threats. Also keep in mind that even if you finish the project, PIs who make threats to ruin you career are not all of the sudden going to become your best buddies. You could very well finish the project and still have your senior PIs blacklist you for further grants. You owe them nothing.

I agree with the thrust of this answer, except that it seems to imply that a postdoc should cease all work on a project the moment their term of employment is up.  To the contrary, it is completely fine to continue to wrap up previous projects after moving on to a new position.  I've tried to flesh this out a bit in my answer.

You should not work without a contract. Whatever is the current academic state of this research project, if your contract is terminated you should stop working on it.
Yes, not delivering on your first funded project can be damaging to your career, but equally for the career of your "co-PIs". Arguably, as they are in  more senior roles, they ultimately have more responsibility for supervising/training you through the project and making sure the results are delivered. They also can not, under any circumstances, to force you work without pay — this is likely to contradict University regulations and they can lose their jobs over it.
Not just this bizarre behaviour of your co-PIs, but also other details of your situation are unclear from your question or contradict the usual norm. There is usually one PI, the person who got the grant, and they are entitled to make decisions about funding, within remit and regulations of the University. Longer, multi-million grants may be led by several PIs, but your grant is 6 months only. In your question, it appears that you are "Lead Researcher" but not a PI on the project.

I don't really think the behavior is that bizarre--sounds like he's being made the scapegoat for failings above his level.

Just to add a bit of information here: I have been working for 8 years in the UK, worked in more than one University and with several different people in each University. It is not the first time that I was pushed to work for free (although it is the first time there are threats). I found It acceptable to do some free work when I was just starting my career (before publishing papers or doing any substantial work), as that was a learning stage for me. But now with several papers published and 8 years of research experience, I don't think it's ok for senior researchers to do this...

It is normal and acceptable for PIs to expect continued collaboration from a former postdoc on projects of mutual interest, even after the postdoc's employment ends.  Furthermore, it is in the erstwhile postdoc's interest to see ongoing projects through to completion (and publication). It is very normal for big papers arising from a postdoc to be submitted well after employment is finished.
However it is not normal or acceptable for a PI to expect their former postdoc to continue working full-time without pay, and it is unacceptable and abusive to use threats of retaliation to compel a postdoc to provide unpaid labor.
In my opinion, you have two reasonable courses of action available to you. First, you might decide that you PIs have been abusive and unreasonable to the point where your relationship is not worth pursuing further. If you are traumatized, depressed, burnt-out, or terrified of interactions with your PIs, this might be a good course of action.  And if this is the situation it isn't your fault.
The second option would be to check with your PIs whether there might be some degree of misunderstanding. You could seek an arrangement where you will work full-time elsewhere (with pay!), but where you continue to devote a significant amount of time to the unfinished project (say 10 hours per week). This additional work would be unpaid, but would come with a set of expectations about your authorship on the final products (these expectations should be discussed and agreed explicitly, preferably in writing).  If the PIs find this relationship to be unacceptable, but remain unwilling to pay you, then it sounds to me like an absurdly toxic environment, and my advice is leave as quickly as possible.
Either approach involves searching for a job right away.

I think this really comes down to who are you working for. Nominally you are employed by the university, but the university really does not care about any deliverables you might provide and is happy for your to leave. Maybe you are working for the funder; if that is the case, they no longer think the deliverables you can produce are worth what it would cost and are happy for you to stop working for them. Your PIs also don't think what you can produce is worth it. In fact, as a postdoc, you are really working for yourself as you are really the only person who will benefit from your work. Your failure to get additional grant money means you can no longer pay yourself (via the university) and now you need to decide if you want to work for yourself for free.

By working without pay, you are fueling the very thing that is happening to you. It's similar to many other areas where college grads are underemployed, and employers take advantage of a college education and a bright and intelligent mind.
That said, if you quit and try to make an economic stand, you'll lose. Someone else will do it. All you can do is quit and know you did the right thing, but you won't be rewarded, and it will be most difficult, possibly more then you can know or I can describe here.
This is what, why, and how technology is developed. It is naive to think a professor somewhere was highly paid to develop Windows o.s., the windshield wipers on your car, and the other things we take for granted.

Also the questions of what is best for you and what's best for people who will be in your circumstances in the future are different and probably opposite.


text:
Co-authorship for a revised but relatively new article?
I am a fresh PhD. In search of postdocs and permanent positions in last 4 months, I learned about two things which evaluating/hiring committee look in their potential employees:
1) How much the candidate has grown post their PhD? If a candidate keeps publishing article with previous supervisors even after his/her PhD it may mean that they have a good working relationship, but it also means that candidate has failed to collaborate with new partners. As the present research world is considered to be highly collaborative. Also it means that even after the PhD, the candidate still needs supervision from his/her former supervisor.
2) The greater the number of coauthors are for your paper, the less weightage you get during the evaluation process.
Now main problem: One of my articles of my PhD thesis was submitted in Phys Rev Lett, and it had received one very good feedback and one very bad. That article basically consisted of an interplay of formulas and some mathematical tricks to derive a desired equation. The idea was mine and I had written the whole article by myself.
My main supervisor contribution's was that he asked me to reverse the order of two paragraphs of the final submitted version of article.  Also during most of my PhD my main-supervisor always helped and polished my work.
My co-supervisor's had initially given some ideas but I proved them to be mathematically and physically incorrect. Also during most of my PhD my co-supervisor hardly contributed anything.
Update: Now I am planning to rewrite the article and submit to the same or some another journal, but this time I will have computational fluid dynamics simulation included in the article which will prove my derivation to be correct. I assume the new article will have 50% overlap with the previous version and new 50% material will be added to it.
Question: Should I include my supervisors as co-authors, or may be just one, or may be none? I do not think I will get any input from them in this particular article.
Background: 1) Academic world acts in 3 ways I guess:
a) Do buttering of seniors, collaborate with many and cite one another, and get timely promotions by feeding on the opportunities of others. I have seen a unqualified person getting promoted from Assistant Professor to Professor in just 8 years.
b) Do not do buttering, but then suffer. I have seen a well qualified person has remained as an Assistant Professor for last 23 years.
c) Make your credentials/ profile gigantic so none could affect you significantly.
So, If I rewrite the article as a single author, it will be a great boost for my long term career.
2) But I cannot deny that a recent postdoc offer I got has some contributions from my main-supervisor since he has highly recommended me to the professor at the new institute, since both are friends. Although the professor knew my work  from before, he had attended a presentation of mine earlier, I cannot ignore the recommendation of my main supervisor. I guess that is how academia works, also it seems difficult to draw a line between buttering and seeking help. I guess when I will be looking for a permanent position after 2 years, I might need the help of my main supervisor once again?
So, how to deal with this problem?

The people who gave input for the 50% overlap with the previous version are still authors, so omitting them would be academic misconduct and not a boost for your career. It's not buttering, it's called collaboration and as such a very important positive for your career. Even if it is not in a direct, measurable way, you do profit from collaboration, from talking about ideas or venting about problems and all of this things.

In this particular case, I would not change the authorship for the revised version (unless there are better reasons than what you have communicated).
You must not forget to keep your personal relations oiled. If you re-submit this article as a single-author paper, i.e. remove your supervisor, your relation to them would certainly not be helped. In the future, it may be important/useful to have that relation intact and well working for ongoing/future collaborations.
Moreover, by having them as co-author they are somewhat in your debt (which cannot be a bad thing) and may return the favor by adding you to one of their papers, even if you contributed as little as they did to yours.

Thanks Walter and Skymningen. A few more information. Let me tell you the impact of this work; this will be the first ever derivation and a validation of an equation that is used in the fluid dynamics of complex media. Also, what contributions will me both supervisors have? At most they may polish a paragraph or so for a better readability. If I become a supervisor in future, I would personally not liked to be given credit of something to which I have not contributed significantly. If it is only about academic-social etiquette, and "being polite" then it is a different matter.

@james Have you already submitted to arXiv?

Also, see this, https://academia.stackexchange.com/questions/21251/is-it-common-to-claim-co-authorship-by-helping-writing-a-paper-without-doing-any?newreg=539fa85aa0594ef8b15be601bc05577f

The so called Vancouver protocol (developed by ICMJE (International Committee of Medical Journal Editors) and its definition of authorship has been mentioned in many questions of this kind here on Academia but I think they deserve being repeated. The protocol describes authorship through three components which every author must fulfil:
Conception and design, or analysis and interpretation of data
AND
Drafting the article or revising it critically for important intellectual content
AND
Final approval of the version to be published.
A key point here is the "AND".

Although all my previous manuscripts were submitted to ArXiv, this article was not, since it was conflicting with some protocol of PhysRevLett. My supervisor had asked me not to submit it in Arxiv. The result was new of its kind. And it was only only mathematical, now I am validating my proof with simulation which took me 4 months to learn and implement.


text:
How to Properly Cite Linux Source Code?
I know, the question of how to cite source code has been asked before, but I did not found anything helpful for my specific situation.
I am currently writing my master's thesis. My university does not dictate any particular citation style so I just use biblatex's default settings. My work is quite OS-specific, so I have to cite Linux source code on several places throughout.
I found the Linux cross reference, which allows me to reference specific code lines for specific Linux versions. I intent to use this for my purpose, so I will cite URLs in the form of http://lxr.free-electrons.com/source/<filepath>?v=<version>#L<linenumber>. However, I do not know how to exactly do this.
I know biblatex provides the online type which should be generally applicable, since I am citing URLs. I have two problems with this, though:

What do I fill in as the author/editor? Linux is written by hundreds of people and surely there would be no benefit in mentioning them all. Should I drop the editor/author and instead fill in the organization? But then, do I refer to the Free Software Foundation holding the copyright to Linux Linux Foundation or rather to the maintainers of the Linux cross reference?
I feel like a larger amount of such source code references would clutter the bibliography. Hence, I would rather have an extra section (like a secondary bibliography) listing only those source code references. Is there a solution for this use case? Or should I save the effort and accept the cluttering?

The official github repository looks like a more stable and authoritative source than the website you suggest.

Didn't know you could reference lines in github too. But with Federico's solution I don't need to be doing this anyhow. So I guess I will be using the github repo with Linus as author.

You can get links to individual lines by clicking on the line number in the source code view. If you are viewing the current version of a file, by pressing y you can turn the link into a permalink containing the commit SHA.

The only official aspect to the GitHub repository is that it is maintained by Torvalds himself. The official Linux kernel repository is there: git://git.kernel.org/pub/scm/linux/kernel/git/torvalds/linux.git

In my mind, I see the Linux source code as a single bibliography entry (possibly with its official kernel.org repository as the source URL). You can refer to the different files in the text as \cite[Version~4.1, \texttt{drivers/android/binder.c}, Line~18]{Linux}.
EDIT: suggested kernel.org instead of github, as pointed out by bdsl, sebleblanc and Bruno.

I really like this solution. It avoids the too-many-references problem and at the same time sets code citations apart from normal citations. Thanks!

I'd use the kernel.org repository, which seems a bit more official.

@Bruno Good point. AFAIK kernel.org doesn't have line-by-line permalinks, but if one isn't going to use them anyway it is a more authoritative choice.

@FedericoPoloni, It looks like there's an anchor for every line (accessible from the number on the left) on kernel.org too. For example: http://git.kernel.org/cgit/linux/kernel/git/torvalds/linux.git/tree/drivers/android/binder.c?id=v4.1-rc8#n18

@Bruno Oh - I am embarrassed I missed them. Ok, then I agree with you, kernel.org trumps github on all accounts.

In APA style (6th ed., section 7.08), the reference should look something along the lines of

Linus Torvalds (2015).  Linux (4.1-rc8) [Operating system].  Retrieved from https://github.com/torvalds/linux/releases/tag/v4.1-rc8

Notes

Linus Torvalds' role is something like the editor or publisher of Linux.
You should have just the one entry in the reference list to the source code as a whole; individual places where you cite particular lines of code should be cited where you refer to them, either in the text or as a footnote.

I think https://www.kernel.org/ is the primary website for Linux, not github. Linus Tovalds keeps an additional copy on github for convenience. Maybe it doesn't matter which one is cited though.

@bdsl - kernel.org would work as well, but you won't find release candidates there.

@CharlesStewart, really? the main page and the refs page list a number of -rc tags, for example this one (as of today).

Would you really cite Linus Torvalds as the author if he didn't author the files/lines referenced by the paper? For example, kernel/time/ntp.c has many authors, none of which are Linus. Would Linus Torvalds still be the one to cite if referencing something specific to this file?


text:
Is an academic degree an honor, a title, or both?
For example: Do graduates receive a Bachelor of Arts degree or become a Bachelor of Arts?
Are Bachelor degrees grammatically and/or etymologically distinct from advanced degrees?
I note that the titles Master and Doctor are still in common usage, even though in practice frequently divorced from the associated academic degrees.  (E.g, a Master as a formal designation is now most frequently associated with a skilled trade – like master electrician.  And many holders of doctorate degrees eschew the use of the title outside of medicine and the academy.)
Etymologically it appears that Baccalaureate would be the correct term for a person who has received a Bachelor's degree.  But I can't find that in modern usage, and its etymology (laureate) emphasizes the award of the degree, rather than the achievement of mastery or doctoral skill.
Or do I have it backward, and it is modern academia that has appropriated these different titles without establishing such terminological consistency?

Note that a person doesn't need to have a doctorate in order to use the title Dr. For example, in most countries medical doctors only need an MBBS to practice yet they are fully entitled to use the title doctor. OTOH, in the US, almost all lawyers have doctorates (JD), but almost no one calls Attorney John Smith "Dr. Smith". So I'd argue "doctor" the title and doctor the degree are two separate things, and doctorates are no different from baccalaureates and masters in this sense.

Trying to figure out the underlying question here; are you basically interested in if it's appropriate to regard a Bachelor's degree as conferring a title upon the holder?

@Nat – First, does "academia" have a consistent view regarding whether people merit titles for earning any degree?  And if so, does it apply to all degrees, or only some?  If the latter, is there a good reason why?  If the former, what are appropriate titles that go with each degree?

The use of master (Meister, meester) has a long tradition in skilled trade, which goes back to the guilds. So I would interpret master electrician in that light, rather than a reference to the academic title/degree.

Depends on the country and education system.
For example, in English, 'bachelor' doesn't mean anything but that you finished that level of education.  In Spanish, finishing university doesn't mean a person gets recognized as having the degree: there are further methods to achieve that (titulaciòn), after which the government officially recognizes the degree and the title that comes white it like 'ingeniero' (engineer) or 'abogado' (lawyer). That is why in some countries the degree is added as a title at the start of a person's name.

I'm unclear as to what precisely is the distinction you're drawing between the Anglo-Saxon and Hispanic systems. Is it that in the Anglo-Saxon system you just have a graduation ceremony, whereas in the Hispanic system you have a ceremony and additionally your degree is published in the official gazette of the state? The recognition of professional title sounds more like colegiarse, and that has parallels in the Anglo-Saxon system (chartered professions, bars, etc).

For generalization of latinamerica let's use México, and lets say a civil engineer degree. Finishing the 4 years (average) of university is just one of the requisites for getting the title of 'civil' engineer, the person aspiring tot he title then needs to pass through a 'titulación' phase to prove they are capable and worthy of the title (Thesis, 3 years work experience + exam, general exam, projects, etc) , after that they are awarded the tile and then can use it in their names. Then to be able to work on the field there's an extra national permit called 'Cedula profesional'.

I'm not sure that's quite what the question is about. I interpreted it as about the use of Lic. as a title (which I certainly see with pharmacists in Spain, and I've seen with psychologists in Argentina, but I'm not sure whether it's related to being colegiado).

It is. A 'licenciado/a' is a title as much as an Engineer.  But it always refer to something, like a 'Licenciado en ciencias de la informatica' (Lincesee in infomatic sciences' or 'Licenciado en psicología' (Licensee in psychology)  Those are the full titles while the shortened version added to the name is the Abb. 'Lic.'

They're degrees, indicating advancement on a course of study.  Hence, bachelor, master, and doctor are different degrees of accomplishment in (usually) the same discipline.

So ... one "earns" each degree?  Or is "awarded" each degree?  But  there is no standard of recognizing one who has achieved any of those degrees with a title?

It's two sides of the same coin. You don't get awarded a degree without earning it. The only degrees that come with title are doctorates (excluding some professional degrees, e.g. MD). The only thing you would be able to call yourself after an undergraduate degree would a 'graduate'.

@Eppicurt An MD is a doctoral degree. Perhaps you mean that certain professional degrees are unusual in that they are obviously not expected to be for teaching, yet grant the historic title of a teacher.


text:
Is it okay to criticize authors because of how poorly their paper is written?
I am currently reading a paper in my area which is very poorly written in my opinion. It is hard to understand the bigger picture of the paper. Now, I am just a student and my opinions might not be of that value but it is really difficult to understand the paper. It appears that everything in the paper is only implicitly stated. I took help of other better researchers (postdocs, profs) but they also face the difficulty of getting it properly. The authors of the paper are established researchers and the results are really great. But, I really want to tell them how bad the paper is so that when they write their next paper they also think about the readers. I wonder if their advisees also turn out like them. I just want to write a mail to them and tell them how a paper is written but I do not know if they will take it as constructive criticism. I am really mad.

What constitutes "acceptable feedback" has a huge cultural aspect to it, so, you might want to state the country this is in. What you can always do is to ask specific clarification questions, instead of phrasing it as feedback.

Before writing any feedback email, please consider it might be the first paper written by a student, and negative feedback might affect them greatly. Let people grow at their own pace.

And what if your opinion about quality of their writing is simply wrong? For instance, in my area, math, it is common to skip on some of the details that a professional mathematician would find easy to fill in, while for a young researcher it would be a very difficult task. This does not make such papers poorly written.

@MoisheKohan I disagree: I think many math papers are poorly written, for exactly this reason.

It's worth noting that it also matters how you phrase your feedback, even if it may be okay to give feedback on this issue in general. That said: when you say it's "poorly written", what exactly do you mean? (Bad spelling or grammar? Confusing structure/organization? Something else?)

This famous snippet from Mark Twain is worth considering: "When I was a boy of fourteen, my father was so ignorant I could hardly stand to have the old man around. But when I got to be twenty-one, I was astonished at how much he had learned in seven years." Dunning-Kruger comes for us all, especially as we advance past novice.

Suggest waiting until you're less mad before you do anything.

Don't criticize the authors... Criticize the paper. There's nothing personal about anything here

Look at your seniors to get a sense of what's reasonable. When sharing the paper with more experienced post-docs and professors, did any of them send a note to the authors, not for any clarifications or questions, but to explain to them how a paper is written? Did any of them get hopping mad about the paper in the first place? I expect not.

Communication is a co-operation between the transmitter and the receiver.  If communication is sub-optimal, the problem may lie with the transmitter, or with the receiver or (more likely) both.  Humility goes a fair way in academia, and it is better to make sure the problem doesn't lie with you before complaining.  That is not an easy thing to do objectively.

Having said which, there is also "security through obscurity" and "proof by intimidation/obscure notation".  The point of writing a paper is not always to optimally communicate an idea! ;o)

If I had a penny for every time something I wanted to learn was poorly written...

About the exact phrasing of your questions: it may be okay to criticize the writing of the paper, but it is not okay to criticize authors.

I once was at a memorial symposium dedicated to Nambu. One of the (distinguished and clearly pretty smart) speakers said smth in the lines of "every time I read his papers, I learn smth new hidden in them". Well, I thought, that's quite a polite way to say that...

Each poorly written paper deriving an important result is an opportunity for you to have a highly cited publication in which you elaborate and review its contents, and maybe add smth on top (e.g., an application to a particular case). Community will appreciate your work if what you claim is indeed the case.

@Tom It looks like that quote is not by Mark Twain. https://quoteinvestigator.com/2010/10/10/twain-father/
Twain's father died when he was 11, so it could not have been referring to himself.

It seems you have read and understood the paper. So the problem is with presentation rather than content. Sometimes disabilities e.g. Dyslexia make the writing of world-class scientists full of typos, etc. Simply recommend having the paper proof read.

As a reader
Its worth asking what you stand to gain or lose by emailing the authors or not doing so. A published paper is not going to change, so you have no chance that you will change the paper at this point. It is also not likely that the authors thank you for your completely out of the blue and unsolicited feedback on something outside of the science, so you are not going to impress anyone. There is some (but very small) chance that your feedback means that their writing will improve in subsequent papers, but for that to be the case, your feedback would need to go beyond just "I can't understand your writing", and contain constructive feedback, including specific suggestions for what particular parts of the writers style could be improved, and how they might go about doing that.  Take it from someone who has provided feedback on a lot of writing - this is hard and long work. The only other benefit is that you will feel like you have done "something" about the thing that is making you mad, even if that something doesn't actually achieve anything.
On the other hand, you are likely to associate yourself with negative emotions in the minds of the authors - the best you can hope for is that they forget you. They don't need to be deliberately vindictive or retaliatory - this can be entirely subconscious. This can be true irrespective of whether they take your advice on board (or even thank you with the conscious part of their brain). This is just human nature. This could be particularly harmful if they are big names in the field.
This is not to say you should never disagree with a big name, or provide them with feedback at appropriate times. Good scientists will welcome feedback particularly on the science as it will lead to avenues for new investigation. But what is achieve must always be balanced against the downsides.
As a reviewer
As a reviewer of the paper as part of the peer review process things are slightly different. Generally, journals will provide fairly specific guidance on how to feedback on guidance. Usually you are not supposed to feedback on "style", but only those things that genuinely hamper your ability to understand the paper. You might say:

Assessing the work was difficult because I found the way it was written difficult to follow. For example, the meaning of 'Lorem ipsum dolor sit amet, consectetur adipiscing elit.' was unclear.

You should also comment where things are genuinely ambiguous – for example:

The sentence 'Cras suscipit massa ipsum, ac tempus massa viverra et.' could be read as meaning either 'Nullam nec varius odio.' or 'Mauris sed ante posuere, euismod urna id, rhoncus erat' and which is not clear from the context.

If there are many typos in the text, point this out if it makes the text difficult to follow.
Be aware that it is not acceptable anymore to tell the authors to have a native speaker proofread the text. This is because:

a) You have no idea if a native speaker has already proofread the text.
b) Many non-native speakers are actually better at technical writing in English than many native English speakers.

In both cases it is never acceptable to criticize the authors. Make sure always that your are criticizing the paper, not the authors. The difference might seem meaningless, but it is vitally important.

Some of these are matters of personal opinion. I have both commented on matters of style and received reports with helpful feedback on my own style. Similarly, the claim that "it is not acceptable any more to tell the authors to have their text proof read" is a statement of personal opinion, not a statement of fact (just like many other claims of the form "... is not acceptable any more"). If anything, the problem is that the authors might not have access to a competent enough speaker, not the irrelevant fact that some non-native speakers may be better writers than some native speakers.

@AdamPřenosil You misquote. It's not "tell the authors to have their text proof read" it's "tell the authors to have a native speaker proofread" (em. added). -- While it was once very common to make such requests to authors with "foreign sounding" names, it's now generally considered gauche, due to the implications. Its still acceptable for a reviewer to suggest a paper needs further proofreading, what's not acceptable is to suggest/demand that a "native speaker" do it.

@adamprenosil it's not just about considering it gauche, it's explicitly against the guidelines at many journals, and may get your comment removed/rephrased by the editor, or your review being disregarded.

@IanSudbery I've seen guidelines asking, essentially, to be tolerant towards non-native speakers, but I have not seen guidelines stating that referees should not suggest that the text be proof-read by a native speaker. I'm not questioning your statement, but if you recall a journal which has guidelines of this sort, I'd be curious to take a look at them for the sake of my own curiosity. (Btw I agree that doing this isn't a great idea because presumably the authors would have already done so if they could. I just disagree that the two reasons that you gave have much of anything do with this.)

@R.M. Sorry, my bad! I changed the quote to fit the character limit, but then I should have also removed the quotes. In my experience, the phrase "it is now generally considered gauche/outdated/refuted" often performs a function similar to the phrase "clearly/obviously" in mathematics. What follows is often not in fact a generally held opinion. The "implications" of the phrase are debatable. Of course, people looking for "implications" can find them anywhere, but in a normal, charitable reading it simply means "have someone highly competent in the target variety of English take a look at it".

Historical context: It's by no means unusual for important papers to be difficult to understand. It's rare that the seminal papers in a subject are the place to go to learn that subject. For example, few people choose Einstein's original papers as their place to go to learn relativity. Few people go to Feynman's original paper on path integrals to learn that. Few people go to Dirac's original paper to learn about the Dirac equation. A lot of people will read these articles for personal reasons or historical reasons. But they are not likely to be the text for those learning those subjects.
There are a few possible contributing reasons for this, some of them these:

The first explanation may arise from the process the author used to get there. This is often not the easiest to understand explanation.
The journal probably has some harsh limits on word count, diagrams, tables, etc.
There has not been a process of refining notation for ease of reading.
There may be language issues if the authors are not native speakers of the language they are publishing in.

So, there is quite a lot of room for writing pedagogical versions of research papers. If you have talent for writing clear prose that gets the idea across, maybe there is a future for you in writing textbooks. Or at least review articles that wind up on every grad student's desk for the next thirty years. I recall a Physics Reports issue on Yang Mills theory that nearly every grad student in particle physics had a copy of.
So a poorly written paper that yet has interesting results might be viewed as an opportunity to produce a better written, possibly expanded, version for a journal somewhat more focused on instruction. You might even get a collab with one or more of the authors of the article that confused you.
That is, turn an annoyance into an opportunity. Much like an oyster turns a grain of sand into a pearl.

Yes, some papers are hard to read and understand because they are about difficult topics or have a lot of assumed knowledge. I was going to suggest: try to write a version of the paper that makes it understandable to students at your level.  When you are happy with that it might be appropriate to share the "translation"  with the author though I would have someone in the field who I know read it first.

If it is a recent article, you could try reaching out to the authors for clarification. Not all authors answer these queries, but some do.

To add to this -- sometimes the first paper written on a subject is breaking new ground on terminology or other ways of thinking about that subject. Over time a community will develop better ways to think about or describe work. But, it's hard to be the first breaking ground, and thus papers doing so are often much harder to read.

"For example, few people choose Einstein's original papers as their place to go to learn relativity." It might be worth to give it a try, though: I read the first part of "Zur Elektrodynamik bewegter Körper" in the final year of high school, and remember it as really well written and easy to follow.

There's a difference between the first paper ever on a subject, and a paper that is just poorly written, yet contains good science. This question is about the latter.

From How to Win Friends and Influence People:

The easiest way to make enemies is to criticize them.
Criticizing people puts them on the defensive. They will dig in their heels and rationalize their actions.

Just consider, how often do you see people respond to criticism with "Yeah, I was wrong. I'll do better next time"? Then compare vs. the number of times people respond with "I did nothing wrong, but you did X, Y, and Z".
Abraham Lincoln is one of history's greatest leaders. In 1863, during the American Civil War, the South launched an invasion of the North that was repelled at the Battle of Gettysburg. Because the Southern general (Robert E. Lee) had appeared hitherto invincible, this was a major victory for the North, but the Northern general (George G. Meade) failed to pursue and destroy Lee's army. Lincoln was upset, and wrote a critical letter to Meade that you can read here. The most remarkable thing about this letter however isn't how restrained it is, but rather that Lincoln never sent it. He knew he wasn't there, he didn't see the battle and death firsthand, or know what it's like to trudge across soggy ground under threat of enemy fire, and he knew all these things didn't apply to Meade. Therefore he shouldn't criticize.

If you absolutely must criticize, praise first. Wax lyrical about how the results are really great, and then say you wished the paper were better written so you could've understood it quicker.

I'm not sure criticizing a manuscript as part of the peer-review process is like sending a letter to a general still bloody from battle, but the sentiment of your post is quite correct: if you cannot be constructive in your criticism, better let it go.

@ZeroTheHero I don't think the question was about criticism in peer review, it seems to be about unsolicited criticism post-publication.

I actually don't like the military language that is often used on both sides of peer review, it seems unnecessary to me.

"If you absolutely must criticize, praise first. Wax lyrical about how the results are really great, and then say you wished the paper were better written so you could've understood it quicker." There's a name for that: a "compliment sandwich." Compliment, criticism, compliment.

Which should really be called a "criticism sandwich"... after all, we don't call bread-cheese-bread a "bread sandwich".

I think I would welcome an unsolicited message criticizing my writing, as long as it was polite and moderate and gave some specific examples of my bad writing and how to improve them. And if I would welcome this kind of thing, I think plenty of other researchers would too.

Papers are not written for students but for experts in the field. It is not uncommon for a bachelor thesis (depending on subject of course) to work out all the details in a paper and show that the student managed to work through it in a couple of month. This working out things, helps you to slowly become an expert in your chosen field. So long story short, my answer is: absolutely no.
What as a student of course you can do is point out errors (if there are) in the publication.

It's a problem for papers to be written only for "experts in the field". They should be written so as to allow a somewhat wider audience, not just, say, the 5-10 people who follow that line of research. Of course there space constraints etc., but effort must be made to keep things as clear as possible, avoid logical jumps which outsiders may easily miss, etc.

@einpoklum I do not think it is a problem and every now and then there is a 100 page introduction article to the topic. You cant add that to every paper.

I believe you're presenting a false dichotomy. The idea isn't to include part of that 100 page introduction article; the point is to make the core of your writing more accessible.

@lalala: what has a 100 page introduction article to do with this? You can make the writing of your paper more accessible while still not writing a general long detailed introduction.

As a student, you're unlikely to be the intended audience of the paper. They may in fact be thinking of their readers; it's just not you. From the context, I'm assuming that the paper is a technical, academic one written by professors of some sort. The authors' goal was probably to announce results in their field to their peers, maybe stake out some territory, improve their odds of tenure or funding, and so on. For publication in a research journal, the authors are presumably writing for an audience of researchers in the same field who already have a substantial background in the subject and are already familiar enough with the area to automatically connect the dots themselves. It could also just be a bad paper; I don't know you or the authors or even the paper involved.
Regardless, I don't think anything would be served by "tell[ing] them how a paper is written." To be honest, I would respond to a unsolicited, angry message like that by summarily throwing it in the garbage, regardless of whether it was from a student or an established professor or a Nobel prize winner. You probably would too, and it's reasonable to do so. It's not even harsh but honest criticism; it's just being angry that someone didn't write the paper that you wanted them to write.
If you like the ideas of the paper but think their presentation is too opaque, you could contact the authors and ask for clarification directly or suggest they write a lighter survey paper. You could even write it yourself. If you do in fact know how a paper should be written, polishing up someone else's badly-phrased good idea for a different audience can be a valuable thing; that's kind of what textbooks are.

If stated really bx a Nobel price winner (or some famous person in the field), I would really think about it. After all, if not even a Nobel price winner can understand it? (However, not if the person is famous for unnessessary critism).

For constructive, or even just specific, criticism? Sure. For verbal abuse from someone who considers me an incompetent inferior and just wants to rant at me? Nah, that's going in the garbage. (Or, if it's actually from a Nobel laureate, it's probably going up on the wall as a novelty and conversation starter, if nothing else.)

Indeed, I would do the same - but the OP seems not to be an verbal abuser and does not seem to consider them an incompetent inferior. If really a Nobel laureate (working in my paper's field) wrote just like the OP would like to do "Hey, your paper is too hard to follow for me", I would really think about how I can improve my writing style (and consult people close to me about that).

I generally agree with most of the answers. If you write some people and say "Your paper is terribly written", nothing good will come of that.
But, if you write them and say, "This result is amazing! I struggled a bit with this bit... if I paraphrase that with , is that correct?".
Then i think it might be appreciated, and maybe even borrowed.
In big labs, students/postdocs can be the main authors of papers and the group leader may barely comment on the paper before publication. Depending on the language This might result in "unpolished" writing.

Just write to the authors with all the questions you have about their paper: "Do I understand correctly that...?", "What exactly do you mean by...?", "One page X are you implicitly referring to Y?", etc. Do not hesitate to ask follow-up questions until you are sure you understand. Having to answer all these questions will punish the authors for their bad writing!

Unless you personally know the author(s) very well, or you are reviewing the paper for publication, I strongly doubt listing every single question you might have (especially when new to the field) will get you anywhere. Also you don't go around punishing authors of published papers for their (bad) writing by sending them angry emails, that's rude.
If one or two questions remain after OP has looked at it with others, a polite email to the authors is, of course, fine. Whether they'll respond, who knows. I would.

After two or three of these, there's a good chance you'll just get a brush-off.  "I'm sorry, I'm busy and am not sure when I'll be able to take time to look at this."  "I suggest studying references [X,Y,Z] for background, which should help make things more clear" (where X,Y,Z are notoriously long and dense textbooks or monographs).  Or just no further replies.  Not really much of a "punishment" for them.

I think that if you have done reasonable due diligence (talk to other people about the papers, read background) then emails the authors with questions is absolutely fine! That's why there is a "corresponding author"!

You should take a good week  (or two) to write that email, to ask really good questions. By that time, you probably don't need to send it any more, because you have worked out by yourself what the authors were unclear about. Perfect preparation to write your own paper later.

You said you sought help from postdocs and professors, but they also faced the difficulty of understanding that paper. This makes me think that the paper is indeed poorly written.
Had your senior colleagues not stumbled on that paper, my sympathies would still be with you. In my opinion (with which some will disagree), a good paper must be written in a language understandable to a graduate student, ideally to an advanced undergrad.
I know an outstanding scholar who is having problems with writing clearly. This is not his fault but his problem of quite a psychological nature: it is difficult for him to model inside his mind how difficult his writings may be for a beginner or for a colleague from an adjacent area. On the other hand, I also knew people for whom writing solely for the anointed was a method of self-affirmation -- which, again, has a lot to do with human psychology.
For whatever reason an author is unable to write clearly, it will be useless to preach to them. Don't waste your time. Also, you may anger the author -- which will do you no good, especially at the start of your career.
Instead, you may send them a polite e-mail, praising their publication, and humbly asking to help you better grasp their so great and important result. After this, the author will probably respond and help you go through his so great and outstanding and ingenious work. Praise is more efficient than reproach.

It's always tempting to immediately critique mercilessly (for me mostly to boost my ego), but first stop and consider why you're reading the paper in the first place. Clearly you're interested in the topic and content they're writing  about and in understanding and replicating their results.
Kindness is King. If this is why you're interested in the paper then think, could there be potential opportunities for collaboration? Could an author on this paper be a future author on a paper you're hoping to publish? If so, then you don't want to ruin relationships now. It's always good to build interest and respect for another person's work whatever stage. You'll find you can make a lot more collaborations and faster progress this way, and a lot more people are willing to collaborate (however big their name) than you might think.
If you're hoping to discuss more with the author, I've found it particularly effective to send an email expressing thanks for their work (Say "Thank you for your paper..." as an email header or something similar). Express honestly what you liked, and/or any intentions for possible citation by your own upcoming work (if that's your true intent). I've seen these kinds of emails are very often replied to, and authors are generally fairly open about responding to concerns for a reply or maybe two.
If you're just upset for personal reasons (i.e., maybe the paper is from a well-known university that you were not accepted to, and you feel you could have written something better) then you're going to find you may be very miserable in a winner-takes-all academic environment. Hopefully this isn't the case.
Why might well-known authors allow this? Other than what @BobaFit said, some professors are far too busy to comb through student's work, or choose to let them publish their level of work in order for them to grow on their own. Sometimes it's used as a strategy (unfortunately) to claim some space so as not to give away too many ideas or keep competing labs away from their knowledge. This allows them to publish more papers in the space without worrying as much about competition. Yes, there are fields where publishing is that competitive and moves that fast.


text:
Academic Job Interviews for Asst Prof Positions in Ireland
I have an upcoming interview for an asst prof position in a university in Ireland. I am wondering what questions are asked in such interviews. I am used to the hiring process in the US. It will be my first time being interviewed for a university in Ireland. Thanks!

https://academia.stackexchange.com/questions/119795/etiquette-for-academic-job-interviews-in-ireland

I am a USA academic who interviewed unsuccessfully in Ireland (but successfully in Scotland). I was partially unsuccessful as I realized a few hours in that I did not want to work there but as they had flown me over I did not want to be unpolite and leave the interview.
Biggest Three Differences

I got to meet all the other applicants. We were in the same room and
called one-by-one to do our presentations. I ended up really wanting
another candidate to get the job.
Only one person on the panel was a faculty member (chair) in the department.
No dinner with faculty, not a tour of the town, no real contact with the department
at all aside from the odd quick hello as we passed their offices.