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How to manage end stage of thesis
I have a few months to go in my MASc program in Aerospace Engineering. I'm not tight for time or anything, but I'm curious if anyone has tips on how to manage results.
My research is highly algorithm-centred, and there are a lot of little knobs and dials on the algorithm that I added as I went along, and I'm still tinkering with it. I know what they all do, but there's no way I can do a detailed analysis on the effect of each setting.
My advisor says it's important to have the results in say figures and charts etc exactly reflect the algorithm as written, which I agree with. But how will I know when the algorithm won't change anymore, that this is how it will be, and these are the final results? Otherwise I'll end up creating the figures 10x over. I could leave the figures out till the very end, but often the discussion is around features in the figures.
I know there's no silver bullet, but wondered if anyone had good tips on managing that sort of problem.

Be careful that your results aren't too dependent or overfit on the dials and knobs you keep adding :)

When I try to present my results, either by text or even more by graphs, plots, figures, I often find questions or issues I have to investigate. So not writing a draft and creating the graphs, stresses me after I finally do so.
To address your problem with doing graphs over and over, you have to automate its generation. I wrote all of my theses with LaTeX so TikZ and its plotting functions were an obvious choice. But you can do the same with matplotlib (Python), Matlab, R, Excel, LibreOffice Calc, Chart.js (JavaScript): Write scripts that read input files or where you have to copy/paste your data. The plot is automatically generated, including postprocessing, scaling, labeling etc.
It is some work, but it pays off! And it adds transparency, because you can always proof that the graphs were not manipulated - or it would be obvious because it is written in your code. Store the code together with the raw data - just in case.
After the final review from my professor, I was asked to drop one data set. I could do this within a couple of hours and it was not stressfull, as 80% of my graphs were automated.

I had a similar algorithm-centred thesis for my MASc. To keep the results manageable, I had to pick a certain easily-justified position for all knobs and dials to be my "baseline" setup. This let me still explore the algorithm design space as the thesis due date got closer, but treating each new result as a special case with a short associated discussion. If you can, it may be useful for your reader and easier for you if each knob and dial can be discussed in its own section. If there's stuff you could have explored in more detail, it's normal to acknowledge that at the end. A hard time limit for master's research is always going to cut you short.


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Is it possible to confirm if someone is enrolled at a particular school?
So I know there's roadblocks like FERPA (this is in the United States by the way), but if I already knew:

Full Name
Date of Birth
Name of school (obviously, since I'd have to know who to ask)
(Supposed) Major

Would a college/university be able to confirm or deny that the student is enrolled, since I'm only asking to have information I already know confirmed or denied, and not asking for any new information? If so, which office/department at a given school would I (generally) direct a question like this to?

So I know there's roadblocks like FERPA — One person's roadblock is another person's first line of defense against nosy people, stalkers, etc.

Probably better to not be finding oneself wanting to do this. If the question is about what other people can do, the answer is "it's technical and ... it depends...". FERPA can give you a way to have your university not divulge your home address, phone (landline or cell), university email, and perhaps even whether you are now or ever were enrolled. But the default of FERPA (as in answers below) is typically that last registration term, current address, and current phone are publicly available, without any clearance or privileged info whatsoever. Maybe this will change in the future...

What is the context? If the student is applying to you in some way, you can ask them for a certificate.

"since I'm […] not asking for any new information?" you don't know whether the person is enrolled. ergo, you are asking for new information.

In the US, under FERPA, institutions of higher education (rules are different for K12 education) are required to define what pieces of information about a student are "directory information."  This typically includes the name, address, and phone number of a student and may include other information such as the student's dates of attendance, major, and any degrees that the student has been awarded.  The list of what items constitute directory information has to be made available to students, and students have the option of to keep this directory information confidential.  Other more detailed information (such as courses taken, grades, class rank, etc.) is automatically confidential and can only be released after an explicit waiver from the student.
If a student has chosen to make their directory information confidential, then the university won't confirm or deny that the student has any connection to the institution.  if the student hasn't opted for confidentiality, then the registrar's office will typically provide the directory information when asked.
There are good reasons for this protection.  For example, consider the situation of a student who has been the victim of domestic violence and is hiding from an abusive family member.  The abuser could call the university, talk them into providing the student's contact information and then use it to track down the student and harm the student in some way.
On the flip side, this confidentiality provision can cause problems with reference checks for former students.  If a student chose confidentiality and years later an employer calls the university and asks "Did John Doe complete a BS degree at your institution?"  The institution would have to say "We can neither confirm nor deny this."
In my experience, a fairly significant percentage of students (maybe 10 to 20%) at my institution opt for confidentiality of their directory information.  Given the problems that this can cause with reference checking, I'm somewhat surprised by how many students opt for confidentiality.
In general, the office to ask would be the registrar's office.  They regularly handle requests from people who are conducting reference checks and background investigations.

Interesting that you have seen 10-20% opt for confidentiality.  In two years at my current institution, I don't think I have encountered a single "confidential" flag.  It may have to do with local culture, and/or the way that the registrar's office explains this option to students.

I can't recall a recent class that I've taught that didn't have the confidential flag on at least one student.  Most of the classes that I teach are quite small (15 or fewer.)  Whenever anyone asks me for this kind of information I just pass them on the registrar's office.

If the student is not at the institution, then would they say the same thing? Otherwise, isn't it a dead give-away?

That's the point of "Can neither confirm nor deny..."  answer.   You can interpret this answer as "Either the person has not been a student or they have been a student but have opted for confidentiality."  The other possibility is that the person has been a student and allowed for disclosure of directory information and in that case they provide the directory information.

@BrianBorchers: can students opt for confidentiality while they're studying (because for whatever reason they don't want their current address to be published) and then change their mind once they graduate (because they want reference checks to work for the rest of their life and the university won't publish their address once they've left)? If so then this might account for such a high rate as 10-20%: they have no current plans that require reference checks to work while they're studying and they are privacy-minded.

Students can change the setting whenever they want.  In practice most probably forget what option they chose...

Unless a student has specifically opted out, FERPA does not cover the information of whether a student is enrolled and the degree that they are seeking (including major).  The exact circumstances under which a school might reveal that info would depend on the individual school's policy.  See here for Penn State's explanation of this aspect of FERPA.

Generically, no, a school should not be giving out that information if the person is not making it publicly available through directories, officially hosted webpages, etc. (By default such information is typically available).
Think about it this way: how can an administrator distinguish you from an abusive stalker who wants to confirm the location of their target?
If, on the other hand, you have a legitimate connection with the student, such as that they are applying for a job, then the student should be able to provide references whose connection with the school is clearly verifiable (e.g., their advisor) and who they can give explicit permission to confirm their status to you.

Actually, I believe FERPA allows schools to disclose "directory information" to anybody. This includes "dates of attendance" which I would think should include current enrollment status. Of course, just because the law allows them to tell you, does not mean they will. At my institution, students concerned about stalking, etc, can have a "confidential" flag set on their record, in which case the school will definitely not share directory information.

Corrected to make the default public status clear.

@NateEldredge FERPA gives students the option to make directory information confidential.  By default, directory information can be released by the institution.  If a student chooses confidentiality than the institution cannot release even directory information.  Other information that is not "directory information" is confidential by default and can only be released with a specific waiver from the student.

@BrianBorchers: Thanks for clarifying.  That matches my understanding.

While it's got a few corner cases that make it unreliable in general - many if not, all universities have a predicable email address setup for each student (my former one is firstname.lastname.yearofenrollment@domain.ac.uk). If you wanted to confirm a student with a name was at the college you would email that address and see if it bounced.
That's the hard way.  If I had someone's name, date of birth and so on. I probably know them well enough to ask them...

That's the thing. They've told me, to my face, in no uncertain terms that they attend this school. Problem is, I have reason to believe that this person is lying to me, and I'm trying to prove it. My goal is to not confront them and burn that bridge until I've made some attempt to quietly verify it directly with their institution.

Also, I did a Google search for "@[school_domain].edu" to get an idea of what the format is, and it appears they have a username generator of some kind that produces whatever mangled form of their name necessary to keep it free of numbers and punctuation, as well as keep it under a certain number of characters (compatibility w/ legacy UNIX system maybe?). This is a prestigious institution (not going to name it, but I'm sure any of you would know it if I did), and aside from inconsistencies in this person's story, quite frankly I just don't see them being the type to get admitted.

"whatever mangled form of their name necessary to keep it free of numbers and punctuation" what type of name do you have that numbers feature heavily?    Ah, then I change my advise- there is NO point disproving a lair - it costs more than it gains - if it's obvious to you it's obvious to others. Best revenge is a life lived well.

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Is it ethical for Albert Einstein to get lecture notes of Geometry class from his personal friend rather than taking the class himself?
In http://www.cvastro.org/ECP1.pdf page 8,

Fortunately his friend, Marcel Grossman attended class regularly and
  took notes which he carefully rewrote. Grossman allowed Einstein to
  use his notes to prepare for the final exams which he subsequently
  passed. This is the first instance of Grossman coming to Einstein's
  rescue.

Albert Einstein got lecture notes of Geometry (not sure if this is exactly geometry) classes from his personal friend rather than taking the class himself. Since he did not attend the class himself and take the notes himself, I feel that he was in an advantage compared to students attending the class and taking the notes themselves.
Not being an ethical hypocrite but I just feel this is unfair (A question comes from sympathy to his classmates in fact.). Personally, sometimes I feel too tired, or the professors bad at teaching but their notes are important (Sometimes one trick the professors ensure high attendance is to suddenly talk about exam questions in class.), or have time clash in the class, I wish I can get notes from someone rather than attending the class or just attending, concentrating on listening but not taking notes. But I feel that this is unethical as many students have the same problems. So if I do so, I have a "time advantage" compared to them.

So you claim that the only source of knowledge should come from inside the class and nowhere else? Even if it is an advantage (which is highly debatable) what is the point? You also have advantage for attending a university in comparison to other students that they do not even have that advantage.

This depends on the requirements for the course.  If passing the course is based only on the exam, then attending the class is not necessary.  Non-attendence is not an ethical lapse.  But, for most students, non-attendence is merely stupid--since, not having Einsteins intellect,  they will fail the exam.

Why would it be unfair? He had to pass the same exam as all others.

@GEdgar but it is not attending but getting class notes.

Don't forget that the point in taking a course is learning.

@Franck Dernoncourt but there are some courses I do not want to learn, having time clash with the course I want to learn, but I am forced to take them and pass the exam within a fixed timeframe.

@kyle in that case, in my opinion, do whatever it takes to minimize the time cost.

Even more amazing: for most courses there's a book that you could just read on your own to learn the same material, and more. ("... education you could have got for a dollar fifty in late charges at the public library!")

I don't see any ethical problem here.  If you don't want to attend class, you are under no ethical obligation to do so.  (Of course, if attendance is required, you may suffer a grade penalty.)
And if another student is willing to share their notes with you, they are free to do so, and you are free to read them (unless of course the professor or your institution's regulations have forbidden this).
If you truly believe your education would be improved by skipping class and reading notes from a classmate instead, ethics permits you to do so.
However, it's my considered opinion that the vast majority of students who think this is to their benefit are wrong.  Reading notes taken by someone else is not the same as attending the lecture and taking your own notes.  You are at the mercy of your classmate's errors and omissions.  And you miss out on the opportunity to ask questions of the lecturer, participate in class discussions, et cetera.

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Is it really legal to submit a work to a venue although we already uploaded it as a reprint somewhere like Arxiv or researchgate?
I am wondering if it  is legal to submit a work as fresh manuscript to a journal although we have already uploaded it somewhere else as a preprint?
Most of the journals/publishers require that the work at hand should not be submitted anywhere else. So I am wondering how the people who firstly put stuff  as a preprint on the researchgate and ArXiv deal with this issue!

It's not a legal question, actually. It is about the individual policies of journals and conferences.

Most of which journals require that? This is certainly highly field-dependent!

The answer is simple: those same journals have an explicit exception for preprint servers.
Consider, for example, the Nature family of journals, whose current preprint policy says, in part:

Posting of preprints is not considered prior publication and will not jeopardize consideration at Nature Research journals. Manuscripts posted on preprint servers will not be taken into account when determining the advance provided by a study under consideration at a Nature Research journal.

If you are wondering about a particular journal, the Sherpa/Romeo database is a good information source and often easier than searching the journal's own pages for the applicable policy.

Not all journals have such an exception, I believe. Check to be sure.

The word "exception" sounds like it should be the rule not to allow for it.  I don't think this conveys the right attitude, I think a word like "regulation for preprint servers" would be better :)  In any case, in physics it is pretty much the rule that it is allowed.

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Is it too late to ask the faculty for a summer research internship position?
I am wondering if it's too late to ask the faculty about the availability of a summer research internship position? When would be the best time for this?
More information as requested:

I am looking for the positions in the US from May 25th onwards.
I am also a graduate student and I'm thinking of a summer internship with an eye towards the possible continuation as a post-doc.

Note that it may be impossible for you to participate in lab or field work due to COVID-19 restrictions- this will depend a lot on the particular institution's policies and may be subject to change on short notice.  For example, at my institution undergraduate students won't be allowed to be in the research labs for at least the first half of the summer.

No, it's not too late to ask. But whether it is too late to get one depends on the local situation and so we can't help with that.
So, ask. If you don't ask you won't get one.
There is a Chinese proverb: The best time to plant a tree is twenty years ago. The second best time is right now.

Thanks for the answer and the proverb, that's a good one.

General answer: it is never too late to ask for anything, nor there is almost no downside to asking. So go ahead and ask around.
Even better news: some summer internship programs are moving online and bumping up number of participants.
More good news: Summer programs (like the one Caltech runs) are structured, so they have deadlines, but if you are in a position where you can work for free, you can always (year-around) inquire about possible volunteering opportunity for specific labs. Even better then to reach out to professors who's work is interesting to you

Thanks for your answer.

There's always someone looking for interns.
My recommendation is to ask researchers that work in fields that interest you if they are able to supervise a research project over the summer. I would recommend you prepare a nice CV that you can attached to your email, so that they don't have to ask you for it and delay the process un-necessarily.
I would also recommend to check their websites, since many of them say explicitly "not currently taking research interns" and therefore if you do email them anyway, they might get annoyed and it could hurt your chances of working with them in the future (it probably won't harm you, but in some cases it can, so it's better not to risk it).
If you need help choosing a supervisor, you might ask friends if they have recommendations, or you can browse university websites after clicking on the department you're interested in, and finding the "department members" page.
If you are really keen and have the time, I might recommend to browse some of their papers, for example on Google Scholar or from the publication list on their website. They will be impressed if your email indicates that you know at least something about what they do, and is not just a generic request to work with someone about whom they have not the slightest clue.
Last of all, good luck with your search for an internship!

Without qualification, I would expect "not currently taking students" to mean graduate advisees, not summer undergraduates, unless that's explicitly stated.

True, I'll edit the answer.

@AzorAhai actually the OP didn't say they were an undergrad student (although I agree that you're probably right). I changed my answer to say "research interns" so that it exactly matches the question. The details are probably less important than the general advice to look at someone's website and get a feel for whether or not they're accepting students. This is at least what I did when I sought undergrad-level, grad-level, and postdoctoral-level positons, and even employment outside of universities.

@user1271772 I am a graduate student.

Thanks for you answer, I am almost doing the same things you suggested above.

@Cardinal Great! Good luck with the search by the way!

@user1271772 Oh, sorry, I forgot some graduate students have "internships" in the summer. It's not common in my field so I just assumed.

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Is it okay to consider publishing in my first year of PhD?
I'm PhD candidate in Applied linguistics, it's been almost 3 months since I've started but I'm seriously allowing for writing and publishing journal articles.
I have asked my supervisor about that, she said that I should devote my time to my thesis and wait until the second year and that writing other forms of papers generally interfere with the thesis.
However, I think I have enough time to simultaneously work on my thesis and also articles, also I have to indicate that the ideas that I'm willing to formulate in articles are not related my PhD focus.
What should I do? Should I wait until next year or just start working on articles and submit them as single author?

Are you by chance considering publishing review articles rather than original research? If so, you might be interpreting your supervisor's advice as "don't publish your first year" when she means "focus on your original research, because publishing a review article as a first year student is not worthwhile."

Thank you for your comment, it is actually a perspective article

I think you should not work on such an article without your advisor's blessing: trust her on this one. Perspective articles are rarely well-received from people not already established in their field: you are unlikely to get such an article published in a good journal even if it's written well, and if it is published it's unlikely to be cited much. People are interested in the perspectives of people who have been studying at an academic level in the field for 10+ years, not from new PhD students.

I fully understand that, it is more of an opinion article, but I have also had collected data for another article. I'm aware that publishing is burdensome process, yet I take it more as a learning experience

Yes exactly: to put it bluntly, no one cares about your opinion (yet). Imagine if a university freshman wrote a book about "how to teach a university course" in their first month of school: how many professors would take them seriously?

I can't agree more, I will keep that in mind. Thank you

I'm sometimes hesitant to recommend editing a post that has already attracted answers based on the previous content of the post, but I do think you should edit this into your post or otherwise ignore most of the other answers you've gotten here: they all seem to be assuming you are wanting to publish original research and your advisor is somehow holding you back from that, which is not the case.

I feel the need to clarify. I haven't fastened on only producing opinion articles; as I stated, I have enough data and materials to have original research. I'm really cognizant of how Academia works, and publishing takes months or even years. So, I suppose having such ambition is to be appreciated and encouraged (otherwise I will be just like any other phd student)

First year is actually a good time to see if you can get the ball rolling with some article publications, I am hoping to publish in my first year but obviously you really need to discuss this with your supervisor.

Advisors are good people.  I would listen to them before random people on the internet.

Whatever you do, you will want to cultivate a good working relationship with your supervisor, so I'd advise against doing something she dissuaded you from just because strangers on the internet told you to. Talk it out with her.
That said, not a single PhD student I've known wrote/writes a relevant portion of their thesis in their first year, and the advice I have constantly been getting from faculty is that early in the PhD is the time to think about publishing other things. There will most likely be a time when your thesis takes all your attention, and by then it's certainly too late to worry about publishing elsewhere.

One way to approach it is to try to determine whether she simply advises against it, or strictly forbids it. Proving her wrong may not help you, but it is hard to say without knowing personalities.

I understand your supervisor's point-of-view.
When it comes down to it, anyone is allowed to publish a paper.  It doesn't matter whether you are doing a PhD, have finished doing one, or never have any intention to do a PhD.
But you are supposed to be studying for a PhD.  Taking time to write a paper on something unrelated is only going to distract you from the work you're meant to be doing.

Furthermore, your advisor might think that you don't have enough content to publish an article, but you need some time doing research (on your thesis) to get it.

I'm PhD candidate in Applied linguistics, it's been almost 3 months
  since I've started but I'm seriously allowing for writing and
  publishing journal articles.

Good going, this is a really good trait to have in academia and will be really helpful in the future.

I have asked my supervisor about that, she said that I should devote
  my time to my thesis and wait until the second year and that writing
  other forms of papers generally interfere with the thesis

This sounds a bit bizarre to me. Make sure there was no miscommunication between you two. Since you only started about a few months ago, I am guessing you haven't started working on your thesis yet. So there shouldn't be any issue publishing now without affecting your thesis. Thesis is one thing, but it is the published articles that actually count in your profile and make you stand out from your peers. Ask her about how would publishing now would impact your thesis and get more clarification. Maybe she is right, which she should be able to explain but do ask.

However, I think I have enough time to simultaneously work on my
  thesis and also articles, also I have to indicate hat the ideas that
  Im willing to formulate in articles are not related my PhD focus.

Explain it to your supervisor and defend your decision.

What should I do? Do you I should wait until next year or just start
  working on articles and submit them as single author?

It depends on the policy set by your departmental or school. Talk to someone in the department before proceeding further. Some have a policy that you have to include your supervisor since you are publishing this work while in their group, unless you are publishing research from your previous degree (say from your MS). But if these ideas are your own then there might be a different policy. So do check and consult with someone in your department who might be knowledgeable about this before proceeding.
Good luck!

Sure, no problem. Just make sure you clarify everything with your supervisor. If you think you have a good idea and you should publish it, then defend your decision with rationale. Maybe she can explain her thought process and even better if she can guide you through the process to fine-tune your idea. Anyway, it will be a win-win situation if you have your supervisor's blessing.

"devote my time to my thesis" might mean "work on experiments, lit review, project design etc"

Yes it could, that’s why OP needs to communicate this with the supervisor.

We try to publish material that we are expert in.  To become expert, we invest time and resources.
Further, when we send stuff out to journals for review, we are impacting the opinions of our current and future colleagues have of us.  If you're a student at this point, you're also impacting the reputation of your mentor.
Without knowing much about you, I'd suggest that it's more likely than not that you're not sufficiently expert to publish something not perfectly within your own research area, and thus you might be hurting your reputation by packaging up a paper and sending it off to a section editor. The time you put into such efforts might be better put into honing your expertise in your own area.
If you feel like you need to be writing, I recommend starting to write a paper on your current topic of research.  The paper will form somewhat of an outline of your research, and will show you what you need to "fill in" before the paper should be published.  The paper will be ready to go out the minute you have the data to support it.  I wouldn't think of this process as "writing a paper", but as more of a statement of research.  It will drive productive discussion between you and your mentor.
At this point, I don't think the advice you've been receiving from your mentor is bad.  She signed up to guide you through your early career, and you should give her her shot at it!

It is certainly ok to consider it. And it is certainly ok to follow up on ideas for research. Whether to actually publish may be more of a political issue, however.
If nothing else, keep a notebook of research ideas and first approaches for later. But your dissertation comes first and your relationship with your advisor shouldn't be compromised.
If you publish something and thereby "prove your advisor wrong" the outcome will depend on personalities. Some would praise you. Others condemn. The answers of sgf and nsinghs provide good guidance.
But the idea of keeping a notebook of things to pursue is a valuable life-long practice. In a fast moving field you may need to move quickly, of course, but often enough things can be set aside while you work on more essential things.

You already said that the articles would not be related to your thesis work. Can you tell that for sure? In some places a collection of published papers is what makes a thesis.
That being said, are we talking publishing in a conference or in a journal? Have you ever published in a journal?
My guess is that you probably have time to publish in a small conference. And you surely have time to write a draft paper for a journal. But publishing a journal paper requires more time and effort than you might be expecting. You'll probably be asked to provide more references than you have, which will consume time to find and read. You have to correct errors, spell check, and so on.
All of this does not happen quickly, you might submit to a journal, get refused, submit to another, be accepted but asked for corrections/improvements. Then you submit again, and it might take some more time before you are asked for further modifications. Depending on the field, this may take more than a year, thus even if you believe you'll be done in 3 months (to send the first draft), you might need to turn your attention back to this publication by your second year.
Now, everything changes if this publication's topic matches that of your PhD.

Along with others, I understand one possible rationale for her advice: the concern is that it will delay your agreed upon PhD thesis work. Your supervisor may not want you to add your name to the growing number of ABD's.  Having said the above, history, culture and norms of your dept environment also play a role.  I published as an undergrad as well as a grad before I finished my PhD thesis and it never occurred to me to seek permission once I obtained a PhD supervisor. So, I recommend, as others have, that you should discuss it with your supervisor and discover why she feels that way? That seems to be the information you are missing (or we are missing, in order to advise you). Best of luck to you.

I disagree with your advisor.  The archived journal literature is what counts.  You can always pull a thesis together.  Get some notches on your belt.
Furthermore, at the end of the day, your career is your career.  Listen to your advisor's advice but don't follow it slavishly.
Edit:  I see you have clarified that this would be a commentary article.  I agree with your advisor on not bothering with that, now.  Original research reports within your thesis area are a different kettle of fish.  I would emphasize publications in that, once you have enough done (and well prior to and before writing your thesis).

I disagree with you - publishing something useful needs some good work to support it.... Perhaps if you are Stephen Hawking then publishing on day one is possible...

Personally, I wouldn't argue.  Just do the work and write the piece.  Then, it speaks for itself.  As it is now, you'll just be having a theoretical argument.  I think the work you do will be usable for either a dissertation or an article, so it's not much lost if you just do the work.  If you find yourself incapable of producing good work, then you learn that from the effort.  Rather than a theoretical argument.

Solar, I'm not Hawking and I produced three articles in first 3 months (summer) of research.  In some fields, this is not very difficult (to get datapoint papers done).  In addition, it is not unusual for accomplished researchers to do publishable work immediately.  If the grad student is not overawed by publishing, than he may be able to quickly move to useful production.  Perhaps the OP is incapable, but so be it.  Nothing wrong with trying.  The effort won't be wasted.


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What does "reject and resubmit" mean?
I sent a paper to a top tier journal in science a few weeks ago. I received the feedback from the editor saying he declined to publish/ accept my paper at the moment but if I corrected/ responded to the comments provided by reviewer, he/ she would consider to publish my paper.
I went to paper tracking website only to discover that my paper is classified as "reject and resubmit". Does that mean if I responded/ did everything suggested by reviewer, there'll be high possibility my paper will be outright rejected?
The comments from reviewer was not that harsh, but I wonder whether I'll be wasting my time if I went back to the lab and did what he said. I only have 2 months to respond.
Also, what is the difference between "reject and resubmit" and "major revision required"? This is my first submission and I'm confused.
Hope anyone can enlighten me.

Also see What does a “major revision” mean?

You are right that your paper may still be rejected, but you shouldn't worry too much.  The fact that the editor proposed a resubmission suggests that he/she sees real value in it.  As an editor, I can say that I would never waste time handling a submission again unless I thought there was a decent chance of acceptance.
Of course a decent chance is not 100%.  Acceptance conditional on minor revisions means the editor is confident the revisions can be completed straightforwardly, while major revisions are always more of a gamble.  They might just not work out in principle, or the authors might not be capable of pulling them off.  However, they are worth a try.
Turning down an offer to resubmit is usually a mistake.  It comes across as a sign of weakness, like you've decided your paper probably can't be fixed and you'd better just submit it somewhere less prestigious/demanding.

Also, what is the difference between "reject and resubmit" and "major revision required"?

Sometimes there's no difference at all: there are fields in which "reject and resubmit" is just what majors revisions are always called.  Sometimes there's a difference, with reject and resubmit indicating a slightly less optimistic outlook (but still optimistic enough to be worth trying).
There are also borderline dishonest reasons some journals prefer reject and resubmit.  Splitting a single submission into two submissions can make the journal look good in two different ways.  Rejecting the initial submission decreases the journal's acceptance rate, which makes it look more selective.  (A journal that accepts every submission after an R&R can claim it technically has an acceptance rate of 50% rather than 100%.)  Furthermore, splitting the process in two decreases the average time from submission to a decision, which is another statistic authors care about.

The key, from an authors point of view, is whether you have been given a fixed date.  If there is a fixed date to resubmit by, then it's effectively the same as a major revision.  If there is no fixed date, then it's a rejection that welcomes a new submission when you've improved the paper.

Each journal will have it's own fairly vague differences between different tiers of evaluation, but what the editor has described and "Reject and Resubmit" are exactly the same thing.
Essentially, your paper has been rejected ("declined to publish accept my paper") but there is the opportunity to revise your paper and resubmit it for consideration again ("...if I corrected/responded to the comments provided by the reviewer"). A paper that has been outright rejected doesn't get to have another go at the submission process.

Does that mean if I responded/ did everything suggested by reviewer, there'll be high possibility my paper will be outright rejected?

What that means is that the editor will consider it again - it's chances depend on many things, including the quality of your revisions.

Also, what is the difference between "reject and resubmit" and "major
  revision required"? This is my first submission and I'm confused.

It will very much depend on the journal. Both are, in rough terms, "This needs some work before we can consider it for publication", though the vagaries of what exactly that means will change.
For the record, refusing initial publication and inviting you for a second round after you've addressed the reviewer's comments is likely the standard trajectory for a paper to reach publication.

Thank you for your answer. My supervisor is also encouraging me to do all the things mentioned by reviewers.

One other point I'd like to add to the above answers is that many journals these days prefer to give a Revise and Resubmit (R&R) over a Major Revisions decision, but both effectively mean the same thing. The fact that there is a deadline attached to the R&R is definitely an indication that the editor has seen some potential in your paper and wants to reconsider it after it has been revised. While your paper still might be rejected, it would definitely stand a better chance of being accepted by this journal than by a completely new journal. This is also because even for an R&R, there remains a possibility that the editor might send it to the same reviewers, in which case, your paper stands a good chance of acceptance, provided your revisions are satisfactory.

Also, what is the difference between "reject and resubmit" and "major revision required"? This is my first submission and I'm confused.

In addition to wonderful answers above: Another difference, which may impact you as an author, is the "submission date" as it will appear on your accepted paper. If a new finding is proposed by two (competing) groups, it may be difficult to see which group can claim the priority. In this case, the decision often is made based on the "submission date", and not the "final publication date", which may be more than a year later due to the time-demanding journal publication process.

For papers under Major Revision the final publication date is delayed by the revision and re-review process, but the submission date remains the same
For papers with the Reject and Resubmit status, the submission date will be the date of resubmission. Therefore, it will be more difficult to demonstrate the evidence of priority in this case.

While I agree with the other answers, that there's differences in how terms get used, I take it to be the case that (for the journals which make a distinction), the distinction is something as follows:
In terms of acceptance,
Reject and Resubmit (or revise and resubmit) (hereafter, R&R) = your article has been rejected.
Major revision = your article is in a kind of limbo state where it is neither accepted as is nor rejected but rather held unto the revisions come in.
In terms of reviewers,
R&R = you have no reason to expect the same reviewers. (You may or may not get them). The review will be de novo in principle.
Major revision = you will most likely have the same reviewers (It's not a perfect guarantee) who will decide whether your changes are sufficient to push it over the bar.

This of course contrasts with three other states I've seen:

Accepted as-is (no more reviewing needed)
Accepted subject to minor revisions (accepted pending minor changes they expect you will succeed in making).
Outright rejection (don't bother working on it again).
Outright rejection with the editor's suggestion to substantially revise and resubmit (de novo review and consideration).


text:
Relative pronoun 'who' or 'which' when referring to article by authors' names
In an academic paper, when I refer to an article by author's name and publication year, then use a relative pronoun, should I use 'who' or 'which?'
For example,

We referred to the method proposed by Smith and  Johnson (2004) who suggested blah-blah.

I'd use who, but probably this question is a better fit for ELU.SE.

I think it is appropriate for Academia.SE because it involves a very specific feature of language rarely if ever seen outside of academic writing.

This depends entirely on the subject of your subordinate (relative) clause.
If the authors are the subjects of the subordinate clause, use who. E.g.

Many postmodernists reacted angrily to the stunt pulled by Sokal (1996), who they felt had acted unethically in an effort to discredit their field.

If the paper or text is the subject of the subordinate clause, use which. E.g.

If you want to improve your mathematical writing, I recommend carefully examining Halmos (1974) which as a text manages the difficult feat of combining  scrupulous rigorous with broad accessibility.

In your example, you'll need who, as you wrote:

We referred to the method proposed by Smith and Johnson (2004) who suggested blah-blah.

Here's an example with which:

We compared our results with those of the method proposed by Smith and Johnson (2004), which is similar to our method except in how xxx is handled.

In your second example, note that the subject of the subordinate clause is actually "method" not "Smith and Johnson (2004)" -- though still a correct answer to the question because I realize the OP specified only the word order not role.

@Corvus - Yes.  I wanted to show the OP how it works, with a couple of simple examples.  But perhaps the OP will want the full grammatical explanation.  I suppose everyone learns differently.


text:
Trying to finish a paper with a professor, but also needing to let them know I switched advisors
I need a bit of advice. I am currently in my third year of a math PhD program.
I have been working with Prof. X for about 2.5 years now. He thinks he is my advisor but I have also been working with Prof. Z who is my chosen advisor for many reasons. In short, Prof. Z a much better advisor for me (nicer to me, better at helping me learn, more available, supportive for me to attend summer research programs, etc.) and I want to work in the research area of Z and not X. I know that I will be successful with Prof Z.
Last semester I was traveling most of the time doing research related to Prof. X's work. In that time, I solidified that X's area is not the area I want to study. I am trying to finish a paper with Prof. X though.
I need to tell Prof. X that I want to finish the paper but then work with only Prof. Z.
I am thinking that telling Prof. X in person is best; however, I am also worried that Prof. X will have a bad reaction (due to his personality). Maybe it is better for me to tell X over email so that the initial reaction doesn't happen with me there.
Any advice would be really helpful on how I should tell him.
Thanks!
Update: Hey all. Just as an update. I told him today. I thought he would be mad but it was more of a sad reaction. I felt bad, but I know I’m making the right choice. Thank you all for your time and help with this :)

Sorry to say, but it is difficult to give an answer to your question not knowing any of the people involved personally. The general advice would be to discuss conflicts in a personal meeting, maybe by phone and never by e-mail. It might feel easier by e-mail but leaves too much room for misunderstandings and uncontrollable escalation.

Thank you very much for your time and help.


text:
Extending work without plagiarism
I am working in a sub-field of computer science (deep learning), more specifically a particular application of LSTMs to learn simple functions. My work is building on the work of another researcher to an extent that I am using the same model, parameters and problem definition. I am writing a research paper based on my findings.
My work is different in the sense that I am introducing some different concepts from another area and trying to make a generalisation about the very nature of ANNs (using his work as an intermediary). And since his work is the only such publication till now, I am taking some things directly in my work eg. Problem Definition or Model.
So the question is whether it will count as plagiarism? If yes then how can I circumvent it as I have to write many things as it is, there's no other way to get around that as I am using them as it is.


text:
Wrong citation? What should I do?
PLEASE SEE CLARIFICATION BELOW
I noticed that one of my citations is "problematic". It is from a book, but I found a Scopus reference that show it as a conference paper, with no authors. So I thought it was simply a mistake (because the paper is very old) and added the authors of the book normally, as the book or paper were published on the same year and the chapters are in fact other revision papers, but they are all the same.
Now it came to my attention that the "authors" are in fact the editors of the book/paper, and I don't know whether I have done something wrong or not by citing them. If someone looks the reference using the "authors", volume and year they will find normally the book, but not the journal I referenced in the paper, which is from the same publisher as the book.
Would it look like plagiarism or another ethical problem just because I mixed the two references, which are identical, but are written differently?
EDIT To be more clear, my citation is similar as if I cited a whole issue of Science (Science, 4, 2010) with the author name appearing as the editors of that particular issue.

I'm having trouble keeping everything straight here.  There's a book and a paper and a journal and a conference, and some authors and some editors...?  Can you give an example, maybe your actual situation with the names/titles changed?  The key questions I would ask about your citation: (1) were the proper authors credited? (2) will a reader be able to find the correct document without excessive difficulty?

@NateEldredge the journal does not exist anymore. But apparently it used to print what they call articles (with no author name) with various reviews in it (from a number of authors). Basically, a book. So, from what I've seen, they had used one of these articles as a book, and the authors of this book, which is a compiled of several articles, are the editors.
Now, what I did (dumbly, I must say) is: I used the citation for the authors as in the book, but with the article details (journal, volume etc)...

@NateEldredge Yes, the reader will be able to find the correct document if they search for the name of the "authors" with the date of publication. If they search for the reference as it is printed in my article, they won't find much.

@NateEldredge Some references cited the "book" with the editors name as authors, so I think I did cite correctly in that context. However, it would probably be better if I cited the author of the "review article/chapter" that I extracted the information from...

@NateEldredge To be more clear, my citation is similar as if I cited a whole issue of Science (Science, 4, 2010) with the author name appearing as the editors of that particular issue.

You honestly attempted to make a citation, but made some mistakes in providing the correct information. This happens sometimes and absolutely is not plagiarism because you were clearly not trying to pass off others’ work as yours.
What you are responsible for is making sure the error is fixed. If the manuscript has not been published then all you need to do is correct the reference in a revision or at the proof stage. If the article has been published you should contact the editors for guidance about the best way to proceed.

Thank you for your answer. The paper is already published. As I said previously, the source is quite old, and it was presented as in an article with other articles compiled, as in chapters (this compiled had a title, journal number, volume and pages, but no author). And it also was presented as a book. I basically mixed the two forms of citation, adding authors to the compiled of articles. I don't know if this would qualify as something for an erratum, since the information I provided, even though mixed, still is somewhat correct...

@arw1990 I suggest you first write out the most accurate citation that you can, using the information that you now have. Then compare this new citation with the one that was published and ask whether there is a real benefit in correcting the publication, either in ensuring that the right people get credit for the work or in enabling the reader to find it. (The answer is likely to be "yes".) If so, then write to the editor asking that a correction of the citation be published.


text:
How big of a deal is it if I abbreviate a school name?
I am writing some thank you's for interviews I had recently. How big of a deal is it if I write UCLA instead of University of California at Los Angeles, for example? I have always spelled things out in cover letters and CVs and stuff, but especially at this point, it just seems like I should just be able to write UCLA. Would anyone not think kindly of this?
Some school names are short/you should always write out like University of Michigan instead of Michigan, or University of South Carolina instead of USC, but when there's no ambiguity like UCLA, it seems silly to write that out every time.
Thanks for the help!
P.s. these are for math positions if that matters.

If you are writing a thank you for an interview at UCLA, then you can write UCLA.  Similarly for USC or Michigan.  (Just don't send the letter to the wrong one...)

UCLA is an extreme example, as the abbreviated form has such widespread recognition that they have actually opened UCLA-branded stores in multiple foreign countries selling UCLA-branded merchandise.  You can probably get away with saying UCLA in almost any context.

I can't imagine that anyone would object, as long as the abbreviation is widely used by people who work at the university.  (UCLA is fine, but I wouldn't call it UC Los Angeles, since I believe that's a much less common abbreviation.)
In fact, repeatedly writing out "University of California, Los Angeles" is more likely to stand out as strange than using the abbreviation UCLA is.

And make sure that your abbreviations make sense. (Writing to someone in California and using "USC" to represent the University of South Carolina may lead to substantial confusion.)

I would suggest following usual rules for using abbreviations. Spell it out on first reference and use the abbreviation on subsequent references.
Obviously if you're addressing a UCLA faculty member you probably don't have to spell out University of California, Los Angeles, but I'd spell out pretty much anything else, you don't know what school they'll think of when you say UM. To me, that's University of Montana but I sincerely doubt that's many other people's first thought.

There are very few universities that are universally known by an abbreviation.  MIT is one of them.  Caltech is arguably another, but I find blank faces on the East Coast of the US when I mention the name, so there is an issue of recognition there to begin with.
USC is another that is ambiguous.  It's easy to assume if you are from the West Coast that "clearly" this is the University of Southern California, but New Yorkers may or may not recognize this.
New Yorkers tend to think NYU is one of the great institutions in the world, but I find most people on the West Coast aren't familiar with it and default to thinking "NYU" means the state university for New York.
Some are suggesting it's weird to spell things out, but I've seen enough resumes to recognize that people spell out all kinds of things and as long as it's clear what is meant, there is generally more to worry about in a resume than that.
So what about your example, UCLA?  I've met very well-educated people from abroad that didn't actually know what it was.  It's true the brand is very strong (especially in Asia), but it definitely does not have the recognition of MIT.  In this case, you might want to put "University of California, Los Angeles" but you run the risk of some people not recognizing this is the same as UCLA (I've seen this happen with people from Asia).  This example shows it's important to recognize your audience.
In summary, whether to use an abbreviation depends heavily on audience.  Lean towards not using an abbreviation if you are unsure, and keep in mind very few institutions are known universally to begin with and known by their abbreviation.

Yeah I know some people don't know what you're talking about, so you do have to know your audience. I was particularly talking about people who are faculty at a certain school. Like if someone at MIT would take offense to me calling it MIT rather than Massachusetts Institute of Technology. I think the consensus is that no, that doesn't matter.

If you use a widely used, well-recognised abbreviation, it shouldn't be a problem, unless in any extremely formal setting (like some legal paperwork). Use e.g. the abbreviation on their web page.
Use of abbreviations for other institutions would be a bit iffy, particularly if not well known or even potentially ambiguous (e.g. USM could be Universidad Santa María in Chile, or University of Southern Missouri, or perhaps even others).


text:
Would it be impolite to ask the time of selection decision, although the information is available online?
I applied for summer internship(BSc level) in applied math in one of the North European countries a month ago. I would consider myself as a good applicant but I suspect that they accept very few international candidates, and range of countries of applicants is pretty wide. It is stated that the time of selection decision is march-april. I'm very curious and impatient about knowing the answers to "am I accepted or not?", "when will I get the answer?". In addition to curiosity, the reason of sending such email is to show that I'm ambitious(?) and serious and didn't applied just for fun. I believe that this might increase a little bit my chances. But I'm afraid that this email might turn against me, because I disturb the committee for almost(?) no reason, and it might give them an image of impatient student.

I decided to edit a little my 3 year old question and it got on the top again. I'm sorry for that. That wasn't my goal.

Now that we're here...did you get in the program?

@Emilie I did not :)

I would not suggest to write an email that does only ask for the status of the application before the announced time of selection is over—even when the email is totally calm and polite. The program has a schedule, the applicants are supposed to know the schedule.
However, you may have some other good reason to write an email. As Thomas commented to another answer: A good reason to ask for the status would be an offer for another opportunity. You could also try to find another good question to ask (but be sure that it is not already answered in the FAQ or wherever). Also, you could provide some new relevant information, if there is any (e.g. some new grades, completed projects,…).

Sending a simple email politely asking about the status of the applications should neither hurt nor hamper your chances of acceptance. Anything more and you risk annoying the committee and hurting your chances.

It might also help to explain why you are asking. e.g. "I need to decide whether to accept a different internship."


text:
PhD completion hanging in balance
I am a Bioinformatics PhD student at a US university. I left the university (stopped enrolling after informing my advisor) in Aug 2014 since I was not making much headway with my research for a long time, and felt that I needed to see the "outside world" for a bit. So I took up a temporary position at another local university to do some other research. My advisor at that point though was wanting me to complete my degree and asked that I continue my PhD research while being away. I agreed to it out of fear that he may not allow me to leave otherwise.
However in the last 1yr my research progress has not been much. I recently got called to the head of the department's office where I was informed that I had been put on "notice" for this bad performance (he did not use the word "probation"). He also said that I risk being kicked out of the program.
I have been called again to meet the department head and my advisor to figure out what to do next. Judging by the tone of the last meeting though, I expect that some pretty harsh punitive steps are in the offing.
I am not that motivated to complete my PhD. I have passed my PhD proposal and have done some work after that and I think what I have could possibly lead to a PhD, but would still need quite a bit of work. I am OK with discontinuing my PhD rather than face the humiliation of being kicked out.
I was wanting to know what actions (removal from PhD, academic probation or anything else) could come my way and how I could handle it. Who could I approach for help/support at the university or outside? I feel that I am being treated way too harshly, and should be at least allowed a dignified way out of the program (voluntarily dropping out).
On a related note, is it even possible to put a student on notice when they are not at the university?
Addendum 1: I just want to add that I have been in the PhD program for 7 years now (including the gap year), and have completed all the requirements as required by the department except PhD Dissertation Defense. My PhD proposal was cleared way back in in 2012. So I think I was expected to have defended the thesis in 2013 or 2014 at the most.
Addendum 2: While as of today I am not that motivated to finish, but I would like to leave the door open on my PhD if possible. Ideally, I would like to revisit this issue in another year and take a call on it (whether to resume or quit).

Are you funded by this PHD? If yes, they have every right to remove you, since you are not doing the work you are paid to do. Also, if you do not want to finish your PhD, how does it matter if you leave on your own or they "remove" you? Why don't you tell them "I want to leave now, thanks for everything". But it seems you want to stay enrolled while you pursue other endeavors and that is not an option on many programs.

I was funded by a project that my advisor had when I was at the university, but not since. I am concerned that if I were to be expelled, it might show up on my transcripts or that my prospective employers could hold that against me (when running background verification). Leaving the program voluntarily does not seem so bad compared to that. I am concerned that if I tell them that I want to leave they might take some serious action, like perhaps expelling me. The rules are very fuzzy when it comes to such things, and there is just too much power in the hands of the advisor and the department.

They are going to expel you, if you give up from the program? I have never heard such a thing. Why would they do that? It is much more paperwork to prove why you should be expelled, than you voluntarily dropping out.

They can't expel someone that drops out, anymore than you can fire someone that quits. Make sure you file the paperwork correctly and in time.

he may not allow me to leave otherwise — "Allow"?  You were worried that your advisor would kidnap you or something?  Just walk away.

@JZee This question is fine.  If you were a woman taking some time off for family reasons, while leaving the door open to come back, no one would bat an eyelash.  You have made a very sensible decision for yourself -- I wish more PhD candidates could take such good care of themselves.  As for your question, how to protect yourself from further unpleasantness, you need to write a formal letter to the department head so that you have a paper trail.  It needs to be polite, with a calm tone, but it needs to contain the basic information in it (cont.)...

... so that if he continues to be a jerk you can take this higher up in your university.  You need to lay out the facts concisely.  Leave out your motivation, and leave out any personal news about how this past year has been going for you (although I will say I personally am glad to hear you had a good year!).  You need to write a letter that provides enough information that a higher up could read it and understand what's going on, and the letter also should make the reader sympathetic to you....  The most emotion you can use in such a letter is to express surprise that (cont.)

... the department head would ____________ (in this case, you'll want to find a euphemistic way of talking about the harassment he did). ...  If at all possible, try to find some university policy to quote that supports your wish to take a leave of absence (or whatever they call it).

I don't understand the problem: if you don't want to finish, just quit immediately. Then they can't "expel" you. Why delay, anyway, if you really don't want to complete the degree anyway? And what kind of reactions from faculty do you expect if you're not doing the work, and give other visible evidence that you don't want to and don't intend to complete the program? It's one thing to not want to complete, but hard to understand why you'd hang around if that's the case. As it is, you've had plenty of time to resign/quit, so why haven't you? There's no obstacle in your path here, unless you really want to remain in this "limbo" longer, for some reason.

When I left the university, I really just wanted to take a break and do something different. I do enjoy doing research and have had quite a productive year at the university I am currently at. My hope all along has been that I could take a rain check say in another year and decide if I wanted to go back to the PhD. If I did not feel like it I would quit then. Problem though is that I am pretty sure my advisor would not agree to this plan. And on top of that, I got called to the dept head's office out of the blue with no prior indication whatsoever.

Ah, ok, that's not completely unreasonable. However, I'd think you'd need to be very pro-active in communicating all these things to your advisor, co-advisor, dept head, etc. If, perhaps, you've not made your intentions clear, then it is understandable that they'd reach their own conclusions. It is also understandable that an advisor might not want to play a waiting game, so... then what?

There are at least 2 scenarios I want to prepare for a)they remove me from the university straight away b)they ask me to either join in full-time in the next semester and spend the next ~2yrs working on the degree or risk being removed. Obviously neither of these work in my favor and I want to take steps to protect myself. Both of these options seem too harsh, given that there have been other students in the department who have been in the same boat as I, and have remained so for over 5 years now. So why single me out for this special treatment?

It seems like I really should approach somebody at the university but I don't know who. For all I know, they could be my advisor's golf buddies !

@JZee   You really do not want to quit, you do not want to be removed, you do not want to dedicate yourself full time. Usually, the world cannot wait for us while we make up our mind.

At some point you have to fish or cut bait - do you want to finish or not? Most universities have a time limit (documented somewhere) for students who are no longer enrolled to finish up their dissertation. The department has started the process to terminate based on the fact that you haven't finished yet remain un-enrolled. How long do you expect them to wait?

@JZee why do you think your advisor is going to act against you? For all you know, the meeting is to discuss and clarify your options. Big people are not necessarily scary ogres.

Of course, if you have not dropped out of the program then they can put you on notice or kick you out.  You should just tell them how you feel, that you are no longer interested in the program and that you would like to drop out; they should not have a problem with that, though they may not be happy.
It sounds like you agreed to keep working towards your PhD, when you had no intention of doing so.  Have you let them know that you want out of the program? It is hard to say they are treating you too harshly, they may just be trying to motivate you to work on your PhD research, thinking that that is your goal (and that you have a set amount of time to complete the degree), and they have not yet taken any action against you.
Just keep in mind, their goal is to give PhDs to strong potential researchers. It makes them look good. Every year someone who will not finish is enrolled in the program, that is essentially wasting the department's resources. Sounds like you should talk to your co-advisor for advice, and maybe they'll be able to tell you what is happening behind the scenes. But you really need to weigh your two options: double down and finish asap, or leave on your own terms.

I am concerned at the way the whole meeting with the department head went. He was very hostile and aggressive and pinned the whole blame on me for things not going well. It seemed like they had already made a plan, and that this meeting was just to give me an advance notice of things to come so that I could start making other plans. I have a co-advisor also but she is a junior prof and generally on my side, but she is very very afraid to say anything openly since my advisor is a senior professor and has been at the university for over 10 years. So I am pretty much left to my own devices.

I'm reading conflicting information between your original question and comments that you've made.
In your question, you state that you'd rather quit than be expelled and that you're "not motivated" to finish. However, in comments you mention that you wouldn't mind another year on leave and then decide whether to go back.
Maybe that's what you should tell him. Be aware though, that your department chair and advisor are probably thinking that you're going to be 2 years out of date on current research in your area of interest, a significant chunk of your brain is now filled with your current research, and it's going to take even more time for you to switch gears and get truly productive when you come back. Will there be funding for your project in another year? Has your advisor been "holding" funding for your? These are all questions that you should think about.
Can you leverage your existing research to help make progress? Is there an opportunity for collaboration between the two groups to make your leave worthwhile to the department?
Even if all that is no, if you think there is any possibility that you'll return, you should be keeping your proposal up-to-date with information from the latest research, and start filling out a detailed plan on how you would finish your dissertation in the least amount of time.


text:
How long and formal should a paper revision letter to the editor be?
I submitted a paper to a journal, they replied saying that they consider it worthy to be published if I corrected a few minor errors, and I have corrected them so it's ready to be sent back.
Someone told me that you should include a letter to the editor stating this and thanking the reviewer. I've never done this before, so I'm not sure about several factors like formality/length/specifics. For example, do I just say "I've made the requested changes" or do I have to list them more specifically?
Could someone show me a boilerplate letter of this type, or point me to a resource that talks about it?

Aside from the usual pleasantries ("we found the reviewers' comments very helpful and thank them for their time") usually your letter will address each individual comment made by each reviewer for the purpose of satisfying the editor you heeded the advice (or had reasons not to do so). I suppose if it were a very short list of simple corrections it would be sufficient and practical to say you executed them all.

The editor needs this letter because she has to make sure that you have adequately taken the reviews into account. She is not going to read your paper to make sure you did.
Thus, in your letter, you have to address each comment and

explain how you implemented it or
explain your good reasons why you chose not to implement it.

Here is a method for writing a letter that ensures that all reviewer comments are systematically addressed.

Just to add:  you can cut and paste their comments and write what you did after each one.  "We changed this line to read 'blah blah'"


text:
Are Researchers at Private Companies Allowed to Publish Papers?
I'm an academic researcher with a very good publication track record in computer science.
I'm considering the possibility of applying for a research position at a well known telecommunications company with a large research department. But I still would like to have the possibility of publishing theoretical work.
1) Are researchers in private companies usually allowed to publish theoretical work produced in cooperation with researchers outside the company?
2) Are researchers in private companies usually allowed to publish theoretical work produced inside the company?

This is likely off-topic here as it is about a company. But the place to get an answer is from Erickson's HR office. Or you could read the contract if you have one. Just guessing, though, is that you will give up a lot of IP rights to the company, including non-compete and trade secret rules, etc.

For future reference, see the Help Center to see what questions work well here and which are likely to be closed: https://academia.stackexchange.com/help.  Anyway. Welcome to Academia.

Actually the issue is the same. There is another site here that is better suited to such questions: https://workplace.stackexchange.com/ and possibly others.

As a researcher in industry, I strongly believe that this question is on topic and appropriate.

Do you mean, are they permitted to by the academy or by their employers?

As someone who has worked for the research arm of a multi-national company, publishing is definitely a possibility.  However, it is not a priority.  Patents are much more valuable.  Consequently, any paper/idea must first be vetted by a committee and lawyers.  If it is valuable to the company, then a patent must be filed first before any paper can be submitted to a conference/journal -- this process can take a while and can be frustrating if one is aiming for a conference deadline.   This is even worst if the paper has a student author, meaning the patent process could delay any publications.

Continuing on my previous comment, if an idea becomes a trade secret and it involves a student, then the said student might not be able to graduate.  Note, a company may have collaboration with a university or you might continue to collaborate with your current university, and hence, students may be involved in your research.  In this situation, great care must be taken.

Speaking as a researcher at a private for-profit company, who also publishes frequently, it all depends on the nature of the business model and the position.
Most people at companies do not publish, either because the company has no interest in publishing or because their particular job doesn't involve much of scientific interest. For companies that are involved in cutting edge work, however, scientific publishing can gain credibility and visibility for the organization just like it does for people at universities. This is the case for the company I work for, particularly given that many of our projects are federally funded research where the government is paying us in part to disseminate knowledge.
Nor is there any necessary conflict between protecting intellectual property and publishing. The three main strategies for protecting IP are copyright, patent, and trade secret. Of those, only trade secret is incompatible with publishing, and it is generally the most fragile and least used in any case.
The biggest obstacle to publishing in private industry is simply priority and time. Writing a manuscript is a lot of work, and if management doesn't see much benefit, they will likely want you to use those hours for things more directly connected to the bottom line. You might be able to publish out of hours, but that can be a more complex negotiation.
Bottom line: it really depends on the particular circumstances. The best way to know if you will be able to publish is to look at whether others in the group you are joining publish. If so, you probably can. If not, there are likely major obstacles, whether formal or merely pragmatic.

Unfortunately this answer fails to make an essential point. Most companies take control of the decision to publish for their employees. There is a gate between you and publishing, even for work not done on company time. The fact that the gate will be opened for you in most cases doesn't change the fact of the gate, nor the fact that its default position is closed. You give up your freedom to decide what to publish and yield it to your employer. You can decide whether that is good or bad, but you can't make it not a fact by wishing it weren't true nor by finessing the outcome.

@Buffy I don't dispute your statement---it's just that in my experience as a private researcher, it is pragmatically rarely relevant.  If you are in a publications-friendly position, then the system will be tractable and generally pose much less of an obstacle than peer-review or collaborators.  If not, then the formal permissions process is probably much less of a barrier than "Why did you spend 80 hours on this crap when you could have been doing your job?"

It is not possible to answer your question unless you specify the company name. Many companies are very active in research, and many companies are not. As you are not an employee yet, you cannot ask the HR, but you can search.
For example, if you search for "deep learning" in ACM, and click on institutions on the left menu, you can see there is Microsoft, IBM and Google there. ACM also keeps company profiles, so you know what topic they are interested in, for example this is profile of Google.
Someone (from Amazon) just told me that Amazon had nearly turned FLoC into a private Amazon event. The conferences at FloC are highly theoretical, and among the most prestigious in logic.
But actually, you don't need to ask this question, as in the companies that are active in research, the directors/principal engineers etc are often former professors, and we followers immediately know where big shots move :-)

Update: thanks @Anyon for pointing out that the company name was editted out. Yes, that company does publish, see its profile in ACM.

Psst. If you check the edit history of the OP you'll find the company name. It was likely edited out so that the question wouldn't depend too much on personal factors.

In general terms, if the publication is, in any way, related to the company's business it will probably be contractually forbidden unless specific permission is given for the paper.
Signing on with a company that depends on IP usually means that anything you produce is theirs, not yours. Read the contract to be sure. Some contracts try to bind you forever, even when you leave the company. The legality of these can be challenged and they may be illegal in some places.
However, if your other work is completely unrelated, then it is probably ok, but it needs to be "released" by whoever is responsible for IP control at the company.
On rare occasions (THE WOZ at HP, for example), a company will give permission to do something that would otherwise be prohibited, but normally because they lack sufficient insight to see the consequences. If they are happy enough to make an exception, make sure you have it in writing - signed and maybe notarized.

But it really depends on the company. Google, for instance, publishes a lot in the Machine Learning field.

@Adrian, I assume you mean Google employees. But I'd be willing to bet that each one has a release for each such paper and that the contracts give the company the power to deny publication.

I assume that too, I just meant that some companies allow their employees to publish (some) of their work.

@Adrian, I think many do, actually. I know  a lot of IBM employees that publish (with permission). But it is the company that gets to decide usually, not the researcher. I'll also note that even some universities have restrictive contracts - especially for patents.

My employer (not Google or IBM) can certainly deny publication if it is inappropriate for the needs of the business, but on the other hand it has a formal procedure in place to approve papers for external publication, conference presentations, etc, and there is a steady stream of papers (of the order of 10 to 100 per year) that are approved for publication.

Buffy - That first line is pretty overdone, I think. While GE Labs, Bell Labs, and IBM Research are perhaps not as prominent as they used to be in technical fields, one can still find many papers from companies in different venues. And, those papers deal directly with the company business. For example, in the semiconductor industry (chip manufacturers and equipment manufacturers), such papers are critical to their ability to show the world what they can do. Few if any in Phys. Rev., but IEEE conference proceedings for sure.

@JonCuster, I made a small edit. But I'll wager that all of those papers have a release from the company. And all of those companies have a specific contractual clause requiring release. They would be foolish not to. In particular, an "open" policy here could get in the way of patent filings. Don't lose track of the main message here. When you work for a company it is highly likely that they own all your IP, whether produced on company time or not, and many try to own it in perpetuity.

Oh - absolutely. But if that is your line, you need to consider all the US government labs as well - they all have processes to allow release of information including publications. Scientists are allowed to publish, they just need to follow the rules.

The US government is a bit different. Most of what is produced there is considered public domain as it is produced with the public's money. I don't know all the rules, but that is the general underlying theory. The government cannot patent anything, for example. Some agencies (EPA, Interior,...)  have recently tried to suppress some research but courts seem skeptical about that.

@JonCuster. See the above comment. There are national security exceptions to openness, of course. If someone on the Manhattan project had published, for example, they'd have been shot.

It isn't national security per se - yes making sure it is not classified is part of it, making sure it isn't patentable is part of it, but formal internal review and quality control is also part of it. And, generally, that has been true at every non-university place I've worked or interacted with. It is a hurdle, yet my groups over the years have managed to publish many many papers (and I've got the auto-generated emails from the review process to prove it!).

@Buffy You're still much overemphasizing a distinction that is in practice often quite minimal in impact. Many university academics also accept similar pre-publication review processes through collaborations and consortia.

@JonCuster To build on what you've said: a nice example of this is NIST. Assured quality in results is a critical part of their mission, so every publication goes through a rather strict internal technical review before submission is allowed.

@jakebeal, the question was about companies, originally a specific company. So, I just addressed that. One of my comments above addresses the university question. I hope none of the comments here are trying to imply that publishing without permission if you are in a company is just fine and go ahead. That would be a serious error. Like I said, check the contract. Ask if necessary.


text:
How to cite oneself as co-author without all names, for resume or presentation?
My questions regards the format of citation.
For the context: I am a student, presenting my work (with slides) and referring to the publications in which I am co-author (never in the first three authors).
It would be nice for my name to explicitely appear, as I also refer to other publications in which I did not take part.However I do not want to list all the authors (more than 10 for some papers).
Should I use (recommendeed by my advisor):

A.Smith, M.Myself et al. "Marvelous publication"

Or

A.Smith et al. (including M.Myself), "Marvelous publication"

My concern is not to appear as being the second author, which would feel like a lie, while keeping a compact formatting.
Is there a common way of doing this ?
Thank you.

Including your academic field might be helpful.

I have often seen "A. Smith, ..., M. Myself, et al. 2018, Nature"

I hope you presented this choice to your advisor and your reasons for not preferring option A. If he/she still thinks it is advisable for your field it probably is, unless your advisor is relatively inexperienced.

For a presentation I would use @Jan Kukacka's answer. Say in the presentation "This work was published in our 2015 paper".
For a resume you've four options as I see it:

List all the authors (put yourself in bold).
List the first x authors (where 10 is a common value of x) then put et al (several journals/funding bodies use this format). Choose x so your name always appears
List all the authors up to and including your name, and then put et al.
List just the first author. As the papers will probably appear in a publications section on your resume, its fairly clear that you are going to be an author.

Which ever you choose, it might be worth including a very short sentence that described your role in the work.

I was recently facing the same struggle. For the purpose of a resume, I decided to write the full list of authors.
A presentation is a bit different matter: it does not give you so much space for text, but you can say a lot more. In this case, I would refer to the papers on the slides the usual way:

First Author et al., 2015: Marvelous publication,

potentially mentioning in the spoken narrative that you are one of the co-authors (since your question gives a hint that this is a part of the message you want to deliver), and possibly including a slide with the full reference list to the end of the presentation (which you won't use during the actual talk but is handy for anyone looking at the slides later).

Yeah in a presentation you can say "... this was published in our 2015 pulblication "A treatise on why the fourth author is wonderful".

Another option is to omit the authors between the first author and your position:

First Author, [...], Your Name, et al., 2015: Marvelous publication`

But I would only recommend this in scenarios where it is important to highlight your participation to these publications, e.g. reports for your PhD progress or similar.

I just put 'co-author' of.  Sometimes people care about which co-author, such as "Second co-author' of.  This is for a non-academic job, and when the employer just wants to know you published.  However, if they actually would probably care about the published work, cite it as a reference, just like the answers above.

I sticked to the Smith et al. scheme but used a different text color for papers I co-authored together with an explanatory sentence at the beginning.


text:
When to refer to a paper as "seminal"
I am writing a paper that relies heavily upon some important work done some 10  years ago. The paper was well received gathering well over a 100 citations and is a must mention within my niche field. I would like to reference the paper as seminal as in "so and so, et. al., in a seminal paper..." but am not sure that would be appropriate. I recognize 100 citations isn't a lot in the scheme of things but at the same time this paper was very important within my niche field.
Under what circumstances can one decide a paper is seminal? Must the person citing it be well renowned? Must the author of the considered paper be well renowned? Is there a citation # that should be exceeded (I really don't like that one, it seems too inflexible)?
Neither I nor my professor are especially well established in the field we are publishing in (this will be my first publication and my professor mainly publishes in another field). Are we qualified to refer to a publication in this field as "seminal"?

Maybe the answer is different if your field is urology...?

"100 citations isn't a lot in the scheme of things" — depends on the field, the topic, and the age of the paper.

Why would you like to reference the paper as seminal?

I would understand "seminal" to indicate that  (a) the paper was the the first in some sense, and (b) that it led to a lot of subsequent research. For example, a paper proposes and tests a theoretical idea, and then lots of other people come along and test that idea building on the original study.
It doesn't matter that you are not established in a field. Anyone can use the word "seminal". It's just that using it correctly requires a good understanding of your field and the interconnections of research papers.
Having a lot of citations is necessary but not sufficient to show that a paper has led to subsequent research. Some citations don't mean much on its own.

From the Merriam Webster dictionary:

[2] containing or contributing the seeds of later development :  creative, original

More specifically, I would call an article seminal if it was the start of a new field/trend/idea, the work that inspired everything that came after, a starting point.
Therefore, if that article fulfills this criterion, you can say that, regardless of how many citations it has, or who are the authors. For instance, recent seminal work will not have a lot of citations :)

Well, if it really doesn't have many citations yet, it's too early to be called seminal.

The first article in a specific field, would be, by definition, seminal. If the field is worthless and nobody would do anything on it, it would still be seminal....

I was just saying that, by the definition you quote, something is not seminal unless things issue forth from it (which should be interpreted in a non-vacuous sense).

Upvoting for getting to the definition of the word; but as others comment, if this paper sows the seeds of a new field, the citations will bear this out. The quality, not quantity, of citations should support this. Did the paper indeed "start a new thing?". If that "thing" is a way to translate 5000 year old Sumerian clay tablets using a Machine Learning approach, it may only have 15 citations (from you and the one other guy in the world that does Sumerian clay tablets) and yet be absolutely seminal.

@Kimball yes indeed. But the "dimension" of what comes next is somewhat undefined, as Floris brilliantly put.

The question is: why should you mention seminal paper altogether?
I would refrain from giving an adjective to the paper.
Firstly, because "seminal" is subjective. Secondly, because it does really add anything relevant. Thirdly, because it may piss off other people that don't find the paper seminal.
There are better ways of recognising the paper's "seminality", e.g. publishing in the field and giving the due credit to the paper.
In any case, the only occasion I would write "seminal" is if I am pretty sure the work is seminal, which does not seem the case here.

Indeed. For that matter, unless the declarer of seminality is themself a big-shot expert, people may think that the declaration itself is pompous and inappropriate. Until one is an authority, perhaps more than a "mere expert", it might be hasty to declare something "seminal".

I have learned one thing how to identify a seminal work is using Google Scholar search engine result showing that the article is cited by another author(s) to support the insights or theories of study. For example, Halperin (2017) uses the social theory within the study employing the structuration theory of Giddens (1984).
References:
Halperin, R. (2017). Learning practice and technology: Extending the structurational practice lens to educational technology research. Learning, Media and Technology, 42(3), 279-294. doi:10.1080/17439884.2016.1182925
Giddens, A. (1984). The constitution of society: Outline of the theory of structuration.

Never, because it will make many of your readers think about semen and wonder whether you're sexist.  Pick a word that doesn't have as much baggage and which also more specific to whatever you mean.  For example you could say it was influential, foundational, or fundamental.
Note that all the above is true even if seminal doesn't have that connotation to you, and even if you think that it's not sexist language.  These are points where reasonable people can and do disagree.  But either way you're going to distract some nontrivial number of your readers from the actual point you're trying to make, and that's not effective writing.
Update:  I just want to point out that this is not a new issue that I made up.  Here's the British Sociological Association including it among a dozen or so words it recommends sociologists avoid (most of the others are chairman and the like).  Here are some other people complaining about this usage of seminal.  I've certainly heard people at the Joint Meetings grumble about the unfortunately named "Steele prize for seminal contributions to research."  Anyway, as I said I don't think this is as clear a case of sexist language as say chairman, but it is a usage that many people don't like and which has few advantages.  It's easier just not to use it.

For anyone who doesn't think seminal has that connotation, I point to the very first comment, which has more upvotes than any of the answers.

I don't think using the word "seminal" will make many people (if any) seriously wonder whether the author is sexist, but it will be distracting or annoying to some people, which is not the desired effect.

I agree with this answer but I think it should be added that the word implies only men can do it.

@AnonymousMathematician it is not the author who is sexist, it is the word itself.

Does this mean I should also avoid the term "seminar"?

I respectfully disagree. There's nothing inherently sexist about seeds, germination, growth, or semen for that matter. While there is certainly a place for courtesy and eschewing controversy to promote discourse, I think the argument that "someone somewhere might be sensitive" because the word shares a root with words that seem "male", is really a stretch.

@NoahSnyder: For what it's worth, my comment was really just a sophomoric joke.  I think educated readers will be sufficiently familiar with both senses of the word "seminal" that it will be clear which sense was intended, and they likely won't even think about the other meaning unless, as in my comment, someone points out the humorous potential.  When urologists write about "seminal vesicles", do their readers get confused into thinking they are referring to organs which are influential or foundational?  I doubt it.

To stretch an analogy, it's like saying that mathematicians should stop using the term "Wiener process" because it sounds naughty.  People giggle the first time they hear it, but then they get used to it.  It's not a reason to stop using it.

this comment could be improved by removing the whole sexist thing and instead suggesting the use of a word that will be understood by more people, e.g. foundational. This would also remove the need to be certain that it was the single first paper. However, I think Fábio Dias sufficiently answered the question.

I was actually kind of surprised to read this answer.  As a side note: this morning I uploaded a paper to the arxiv.  Just before I did so, I replaced an instance of "seminal" with "pioneering." I'm not tryin' to be sexist...

As I understand it, the issue here isn't just that "seminal" sounds like a sexual word, but rather that even its non-sexual use is tied up with the baggage of stereotypes of male virility.  The counterargument that this was not the original etymology is what makes this a case where reasonable people can disagree.  But I don't think it's an open-shut case either way, as it's hard for a word to have two related meanings for hundreds of years without people to some extent associating the one meaning with the other.

I can only say that once reviewer put objections on the paper of my senior colleague because he used the term F-ART because he thought it looks similar to fart.

authors: كورة اونلاين


text:
How to explain in PhD interview about leaving current PhD due to lack of funding?
I am invited to interview for a PhD position.  I am very afraid about the questions which will be asked. However I have a big fear, and it is that I am currently PhD student, started 1.5 year ago. I was the only PhD student in the group who was not paid, so I needed to work extra for an international research project to finance myself. Some months ago I again spoke with my supervisor and he told me he has no budget and I am free to leave the group whenever I like!
Due to all this, I decided to change my group. Now I am invited to interview for a competitive PhD position ( in another university but the same city). I would like to get this fully paid position which also fits well to my experiences, however I do not know how to tell the new professor about my current PhD?
I did not mention my current PhD in CV, and just wrote about my working experience in the last 1.5 year.
How shall I explain this issue to new professor?  Can this issue be a reason that he does not accept me?

I think leaving your current PhD out of your CV is probably a bigger problem  than being currently enrolled in a PhD. Why did you do that?

@ff524: I have not recieved my PhD degree yet, and I donot want to finish this current PhD. I think when you donot have degree and you donot want to finish it, it is like you donot have it.

Leaving it out of your CV makes it seem like you are trying to hide it, which looks bad. Typically if you are enrolled in a degree program, you list it on your CV as a degree in progress.

You don't have the degree. You were registered as a graduate student for 1.5 years, and that should be on your CV. If you had listed it, there would be no problem at all: "Unfortunately, my current program was unable to fund me. I would prefer to give my full attention to my PhD studies and research, without the need for an outside job."

@ Patricia I didnot mention that. I just wrote about what I finished. I was actually thinking not to mention it also in my Interview, however I decided that is better to tell it. How shall I do that?

@user42190 Just be honest and explain your situation, but spin it positively. Tell them due to the work commitment you were not able to focus much on the PhD, but nevertheless you learn some thing from it. With the new PhD with funding available, tell them you will be able to concentrate 100% on the work which you enjoy.

@PatriciaShanahan Can you please turn this comment into an answer so that I can vote for it?

You don't have the degree, but you were registered as a graduate student for 1.5 years, and that should be on your CV. If you had listed it, there would be no problem at all: "Unfortunately, my current program was unable to fund me. I would prefer to give my full attention to my PhD studies and research, without the need for an outside job."