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Feeling regret for sending my code to my classmate
As an international student, I found hard to integrate well with other classmates. I only have two relatively close friends in my class. When my classmate asked me to send my code to him, I did not reject him as I was afraid of losing this friend. Now, I feel extremely regret as I am facing an accusation of plagiarism. I will never allow others to access my work. I actually have evidence that all works are done by me.
However, I worked extremely hard on my assignment and amended it four times before submission. I do not think that I deserve mark reduction. Are there any things that I can do to change the professor's mind instead of mark reduction? I hope I can do any other things to compensate for my fault instead of mark reduction.

What have you done already to discuss your case with your instructor? What level course is this (freshman ... senior)? Were you told at the start that all work was to be done individually? The approach you can take depends on the answers to some of these questions.

Actually, I handed in two assignments. I allowed my friend to access my codes for these two assignments. The first assignment was flagged for plagiarism. My professor sent me a warning email a few weeks after the submission of the first assignment. He mentioned that that email is the final warning and I will be accused of plagiarism if flagged again.  However, I already submitted my second assignment when I received that email. I have no chance to change the content of my assignment.

Regarding your questions, I talked with my professor and he said he is pending for plagiarism report. I disclosed everything to my professor at that time. I cannot make any decision at this moment. I am a freshman. I was told at the first lecture to do all works individually. However, after checking the slides of the first lecture, the professor did not explain very detailedly about plagiarism. My friend asked me for my code at the middle of the semester. Professor's wording did not come up from my mind at that moment.

You may plead your case to your instructor in writing as you have here. Your best option is to demonstrate that you did not get the warning of the first offense until AFTER you had already committed the second offense.
Agree that what you did was wrong. Admit that you did the wrong out of partial ignorance (you knew a rule existed but did not understand its implications fully). Demonstrate that you were given a warning of the first violation only after the second violation had already occurred. Show that you immediately stopped the unlawful action at the warning. Ask that your total penalty be reduced (but not removed) in accord with a plea of doing the wrong from partial ignorance rather than willful intent. See some of these legal readings for insight.
https://www.lawyers.com/legal-info/research/ignorance-of-the-law-may-be-an-excuse.html
https://en.wikipedia.org/wiki/Ignorantia_juris_non_excusat
http://www.duhaime.org/LegalDictionary/I/IgnoranceoftheLaw.aspx
This is not necessarily a criminal case, it is more a civil one. Also, this is not necessarily one where the full implications of the rule were made clear enough at the outset.
On this latter note, since you have read the code now, you absolutely cannot plead ignorance that a code even existed. You can only plead ignorance of the full implications of the code. You should keep your personal story of a need for friendship out of the discussion. You gave the other person the code with the intent to offer insight, not to offer an answer key. You ignored the fact that your action could be easily abused (by a "cheater") and you were ignorant of the fact that such abuse by a cheater had real consequences not only for the cheater but also for you.
Having had cases such as yours multiple times in my career, I am well tuned to the distinction between intent and ignorance. Your instructor may be as well, and he/she may be willing to provide grace with sufficient grounds that remorse is sincere. On the other hand, I am also just as well tuned to spot someone who wants to play games when pleading for reduced penalties. Do not go down that path, lest your instructor is equally well tuned.
Finally, chalk this one up to experience. Some students take a lot longer to have this type of situation hit them. By that time, they often more than deserve the strong penalty that follows. You can now move to the next level of your life with greater confidence that such will not be the case in your future.

Thank you very much for your detailed reply. Now I understand the meaning of ignorance and intent. I have learned a lesson, not just about plagiarism, but also about some legal knowledge.

You are entirely at your professor's mercy or lack thereof.
As a student, you are responsible for knowing the regulations of the course and the school. This includes plagiarism and academic misconduct charges. You were told to do all work individually. On multiple occasions you violated that principle and knowingly did so because you did not want to lose a friendship. You intentionally made a choice and now you must face the consequences for making that selection which fell afoul of regulations.
The fact that you did all the work individually does not clear you of misconduct because you intentionally aided someone else in violating the academic misconduct regulations. If your friend had stolen your work without your knowledge, that would be an entirely different issue. However, you willingly participated in the process, which makes you just as much of a "cheater" as your "friend."
So, you may try to argue about your lack of culpability but your instructor is within rights to pursue academic misconduct charges against you. Any offer of a "reduced" sanction or punishment is entirely at your instructor's discretion.

Thank you very much for your reply. I understand that I am guilty of violating the regulations. But I do not think that my intention of violating the rules is as strong as that of cheaters. I did not initiate the whole process. I also told my friend not to copy, just get some ideas and solve the problems himself (although I cannot provide written evidence for this to the professor, I did say this). If I am a real cheater, I do not deserve any marks as the marks should reflect the effort I put. For my case, I think I can have other ways to compensate for my fault.

I was totally screwed up and feeling guilty for the whole week. I think it is also a punishment for me.

Under many academic misconduct codes, there is little distinction, if any, made between the initiator of misconduct and other participants. If a random student asked you to help the student cheat on an exam and you agree to help, you are still guilty of misconduct. You might argue the level of misconduct, but you have conducted misconduct. Helping a cheater is still considered misconduct.

Thank you very much for your reply. I agree that I conducted an academic misconduct, and I think that I should have a lower level of misconduct. I just want to find whether there is anything I can do to compensate for my fault instead of mark deduction, as the academic misconduct code of my uni includes remediation as one of the sanction. (I read through the code thoroughly after the case happened)

@wintershelter Misconduct has no "lower level". It is or it is not. We have a saying ... Ignorance of the law is no excuse. However, see my note below.

I'd note that the professor did provide "mercy" here, in starting with a warning. "Mark reduction" is more mercy still, as it is probably within the professor's power to fail the student.

@wintershelter Please note ASimpleAlgorithm's comment here, I think it is very very important to realize that a mark reduction is already a lesser punishment than what is possible, especially after a warning was given. In any approach you take to try to lessen your punishment more, it is very important to realize the  leniency you have already been granted, otherwise you may come across as unappreciative of the severity of the offense which will make it harder to grant you any further leniency.

@A Simple Algorithm @Bryan KrauseThank you for your reply. I understand that I was wrong. I will admit the things I did and wait for the decision of my professor.


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How appreciated is "Part III" in the US?
I will complete an MSc in physics, including a thesis, this year.
I have received an offer for a 9 month taught math master's course at Cambridge called Part III, although I don't yet have a funding offer for it, sadly. Some funding sources are available but it is competitive.
My main reason to take this course (beyond the degree itself) is to improve my chances of being accepted to a PhD in physics at Oxford or Cambridge.
Yet I also wonder how much this course is appreciated in the US and if having done it will improve my chances of being accepted for a PhD in top graduate physics schools there were I to apply there as well.
For my doctoral programme, I aim to research topics such GR, QFT, string theory, quantum gravity.

http://math.stackexchange.com/questions/488360/mathematical-tripos-part-iii-at-cambridge-university

Note that Cambridge likes a lot to have their own naming and idiosyncrasies, but Part III is just a MSc in Mathematics.

@AnderBiguri It's an MMath for students who completed their undergrad at Cambridge, and a MASt for students who didn't. Cambridge doesn't award an MSc in Mathematics, and even the undergraduate course is a BA rather than a BSc.

@kaya3 I know, I work there :) But Cambridge idiosyncrasies aside, its not materially different to an MSc in mathematics, that was my point. If you go to a different university and you get a BSc in Maths and then a MSc in Maths, you have an equivalent degree. Particularly to apply to a PhD. Of course, the name of the uni matters, I guess, and given how hard Part III is, im sure it helps. Also the difference between a BA and a BSc in mathematics is none, its an undergrad in maths. Particularly, again, when talking about PhD applications.

Part III of the Tripos is reasonably well known amongst professional mathematicians. I can't comment on physics. Good marks would surely boost your competitiveness for PhD slots in math.
Having taken one of Oxford's similarly pitched courses 8 years ago or so, here's a broadly applicable set of logistical anecdotes related to subsequent US PhD applications. They all flow downstream from the fact that Part III starts in October and US PhD applications are often due in December.

You will have to prepare and send off PhD applications alongside some of the hardest segments of the Masters course.
By the time PhD applications are due, you will have no marks from Part III nor will you have new recommendation letters because there is not enough time. The course is correspondingly unlikely to boost your PhD applications very much in the immediate term.

Thank you, can I also ask if you know whether part III or Oxford mathematical physics MSc will be more appreciated by universities? I tend to think that part III from information available online, but I would be happy to hear from someone who studied there

@ziv This site has a general rule not to rank programs etc., born out of reasoning that the Q&A format doesn't really handle this well. If you're an undergrad now, why not talk to a professor in your current program about these questions instead? On this particular point: I am a mathematician and took a math course at Ox, so I'm especially unable to guess what the physicists are looking for.

I think Part III is quite common amongst US students nowadays, and is thus well-known to graduate admissions committees.  Probably the effect on your application will be good, since if nothing else it shows you are serious about studying mathematics; a school can also reasonably expect you to be considerably better prepared coming after a year at Part III than when you finished your BA.  So if one of your issues was a weak curriculum as a BA student (as opposed to poor grades or weak letters), then Part III could help quite a bit.  On the other hand, I wouldn't count on a dramatic change in your graduate school admissions, in part because as you note, you won't have your grades or a strong recommendation from Part III in hand when you apply for graduate schools the next time around. I wouldn't worry about the fact that Part III is not research based; obviously doing research before starting graduate school is great, but most graduate schools in the US are not really expecting you to have done much in the way of it beforehand, or to be even close to ready to start when you enter.
I think if money is no object, then Part III is probably as good as anything else you might do for having a strong graduate application in the coming cycle.  EDIT: I should probably also say that a matter of substance (as opposed to application strategy), Part III is probably on average better than spending a year as a grad student at a random respectable grad program in the US, since it will bring you into contact with a wide variety of other students and ideas.
However, I think you should weigh that next to the possibility of starting graduate school at one of your lower preferences, and then trying to transfer after a year, or when you get a master's degree.  There's no guarantee this will work, but the same can be said of Part III.  If you've been offered funded admission at a respectable school in the US, and would have to pay your own way at Part III, I would look hard at whether you think it's worth the money.
EDIT: I wouldn't count on the "glamour" of Cambridge itself to have a strong effect.  I honestly don't know how selective Part III is (maybe someone who knows can comment.), so I wouldn't rely on assuming that admissions committees will consider it as such.  There's some psychological "band-wagon" effect where getting one prestigious position reinforces getting others, but it won't work if the substance isn't there. Getting a BA from Harvard or MIT is helpful for getting into graduate school (if you have a strong record) because an admissions committee is more confident that getting an A in math class at Harvard really means something, and that a professor at Harvard has a lot of experience with talented undergraduates and thus can speak with some certainty about what it takes to succeed in graduate school.  So, if you went to Part III, got good scores on your exams and got a strong recommendation from a professor there, that could strengthen your application a lot as a "second opinion" reinforcing the recommendations and grades you have from your BA.  However, as discussed, those would only be available for the fall 2016 admission cycle, not 2015.  One possibility is to see about accepting one of your safety schools with a deferment to go to Cambridge, going to Part II in 2014-5, going to the safety school in 2015 and applying for transfer in 2016 or 2017 if you're unhappy there.
One piece of information we're lacking is what your "lower preferences" are (don't put too much stock in USNW rankings, but they help to be concrete in a discussion like this).  It makes a big difference whether we're talking about a school in the rank ~25 (like UCSD), ~50 (like UVA) or ~100 (for example, South Carolina).  In the former case, I'd say it's a waste of time to try to try to move up unless you go and are miserable, whereas in the latter it makes a certain kind of sense.
LATER EDIT: Incidentally, yes, given that your undergraduate grades are already "baked in," the main things you can still hope to change are your letters, and also your GRE scores if those were bad.

From your answer, I suppose then the more important thing for me is to secure a stronger letter in the next 6 months. I will have to weigh the financial options. One last question: You say a potential benefit of taking the course is that it shows I'm serious about studying mathematics. I was wondering, does it also impress admissions people in any way? For example, if the first thing one sees is that the applicant is from Harvard, you might think there is a decent chance the applicant is a strong student. Does Part III have a similar effect? Thank you for your answer Ben.

@Craig I added more about your question to my answer.

"I honestly don't know how selective Part III is" -- it's fairly selective: https://www.dpmms.cam.ac.uk/~twk/PartIII.pdf, "... normally require First Class Honours from students coming from other British universities ... you should be able to profit from
Part III if you are in the top 10% of mathematicians graduating in your country". I guess the questioner's previous unfavourable PhD responses already had the same information that Cambridge used to accept him for Part III. If they rejected due to lack of Master's-level study, then Part III is exactly that by international standards.

@SteveJessop I actually read that earlier.  I don't read "you should be able to profit from Part III if..." as the same as "we will only admit you to Part III if..." as synonymous.  Of course, I'm sure it isn't all that easy to get into Part III, but I wouldn't take it as a sign that somebody has a really strong file, like I would someone getting into, say, Harvard.  That was also meant to suggest that other people may not know how to interpret it and thus won't put a lot of weight on it.

@BenWebster: fair enough, it's all about how people interpret it after all, not how selective the course really is. But given what I know of Cambridge and the language of UK universities, I would not expect a course to admit someone if, in the opinion of the admissions people, they don't meet the criteria to benefit from it. Strictly speaking those criteria are stated as sufficient but not necessary anyway, so it's ambiguous however you cut it :-) "Normally require First Class honours" is an indicator, but of course you can prove that to the PhD program with or without Cambridge's say-so.

Also I don't know this, but based on how the MMath course I did at Oxford works, I suspect that if you get into the Cambridge undergraduate course, and do reasonably well on it (on course for a first), and want to take Part III, then you'll get a place. That is just a guess though, I don't know for sure that they don't apply a serious selection procedure to their own undergrads. So you might well consider that an indicator that although it's fairly selective (this is maths at Cambridge after all), it's not hyper-selective.

... the reason I guess this is because top UK universities are keen for students to take the MMath, and this is the form Cambridge offers it in. Getting off topic but the reason they're keen is the state of maths education to 18: for example some students now arrive at university without any abstract algebra. So the pace of bachelor's degrees has slackened. The MMath is, in response, a "proper maths degree". Cambridge may be different but usually it doesn't imply genius, just that you can do something non-trivial with homotopy groups (or whatever subjects you pursue in the 4th year).

My best offer was at a school that usually ranks between 10th and 20th. Could you elaborate on why it is a waste of time to try to get into a better school (5th-10th in USNews say) in that situation? Is it because it is very unlikely for some reason, or because the improvement would be overall negligible in the long term?

Briefly: while I'm sure it is better on average to go to top 10ish school than one in the 10-20 range, I don't think the difference is large enough to justify the effort, when the chance of successfully "trading up" is low.  There just aren't very many seats in top ten programs (on the order of 200 per year) and you're competing against the whole world.  The benefit is also uncertain: not having attended any of these schools, you have no idea what's going to work personally for you.

If you've gotten a funded offer at a school which is generally regarded as top 20, unless you have some very specific reason not to go, try it out for a year.  You won't have to pay, the education should be a similar quality to Cambridge, and you might find you really like it.  If not, you can always get a masters and try to get in somewhere else, though I think if you want to get in somewhere top 10, you've got to really knock their socks off.

I am just finishing Part III after doing an MSc in my home country and my focus has been on the topics in theoretical physics that you listed. As others have pointed out, by the time applications are due, you will have no grades from the course since all assessment is at the end of the year. Therefore you are essentially trading on the reputation of the university alone. In the UK and Europe, Part III is held in high regard and so you will be at the top of the pack for PhD applications here but note that there are ~70 theoretical physics students in Part III so you'll be competing with them for the best places. Of those 70 students, ~10 get offers for PhDs in DAMTP HEP/GR and probably less for Oxford math HEP/GR (since you compete with more people outside Part III).
Having spoken to people in Part III who have applied for US PhD programmes, Part III will definitely help your chances, but there is still a large bias towards those who did their undergraduate at a reputable US institution. The only students I know who were accepted by a US programme had come from good US schools previously. This is only what I have observed from a small sample size and many in Part III just don't want to go to the US.
For what it's worth, I got everything I wanted out of Part III. It has been great training for a PhD in quantum gravity, the courses were awesome and I could trade on the reputation of the university to get the PhD position that I wanted. At the same time, I've found it really stressful. You begin the year worrying about PhD applications, then you work through the first holiday to prepare for the Cambridge PhD early offers test (HEP and GR only), then the rest of the year is spent worrying about getting the grades necessary to keep your PhD offer if you were lucky enough to get one.
Despite all that, doing Part III will most likely have a great impact on your career in theoretical physics or outside of physics and it really comes down to whether you can stomach the cost and a year of uncertainty.

Thank you very much for the useful information. Can I ask what skills you need to excel in the HEP/GR PhD exams? Do they check your overall understanding in physics and mathematics? Or do they specifically examine your skills in GR/QFT, relying on the fact that many students already have some background in these subjects? Is there a place where I can find more information on this exams?

Also, do you know how many of this ~10 successful PhD candidates get funding for the PhD?

I haven't seen any information on the early offers test online. It's entirely based on coursework in Michaelmas term. There is a question for each of the big theoretical physics courses (GR, QFT, Symmetries particles and fields, cosmology) and you answer 2 or 3 questions in 3 hours. Best way to start preparing would be to start looking at the course material. e.g. the QFT course is almost always based on David Tong's lecture notes which are publicly available.

I think funding is not a big problem for those who get offers in DAMTP HEP/GR but it can be a struggle for international students applying to other UK institutions.

I see... And are the exams done with open materials?

No, all exams in Part III are closed book exams. They tend to be very heavy on book work. It's the tradition of the tripos apparently.

Let us continue this discussion in chat.

When I took Part III exams (in 2010), the exams I took were all closed book, but exams for some of the other Part III courses which my classmates took were open book. I think an astrophysics or cosmology course was one example. I don't know how this is in 2024, but there is no long-standing strict rule preventing professors from setting open book exams.

As a physicist who has moved between the US and UK, and thus has experience with both systems, my advice is that part III (or the equivalent at Oxford) it not really a good idea if your main goal is to go to the US for a PhD.
First, there are the logistical issues, as user176372 mentioned in their answer.
Secondly (and most importantly), it may not help much, even if somehow you are able to use your part III results for your application to US PhD programs. The US and the UK actually have very different "cultures" when it comes to PhD admissions.  The US is very research-focused: what matters most are projects that you've done, letters of recommendation from professors that you've worked with, and any publications you already have.  The UK, on the other hand, is very coursework and exam-focused, probably a legacy of the tripos at Cambridge and the surrounding culture.
For example, performing very well (i.e. ranking top ~5 or so in your cohort) in Part III (or the equivalent at Oxford), will almost guarantee  you a PhD position anywhere in the UK; but performing extremely well on courses/exams will not be a huge boost to a US PhD application, unless you have research experience to support it.  In fact, doing a Part III (or the Oxford version) might be a net negative in terms of going to the US afterwards, since you will have to spend a whole year on classes with no time for projects or research.
Third, it could be a waste of time. Most US PhD programs have a required coursework component that cannot be (completely) skipped, even if you already have taken similar courses or already hold a Masters degree. Since you already have an MSc, if you do Part III + US PhD, you will end up basically doing three (!) masters in physics. This is not the best use of time: the only way to advance your career as a physicist is to do research: it is necessary to have basic knowledge foundation, of course, but after a point more coursework becomes a waste of time.

If you are dead-set on doing your PhD in Cambridge/Oxford, then go for the Part III.  Otherwise, since you already have an MSc, it would be a better idea to apply to PhD programs in the US, and also in continental Europe. (Germany/Switzerland etc. are also great places to do a PhD in physics, and may be the best for you as it would allow you to directly get into research).  You can also apply to PhD programs in the UK, although as you already know, your ability to get into Oxbridge might be limited by not having the Part III/masters—but it is not impossible; I know several people doing their PhD in theoretical physics in Oxbridge without having first done the masters from the same institution.

note: my field is condensed matter/quantum information theory. What I say here should apply to high energy theory as well. Pure math (and the parts of physics truly bordering on pure math) will be a bit different, as in there (I think) there is more emphasis on courses/exams/competitions, even in the US.

@Trunk theory, but thanks for the reminder. see the edit

I was going to write an answer, from the perspective of a high-energy theorist in the US, but this one already says what I would have said. Part III is certainly well-known, but (apart from the fact that you'll have barely started when you apply, unless you have a gap year in between) the downside is that we are mostly looking for research experience, and Part III doesn't help with that. Letters from the UK are often not useful because they just comment on relative rank in coursework, not research.

Where are you now? I am guessing not at either Cambridge nor Oxford. You will have a master in physics already in time but not from either of those universities(?). Do you want a second master in mathematics because that is what Part III is! Are you sure that your current course does not already covered those topics that you will be studying in Part III? There are options in Part III that you can always pick new courses to study, of course. Do you want the prestige of being attached to Cambridge or Oxford because if you don't have funding, it will cost you a small fortune for that. But then if there is a specific someone that you want to work with there, you should try communicate with that person to see how likely you can continue to do a Ph.D with him/her after Part III as well as the potential funding for the Ph.D.. It will be an obstacle course for you. If you can get the funding, then I would do the Part III especially if you can take new topics that have not been covered by your currnet course. On the other hand, if you cannot find any monetary support, then you will have to decide. I would say that it is still helpful with a Part III under your belt if you want to look for a Ph.D. position in the U.S afterwards.

Thank you, Yes I know it is another master's. Apart from my will to research with specific professors there, it cover topics that are almost not researched in my country at all. I am sure that this course really fits me well, but having to spend 50k pounds makes it hard to evaluate, so I am trying to understand if it has other benefits

Yes... And the most frustrating thing is that I can study in my country for free with 2k pounds fellowship per month, the problem is that the research topics are not exactly what I want

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How to tell your advisor that you lost motivation for a PhD and need a break?
I was very passionate about my PhD. The institute, research topic and funding is good. One year has passed and I covered PhD coursework credits with good grades. However, during the last 5 months, I gradually lost all motivation for my PhD.
For the previous month, I did absolutely nothing. We have a weekly meeting. Last week I told my advisor that I was sick and couldn't work. This week, the meeting is approaching and I can't even write 5-6 lines of my research topic abstract (or I don't want to write, maybe due to procrastination). Last week, I gave my advisor some hints that I lost motivation and can't work. He just said it's normal and encouraged me with some concrete goals for this week that I never met.
This situation gives me a strange stress and I face behavioral and mental problems. How to get out of it? I sometimes think to quit the PhD and do a job. But still deep inside me, I want to do PhD and want to do in the same topic and same institute. I feel I'll regret if I quit. Please guide me. I did much online research but nothing helped me. I've been a quite good researcher and published three works in my master degree. But now I feel low energy, exhausted and demotivated.
(this paragraph includes details for diagnostics, skip if you want) In April, I visited my home country for my marriage. I promised my advisor that I would work remotely and will take vacation for only 1-2 weeks during the marriage. But I could not work at home and didn't do any work for 1.5 months. Then I went back to university but missed my wife. I tried to bring her to the country where I study but could not due to visa problems. So, I was always distracted and extremely less productive. After spending a couple of months at university, I lost my mother in my home country and I left university again and came back home. My advisor gave me all the mental support and never pushed me. After spending a couple of weeks at home, I felt like I should resume research. So I emailed my advisor that I want to continue remotely. However, a month has been passed and I did nothing productive.
At the end of this month, I plan to go back to my university and I hope I shall be on track there. However, I am not sure and feel guilty for my advisor.

and I have proposal defense approaching after a couple of months

Is your project part of a larger project of the advisor or a personal one? The latter is typical in math, for example.

Sounds like you have been taking a break already, you just don't want to admit it to your advisor. Lots to unpack here, unlikely that we can give specific advice.

@Buffy  the project is a part of a larger project of the advisor

That makes a solution much harder, of course.

@Buffy i would like to know your thoughts

"the project is a larger project of the advisor" is not making much harder by default. Large project, with well defined work package are easier to be split. If the project is a medium-large project and the advisor is the PI, it is likely that the advisor has no time to spend with each individual project contributor, so being phisically close to the advisor office may not be of any help.

Based solely on your exposition, it reads as tough you are suffering from depression. Please remember, depression doesn't mean "sadness" Rather, depression is a well-recognised condition which on one hand could handicap everything you try to do and on the other hand, can be be readily corrected.

I'm a little surprised @RobbieGoodwin was the first to mention depression (though at least other answers have mentioned mental health); these are pretty much text-book signs of depression. Your university likely has some form of campus health or counselling centre where you could at least get information about local services if not direct help/counselling, but I definitely encourage you to seek out some form of support.

I face behavioral amd mental problems. How to get out of it?

Depending on where you are, free or inexpensive counseling, psychiatry, and mental health services might be available to you. For example, in the US, it is common for universities to provide these to their students.
If possible, I recommend that you seek them out. It sounds like your advisor is a kind and supportive person, but PhD advisors are not trained in mental health counseling, and you might benefit from speaking with someone who is.
Very best wishes to you.

I will bring a couple of strong points.
First (of four): what you face is not that uncommon among PhDs and Postdocs, not even when they pursue their goals in an environment close culturally and socially to them. The problem is that the academia is not ready to accept it, on the contrary, since who is now a professor survived that, the average attitude among managers and porject managers and research managers is "if it does not kill you it makes you stronger". I have a bit of hope that your supervisor is not one of them, but surely he/she has some of that pressure from the top.
You are facing immense hurdles, although you did not realize it, because in the first year you worked intensively (quality, see your marks) and extensively (quantity, since you worked in pandemic times, managing to complete a big chunck or even all of your courseworks), but you repressed your social life (remote calls are not a substitute, they are a mere surrogate).
You do not say that, but I have been in research long enough to see a pattern (no judgement fom my side, but if you come from a non-christian non-european or non-US country you face immense differences and even bigger misunderstanding).
Second: it is time to be frank with your advisor and with yourself. You do not want to live any day away from your family, but you do not want to miss on the PhD opportunities so you are being split. If you are not doing lab experiments, it is time to exchange some of the money you receive for freedom. Take a non-paid leave, try to see if you can pursue your PhD staying in your country with your wife and working fully remotely.
If you are doing lab experiments: the same, but on top of that you have to move to a different thesis, either analytical or numerical or bibliographical work.
Third: the fact that you could not reunite with your spouse in the country where you are pursuing your PhD is both a sign of luck (in case of positive outcome from my second point), it may allow you to stay with your family in a country where your family feels at home instead of being the wife at home in a foreign-hostile country) and a "test" you would have had to take sooner or later... (prospects of) career or family?
Trust completely your supervisor, either they will prove to be a reasonable person or a total idiot. Then make up your mind, if you value more your PhD or your wife and then cut the branch you care less.
Please be absolutely egoistic, consider only your wellbeing and ignore social pressure and cultural pressure from your culture or from the country where you pursue your Phd while doing this choice... a person may vote in favor of the fmaily, another in favor of your career, the median western anglosaxon culture would consider career to be dominant, but in the end
Fourth you have your life, it is one, not a median-plusminus-3sigma life, so it is up to you.

very insightful. Yes, I come from non-christian, non-european and non-US background. Also, did my masters in China, which was also a foreigner country to me. And now Phd is in Europe. Strange thing is, I could not travel back to my home country from 2018-2022 (thanks to covid). Now I feel stranger everywhere, even at my home country.

You reached a very special (un)lucky point in life: it is not where you live that defines you, but you define where you live. Someone (I would even say most of the people) never reach that point. Good to them, life is easier, but once you get there, you cannot go back.
Good luck and all the best!

I have thought about suspending the studies for some time. And when I lost my mother, my advisor told me that I have that option. But big chunk of my home finance (especily after marriage) runs from my scholarship. And if I suspend studies for an year, I shall have to reapply for the visa which is a big headache. Anyway, just see if you could guide me a bit firther. It seems that you've been through such circumstances. In my family and society circle, I am the only PhD, so I find it hard to get the relevant guidance. Everbody becomes motivational speaker (just like when I was in Master study).

Since you have a scholarship, it is "your" money and we can safely assume that the advisor did not have to put their money for you, so you are free workforce for the advisor and for their project.
Just state to your advisor that from now on you will work fully remotely because you cannot be detached from your family and your wife cannot join you in the country. Proposal defense, article, reports ... there is no difference, if you need support from them to get through them, you will find the way to get the support also remotely.

I have a question: is the scholarship monthly pay as high as your fellow PhD students being employed in the same project?

Covid travel restrictions, the passing of your mother, getting married, and being unable to be with your wife must have all added up to a huge amount of stress, on top of the stress of pursuing a PhD and being a stranger in a strange land... A single one of these events is stressful, but you are faced with 5 or even more.
My advice is that you must seek out professional help, perhaps via your university's mental health services. Seeking help for "Mental Health" carries a stigma, and you may think that you're strong enough to deal with things yourself, or that you're not the kind of person who needs to resort to this. That perspective is a dangerous trap. For your sake please do seek out this help today. We can all cope with stress well enough up to a certain point, but once someone is close to their breaking point the risk of self-harm becomes very real very suddenly.
A professional will help by providing proven techniques and teaching coping skills that help manage stress, burnout, thoughts of self-harm, etc. A burnout is a medical condition, just like having a broken leg that requires a cast, and nobody would expect you to run a marathon with a cast. A professional diagnosis will also make dealing with your advisor much simpler, as the mental health professional may even notify the university that you're unable to continue for a valid and diagnosed medical reason. This would make putting the PhD on hold much simpler.
Also, in an unrelated matter, as a parent of 3 kids I'd advise against having kids until after the above is sorted out or at least improved, and you have a stable professional situation.
I suppose we're not supposed to diagnose people online, but in my opinion only helping your with how to communicate with your advisor would be a disservice.

My reading is not that you are demotivated, which happens to many people. Sometimes (my case) it is/was burn out from a too intense experience. But I think that the issue is that your life has been thrown into chaos for reasons mostly outside your control and not because of your own actions. You need space in which to sort things out. The chaos is affecting you emotionally as well as reducing your effectiveness.
I suggest two things to try to get to a better place. First is to talk to a counsellor about your entire life situation and how you can better deal with it. Many larger universities will provide this as a service. Some religious institutions do this also.
Second, you need to ask your advisor for a sit-down, not just to ask for a break, but to work out between you a good path forward to your degree and career. Everything should be "on the table" in such a discussion.
Two additional things can interfere with this plan, though. The first is your funding and how it can be maintained. The second occurs if your work is essential to a larger project that must continue. Both/either of those can cause a larger disruption, even a pause in your plans so that you can return home but maintain a slot for your return. Is a year off feasible? Is a distance relationship with the lab feasible? Is a half-time position feasible? Is quitting and starting over later, perhaps somewhere else, feasible?
Think about your life as a whole and see if the advisor can support necessary decisions. And see what options they might be able to suggest. It is more than asking for a vacation.

It seems like you're in a difficult situation. But I also believe everyone, at some point in their career, whichever it is, get demotivated and feel like they need a break. I don't have a PhD, but I'm finishing my master's degree right now.
I've faced the same problem you did during this master's degree and also at work. What I can say is that there's nothing worst for your sentiment of guilt than taking an "unofficial" break.
Right now, you feel like you need a pause, but at the same time you aren't asking for it. So every time you're not working, you're feeling guilty. This guilt makes you feel bad so you don't work, which makes you feel worst. If that's how you're feeling right now, what you need to do is ask for vacations. Real ones, that are official, where you'll be able to free your mind for a bit.
From what you've written, your advisor sounds like a reasonable person. Explain to them how you're feeling and state that you think you need time off, just to reset. Feeling guilty of being unproductive will probably only make you more unproductive.

Yes, me and my advisor both agreed for a 2-week full vacation till the end of the August. Let's see what happens.

@ghost_programmer Well now, take time to relax away from everything that causes stress! :)

In addition to what others have mentioned, please note that going from coursework to research is not a trivial step. Three papers from Masters don't tell much. It may be that you are unable deal with the change from being told exactly what to do to figuring out steps for yourself. You may need a change in the way you look at phd research.

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How to offset poor undergraduate performance in core classes?
I recently did not do so well in a couple undergraduate core classes, what are my options to make up for this on a grad school application?

Your question is very long and missed a few important points. What were the classes you failed the 3rd semester(this one)? Besides building the student organization, is there any other reason you failed the classes?

I will edit it to include the course names.

Please let me know if there is anything else that might need to be added in for clarity.

There are many mathematics professors on this site, I'll let them answer your question. But, I'll have an opinion here. You failed Galois Theory because you did not grasp the basics of groups/rings/fields well. How do you study graduate level Algebra without enough knowledge about groups/rings/fields? That is, even if you get in one of the good graduate schools in Math?

As answered in http://academia.stackexchange.com/q/38237/19607 doing well in a master's program is a good way to offset poor undergrad performance.

You seem to be aiming for more success by retaking at the graduate level the courses you failed. Isn't that the kind of thinking that got you into trouble in the first place?

In my opinion what led me to fail was lack of effort and preparation. My plan is to spend all summer working through a couple of books to learn what I was supposed to learn in order to be successful. And it is possible to take graduate courses at my school, so I would not need to go elsewhere to take them.

@aparente001 If you are being sarcastic regarding the bipolar disorder comment, point taken. If not, I'm not exactly sure how you would get that from this post.

I will answer the first question here.
If the course you're skipping is a "mandatory" course in your major, then taking advanced courses to make up for the earlier failures is not sufficient unless you get the necessary approvals to do so. (Usually there is some sort of departmental advisor whom you can petition.) However, I should mention that given your past record, it is quite likely that such a request will be denied.

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Some typos in my formulas in my thesis
I found some typos (or errors) in my thesis, one formula, the label of one figure, and one citation. My thesis is done. What should I do? I know some students faked data and their degree were revoked. I did not fake data, but I am not sure how serious these typos are.
UPDATE
I cited and used 5-6 statements from an online report A and changed a little of them. They looks similar. But citation is wrong. I cited B in reference. What should I do? Is it Plagiarism?

Define "done". Is it signed and submitted to your university already? Have you defended it?

Yes. Already submitted to my university.

Have you checked (presumably online) to see if your university has a policy on errata for theses?

I did not find any such kind of  policies on my university website.

I read this post, but still have no idea what to do.

What did your advisor say when you showed them?

At least three persons reviewed my thesis. They did not find these problems. Neither did I.

You get your degree revoked for academic misconduct. Having typos in formulas and text is not misconduct. It is at worst carelessness; in reality, everyone make mistakes of some kind or other. You will just have to live with it.

Now that you have discovered the issues, you need to get to the bottom of whether they matter. If they typos make the conclusions wrong, you have a more serious issue than if they don't change the overall results.
It doesn't seem like a figure caption is likely to matter (unless it implies the exact opposite of the correct caption, like "Death Rate" instead of "Survival Rate").
An equation typo is unlikely to matter unless it invalidates a proof or gives the wrong values in the final form of an expression. You ought to be able to determine this now.
The citation mistake is annoying because a stickler could accuse you of plagiarism. I think that's unlikely, but it's probably worth fixing if you can.
My recommendation would be to show these three errors to your advisor (assuming your relationship is good) and ask for their advice. Helping out with these kinds of issues is their job. Also, they can probably help you navigate/find your university's policy for dealing with thesis errata. Given that pretty much everyone makes mistakes, I'd expect there to be some sort of mechanism for correcting inconsequential mistakes.
If the errors are more important or change the results of your work, you're really going to need your advisor's help. I think talking to them and working through the consequences together are your best bet.

(1) As for the citation, I would like to cite paper A of person X, but I cited paper B from the same person. Because I need to cite his algorithms. (2) As for the equation, it is one variable used in my simulation. It will confuse readers. (3) as for the figure caption, the figure is to compare two algorithms. what we care about is the gap between them, but now I added wrong descriptions. But the gap is there.

These sound pretty minor to me. I still suggest you discuss them with your advisor and try to get them fixed. Definitely fix them in any papers that come from your thesis.

In my published conference paper, there is a equation typo. It does not have the citation and figure caption issues. But I will double check. after that, I will try to contact university and conference organizers.

@codedog, of course I meant fixing them in any papers you publish related to your thesis from here on out. You may or may not be able to get the already published conference paper modified by the organizers.


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I believe my department is failing to enforce standards in doctoral examinations. How to proceed?
I have witnessed multiple doctoral examinations at my (top-10 rated) university in which the student did not, in my opinion, demonstrate the required level of knowledge and understanding under questioning but was awarded the degree anyway. The committee consists of the advising professor, usually one or two additional professors (one of whom may have been a co-advisor), and the professor that chairs the doctoral examination committee in the department.
I suspect that the degrees are awarded at least partially out of expediency because failing the student after admitting him/her to the examination would be unfair to the student and indicate a failure by the advisor and be embarrassing to both, especially because the examination is open to the public (so other students as well as friends and family are present).
In addition, I believe that choosing one examiner to be a co-advising professor is a blatant conflict of interest, since failing the student would also amount to a failure of the co-advisor and is therefore not in his/her interest. The third examiner is sometimes selected by the advisor strategically from a pool of  current or former collaborators.
Finally, I get the impression that the chair of the doctoral examination committee defers to the recommendation of the advisor and does not serve as an additional arbiter of standards for the department (as I assume would be his/her duty), again out of expediency, because if he/she did refuse to sign the departmental forms, it would create a conflict and presumably a lot of additional work.
I know I'm not the only one who feels this way about the situation, but so far nobody, to my knowledge, has spoken out. I'm inclined to speak out anonymously because I find the lack of enforcing  standards to be embarrassing and sickening, especially given the rating of my university. Speaking out, even anonymously, could create problems for me, which is why the best way forward is unclear to me.
Does anybody have any recommendations about how best to proceed? Are my expectations unrealistic?
Edit: One commenter asked me to be more specific about what I thought they lack. Briefly put, they all struggled to answer questions about the problems they investigated. These questions required nothing more than a fundamental understanding of the relevant physical processes. Some of the required understanding is part of MSc courses and would not have been acquired as part of the PhD research itself. What troubles me is that rather than continuing to question the student, the committee members seemed to be going out of their way to give clues and avoiding pushing the student too far in the sense of making the deficiencies too obvious.

Most of the content in this post - about the makeup of the thesis committee, and the potential for extra work and/or embarrassment on failing a student - can apply to a huge number of departments. Do you have any reason to believe that the thesis committees at your institution are different from all those other institutions?

Actually, the system you describe seems to be the norm (for the US), in my experience. I think there is a conscious deference to the advisor, as the person who is best qualified to judge the quality of the student's work; the advisor would likely be overruled only if they were utterly out of line. You may not like this system, but I don't think you'll be able to shame your institution into changing it, since everyone else is doing the same thing.

One problem is that there are usually only very few specialists in the world that will be able to judge the candidate's work, since Ph.D. level work is by definition at the frontier of knowledge. Consequently, they all know each other, meet regularly and collaborate. Or have blood feuds going. Either way, it's probably unrealistic to expect an unbiased assessment of a candidate who you have been co-authoring with for two years, or whose advisor you have hated with a passion for ten years.

Where I did my PhD, anyone with any co-authorships in the past 5 years with any (co-)advisor was barred from sitting on the committee (which, incidentally, meant committee members were often coming from overseas), and still I witnessed a case where a PhD student in atmospheric science was awarded a degree after a public defence where she was unable to explain what causes wind (among other embarrassments).  Therefore, I do not believe removing the conflict of interest is sufficient to resolve this problem.

I believe institutions sometimes give students a PhD to get rid of them and it's frustrating to other students. But the title alone will not serve them much in academia if their background and research output is poor. Unless all they want is a cosy government job back in their country of origin in which case the fault is on the people hiring them. There's not much you can do about it.

If you are a student, you don't "witness" oral defenses (as you say you do). If you are a professor, there is no way I believe you are not familiar with how they work, and that they are not a second qualifying exam (or similar), yet merely an opportunity to talk about your research. And there is nothing wrong with that, obviously. I smell a troll post.

"failing the student after admitting him/her to the examination would be unfair to the student" Huh? Not at all! It's unfair to the other students who did meet the examination criteria. I will never understand how it can be deemed "unfair" to fail a student who does not meet the criteria. What, then, is the purpose of an examination?

@gnometorule: in some countries (e.g. France) the PhD defense is public.

Of course, no leeway should be given for the fact that the students are (1) really nervous, and (2) spent time preparing almost exclusively on their actual thesis content? The defense is not an oral exam covering everything in the world. If you are a student, all I can say is good luck.

I find that question weird, because, honestly, the defence itself is just a formality, a show. Bad students, do not get there.... if you got to the defence, that means you did your phd, regardless of the outcome of that particular event...

Are you a student or faculty?

I have no idea of whether this applies in your situation, but I think some academics (including me) have a tendency to be critical of students for not knowing something we think of as basic, either because we forgot that these things are not as simple to learn as we view them now, or because we don't see all the things they do know.  I don't know a name for this but, this is a sort of opposite of the impostor syndrome.  So one should be careful about this kind of critiquing and, as much as possible, it should be clear to both students and faculty what is expected at defenses.

@Lightness Races in Orbit: I did not say that I thought it was unfair. I said I suspected this could be an explanation for what I have been observing. To be clear, I do not just think it's unfair to other students (in addition to sending a bad/mixed signal) but also (a) bad to the defending student because eventually their lack of understanding will be exposed and (b) therefore bad for the department and the university.

I am a bit confused by the question: the body of the question speaks of a doctoral examination, but one of the tags is defense.  An examination is very different from a thesis defense: the former occurs roughly halfway through a PhD program and is one of the hardest exams that academia has to offer.  The latter occurs at the very end, and according to the current standards of academia, is most often a formality.  So which of these two very different events is being discussed here?

Also what country and field is being described?  The formalism differs.  In my neck of the woods -- mathematics in the US -- there is no graduate level exam in which there is a "head examiner".  Nor is there even an "examination committee" which is separate from the student's thesis committee.

@gnometorule: I don't understand why you think it was a "troll post" - your sense of smell has let you down. Yes, students can attend examinations in the institution I am writing about. To be clear, I've attended examinations as a student in the audience as well as a committee member and so I am familiar with how they work.

@Pete L. Clark: I'm using the terms interchangeably and I'm referring to the oral examination at the end of the PhD. I agree that it should be a formality - if the advisor has done his/her job properly, meaning partly that students that are not ready should not be allowed to get to the examination - but in my case formality means that even students that do not understand the fundamentals in their field pass the exam.

@G.L.: What I am saying is that in programs I am familiar with, there is no oral exam at the end of a PhD.  There is a thesis defense, which is not the same thing.  The testing of fundamentals of the field should occur much earlier in the program: maybe you should be concentrating your attention there.  I don't know what a "head examiner" is or anything like that.  Once more I ask you to specify your country and field.  There is so much variation in the academic world that without this you are going to be getting a lot of information and comments that do not apply to your situation.

Sorry, I see that you didn't use the term "head examiner" either.  Please substitute "chair of the doctoral examination committee".

@PeteL.Clark: There are institutions (even in the US) where the local terminology is to refer to the dissertation defense as an "examination", even if its content is just the same as an ordinary defense (candidate gives a talk, committee asks some questions about their research).  At Cornell, for example, the dissertation defense goes by the idiosyncratic name of "B Exam".  I agree that there is some chance that the OP here is reading too much into the word "examination".

If everyone who is awarded of a PhD title were excellent, we wouldn't have bad researchers, average researchers and good researchers. The fact that, instead, researchers are evenly distributed among all those categories (however one decides to define them), should let you think that probably you have an idealized view of the " required level of knowledge and understanding" for obtaining a PhD.

If you really think people should fail out of their degree, you probably should be thinking about earlier stages.  Typically this would happen at the oral examination or written examination, which happen ~halfway through grad school and are frequently failed by grad students.  The oral/written exams is where the department is supposed to test domain knowledge anyway - the final PhD defense is just a "did you really do this work" formality.  So it really seems to me that your issue is with earlier stages of the process, and you should concentrate your attention there.

Devil's advocate response: enforcing standards helps none of the players (in the short term).

This is currently happening in my department and I find it hard to speak out firmly because most of the board member taught me as undergraduate student. I only spoke up and insisted when a student was actually carefree about not knowing the fundamentals of this course which means there was no way he could have a complete thesis if he doesn't know the basis. I have heard comments like "you schooled abroad and it's not the same here", "these students don't enjoy the opportunities you were given abroad". These are all excuses to pass them.

The observation that the level of knowledge, skills and achievements shown by someone finishing their PhD varies wildly both among institutions and also among students at the same institution is a very widely made one, but nevertheless is still striking to those who observe it for themselves.  At my current institution, we have some graduates that I really wonder how they could possibly have gotten through the program, and we have other graduates whose superior work shocked me: once every few years a graduating student in my current department (UGA math: about the 50th best in the country) has a thesis that would have been regarded as distinctly strong at the department where I received my PhD (Harvard math: always in the top three).  Is the variation lesser at a place like Harvard?  No, I think it's greater.  In 2003 I graduated from that department with a respectable thesis.  One of the 2004 graduates had a thesis that was, suffice it to say, orders of magnitude better.  Do Harvard math PhDs have an understanding of the relevant mathematical processes?  On average, yes, to a reasonable degree.  All of the time?  No, probably not.
I don't think it is helpful to cast the problem in "whistle-blowing" terms.  That suggests some kind of clandestine nefarious activity, but so far as I know most interested parties are acutely aware of the issues raised by the OP and described above.  If the OP is a tenure-track faculty member at the institution he describes, it is (to say the least) entirely his right to take action to enforce higher standards in the PhD program.  I don't understand the need to do so anonymously -- you don't need to do your job anonymously, and doing so sounds difficult.
Here are some thoughts about how to get involved with this.
1) Pace yourself.
The cliche is that young faculty members come in wanting to fix the new department.  In my experience these desires are overall quite positive, but they need to be tempered with an awareness of how the department actually works (which will not be exactly the same way as the few departments they have previously been involved with) and also need to take time to get to know the personnel.
While you are an assistant professor you should start serving on thesis committees of other students.  You should be conscientious but less vocal than you plan to be in the future: you have a lot to take in.  In particular I think it's best if you spend at least a year observing PhD students and the PhD program before taking on students of your own.  So long as faculty are invited to exams and thesis defenses, make a point of showing up, even if you are not on the committee.  If such events are not typically open to faculty members, consider asking if you can show up "as an observer".
2) As long as you are confident that you will not be making real trouble for other students and faculty, don't be afraid to enforce your personal standards.  You need not be held to the lowest common denominator.
As a faculty member in your department, some portion of the task of setting the standard for the students falls to you.  You can be stricter or more exacting than some of your colleagues, so long as you are not making bitter enemies or ruining people's lives.  In my department, the oral exams run by my research area are well known to be longer and more grueling than anyone else's oral exams.  Maybe this dissuades a few people, but not too many since more students study in my research area than any other area.  A faculty member who has a reputation for high standards and working with students to meet them often becomes very popular and influential in the department.
3) Realize that the thesis defense is too late to "hold the line" for any standard other than the requirements of the thesis work and the written thesis itself.
Academic traditions must differ a bit, but I have never seen a thesis committee test for basic knowledge during a thesis defense.  The job of the thesis committee is to make sure that the thesis is an acceptable written document and of course to convince ourselves that the student was responsible for it.  That is not a formality: it often involves hard work down to the wire by the student, the advisor and some of the committee members to get the thesis in acceptable shape.  The thesis defense itself really is a formality: in my experience whatever issues may remain with the written thesis are not even much engaged at the defense itself, though they may still be dealt with later.  If the committee doesn't think the student is ready to get a PhD, the thesis defense should not be scheduled.  Period.
If a student exhibits a lack of basic knowledge at the thesis defense: yes, that's a distressing failure worth doing something about.  But the failure took place years before.  Most PhD programs have several rungs of exams, both written and oral, extending over several years.  A student should not be able to pass these exams without a knowledge of the fundamentals of the field.  Moreover the typical culture of academia is that not everyone passes these exams the first time they take them. Generally speaking it's quite culturally acceptable as a faculty member to say "Sorry, Student A doesn't know Subject X well enough to continue on with his studies."  In my experience, these kind of exams are often done relatively quietly in the department.  Some faculty -- maybe those who are directly affiliated with the most relevant coursework -- are involved in administering the exams.  The majority of the faculty may not be.  If you're crusading for higher standards (not a bad thing!!), this is your place to get involved, get active, and draw your lines in the sand.  Take time to figure out exactly what the problem is.  Are the exams not being graded seriously enough?  Are the syllabi not testing what you want or not testing it to a high enough level?  Are the advisors of students given an undue influence over the result of these exams?  (E.g. "It is a waste of my Student A's time to know Subject X.  I want him to work on Subject Y only.") Once you've identified the problem(s) you can get to work on the amelioration process, patiently but implacably. Because it is in fact not a criminal conspiracy, if you are passionate, smart and keep your eye on the ball over a period of years, you will have more of an influence than other faculty members who are a bit too lazy, too "nice" or too whatever to run things in the best way.

"The thesis defense itself really is a formality" -- I thought the committee was to verify that the defendant actually did the work themselves. If they can not answer basic questions about it, this conclusion is threatened.

@Raphael: Yes, as I mentioned in my answer part of the task of the committee is to verify that the thesis work was done by the graduating student.  Given that the thesis committee has been working with the student for several years at that point, in all of my experience this does turn out to be a formality.  If at a defense a student cannot answer basic questions about their thesis, that would indeed be a problem.

Well, the OP seems to suggest that the committee should not consist of people invested in the student's success (which I think is a great idea, independently of concerns about standards). Then, this part is less of a formality but a crucial necessity that is integral to the whole process. (Sorry, I seem to have missed that you included that point.)

@Raphael: The gist of much of my answer is that it is both desirable and necessary to be able to say "sorry, not good enough" to students in a PhD program, but it is the least efficient and productive to say this at the very end.  I have known many students who were capable of attaining the standard of PhD work but did not get enough support from their committee to make it to the finish line, so from my perspective "too much investment in a student's success" is by no means the problem.  Certainly I can't speak for the entire academic world...

With "invested", I meant not that they care about the student or have been part of the process. Problematic are motivations like "we need high graduation rates" or "if they fail, I'll look bad" or "if I make this complaint now, I'll look stupid for not noticing the problem earlier" or "I need more graduates than X so I get a decent share of department funding". That does not only exclude direct supervisors, but arguably any one from the same department. (I know that in some places, the committee can not contain the supervisor, and must have one external member.)

@Raphael The term "committee" also refers to some fairly different concepts depending on the place. In the US, the committee is part of the process, meeting the student occationally. In Denmark, for example, the committee is not formed until about the same time as the thesis is handed in for evaluation, and the committee has no other job than to do this evaluation (it consists of the advisor, someone else from the department who is mainly there to see that formalities are in place, plus two external examiners chosen for their expertise in the area of the thesis).

Yes, I have seen some similar things in my life and this is indeed a very tricky question. There is a strong tension between our ideals regarding the quality of PhD's (and other degrees) we feel our institutions should be awarding and the practical realities on the ground, which involve messy and awkward decisions that have a direct influence on people's lives. This reality is such that sometimes we feel we have no choice but to compromise our lofty ideals to some extent. As long as the compromises are small, this is probably as it should be, but when the compromising reaches alarming levels, it is reasonable to start becoming seriously concerned.
What I would suggest is this. First of all, it may be worth remembering that the behavior you are describing is not your doing nor your responsibility. The chair and the members of the doctoral examination committee are the ones who are making those decisions and putting their own reputation and credibility behind them. So, although you find the behavior concerning and perhaps for a good reason, you cannot reasonably be expected to fight all instances of poor decision-making at your university. Thus, one option is to simply do nothing except to resolve privately that if you ever preside over a doctoral examination yourself, you will follow your conscience and let the chips fall where they may, and thus play at least a small role in making your department and university better.
If you want to be more proactive, an honorable course of action would be to actively pursue the role of chair or member of the doctoral examination committee so you can put the goal of raising standards directly on the agenda. Or you could strive to be appointed to the departmental committee that decides the makeup of the doctoral examination committee, and thereby help get people with high standards be placed on that committee and help prevent the kind of conflicts of interest you are describing. Through such behavior you will be setting a personal example and showing that you are not just criticizing others but willing to take action yourself for the goal you believe in. Since you mention that you believe others in your department feel the same as you, you may find that you have a good number of allies who will support you in your mission, and even your opponents will respect that you are acting on your convictions. Of course, it will take time and effort to bring about change, so be prepared for a long struggle ahead.
Finally, if your position within the department does not make it realistic for you to seek the kind of active, visible role I suggested above, or you are unwilling to make such a large effort to see change happening, I don't have much to suggest. I don't think there are easy fixes; someone will have to do the work to change the culture of your department. If it's not you, maybe you can work behind the scenes to identify more senior allies willing to take on that role. You might get lucky and find someone passionate enough about the subject, but probably you won't.

I have observed the same problem in a number of high-ranked universities in the North America and Europe. In fact, I would say that I have only observed two or three defenses where the student exhibited true competence and control over the subject matter (factual and logical) -- all were my own students. Coupled with student-progress related discussions at faculty meetings, this led me to reexamine my assumptions about what the degree Ph D "means". Rather than consider only what I believe the standards should be, I concentrated on what they actually are. Consequently, I saw that none of these dissertation defenses were shockingly below the existing standard, even though they were sometimes disappointingly low. I came to understand that the students' shortcomings were largely a failure to consider alternative and a failure to know facts, but generally not a failure to have any idea how to answer the question.
As a member of the examining committee, you (may) be in a position to clearly indicate that the student is not ready yet, and if that is the case, you should not shirk your obligation to maintain appropriate academic standards. If you are not in that position, you have two realistic options. One is to focus on asking relevant questions from the floor. Institutions vary in terms of how "outsiders" can interact with the defense, ranging from completely closed to open to the public and anyone can ask questions. The goal should not be to prevent the student from getting the degree, but rather to make it publicly known that there is a problematic failure to enforce proper standards regarding core knowledge in the discipline. The second is to make this be an agenda item for discussion at faculty meetings, where policies regarding graduate programs are (possibly) set. It may be that requiring a specific course at the PhD level would address the problem.

Nobody knows everything.  My experience with defenses is that the questions keep getting more and more difficult, until the student says "I don't know", at which point the faculty make an effort to walk the student through the issues.  After the committee is convinced that the basics are really in place, this process repeats itself.  AT many universities, this process takes place behind closed doors with the committee, AFTER the public presentation.
So, what should you do?  Assuming, for the moment, that you're faculty, if there has been a closed session after the defenses you were not privy to, you really have no idea how the student performed in the closed session, thus you have little to say officially about the matter.  That said, if you believe that the student does not merit the degree, and that releasing said student to the world would harm your department's reputation, you might mention your concerns to the chair of your DEPARTMENT'S grad program or your chair (not the Dean's office, university officials, etc.).  Keep it in the house.
If this resonates, this might rise to the level of a committee or general faculty meeting, in which case you can offer your suggestions on how your department might better groom your candidates for defense -- Perhaps a more rigorous proposal process or more frequent committee meetings or even create a system where the student gets more practice and feedback on presentations and QA sessions (we have a summer presentation series of grad students presenting to other grad students with no faculty presence that seems to help).  If this conversation doesn't happen, and you still feel strongly about it, talk to your chair about placing you on departmental committees that have some oversight, like your graduate committee, and gently try to sell your point there.  As others have said, this becomes an issue of changing the departmental culture.  My own opinion is that this difficult task is best approached through a "what can I do to help make this better?" strategy, rather than a dig in your heels,  "We're doing it wrong" stance.
One thing that I've seen that puts students in bad situations like you describe is late formation of doctoral committees.  Committees should form early, and meet with regularity.  If you don't do this, you can wind up in a situation where a faculty member gets involved too late to do any good.
The one approach I WOULD NOT recommend is playing pariah on a students committee at defense.  If you want to make your statement, the time is actually WELL BEFORE the defense takes place.  You can nudge a committee you're on into laying out a careful schedule of benchmark reviews with the student, and whip him or her into shape if things aren't looking good, and even hold up the defense date until the student is ready.
Interestingly, at our university, the policy following distribution of the dissertation used to be that the committee chair (who is external to the department) would informally ask other committee members if the defense should not happen.  This has changed to a more anonymous electronic mechanism where each committee member needs to affirm that he or she believes that based on the dissertation, the student is ready to defend.
If you're a student observing the sort of pattern you describe, you might mention it to your adviser or chair, but I wouldn't expect this to be well received.  I'd put this in my "stuff I've observed that I can do better when I launch my career" pocket, and try not to forget it later.

Of course I would not bring this up as an examiner during/after a defence - that would be extremely unfair to the student. Your other suggestions are good ones, but as I mentioned in my post, for reasons I cannot get into here, I cannot do this in the open, i.e., non-anonymously. One other thing I want to make clear with reference to your first paragraph: I am not referring to questions about topics that are at the "bleeding edge", but questions about the fundamental processes in the field of research of the students.

@G.L., I see that the question is marked with the "whistleblowing" tag and that you mention you want to maintain your anonymity. It did occur to me after I wrote my answer that you may be thinking of a strategy of anonymously exposing what you perceive as some sort of scandal. This may seem like an easy solution compared to the strategy I proposed, but honestly I don't think you will achieve anything this way. The decision whether to award someone a PhD is so personal and subjective that I strongly doubt you will be able to convince anyone that the committee members made a wrong decision, ...

… unless you take a more activist role where your accusations are made in your own name and backed by your own actions and credibility.

Great answer.  One of my favorite parts: Create a system where the student gets more practice and feedback on presentations and QA sessions.

An issue not yet raised is that of expectation. If the defense is sold as a "thesis defense", as it frequently is in North America, then it is unreasonable to expect the student to have prepared answers to questions outside of that scope. In the defenses I have been party to, it was strictly about the thesis itself. The outcome of deliberations had to fall into one of four narrowly defined categories:

Accept thesis as is
Accept with minor corrections
Major revisions required
Reject

(I have seen categories 2-4 used; 1 I take to be exceedingly rare.) All of these categories have to do with the thesis. Nowhere does it state that the candidate must exhibit sufficient expertise in the general subject area; this is supposed to have taken place during preliminary and qualifying examinations. (With the continuing specialization and narrowing of focus it is not even clear that the subject area can be properly defined.)
As Dan Romik states, changing this state of affairs requires a deep change of culture and lots of time and energy.


text:
My institution requires publication in Clarivate-indexed journals - what should I do if paper is accepted by a journal at risk of being de-indexed?
My department requires that papers are published in a journal that has an impact factor and is indexed in Web of Science.
I submitted a paper to one of these and went through four rounds of review, and now my paper is accepted. However, the journal is now considered "On Hold" by Clarivate and is at risk of being removed from their indices:

On Hold

Concerns have been raised about the quality of the content published in this journal. The journal is being re-evaluated according to our selection criteria; new content will not be indexed during the course of the re-evaluation.

When the evaluation is complete, the publisher will be informed of the outcome and the journal will either:
be removed from coverage if it no longer meets the quality criteria
or remain covered if it continues to meet the quality criteria.
If the journal meets the quality criteria, any missing content will be indexed. If the journal is removed from coverage, content will not be backfilled. In the most serious cases of breaches in a journal's editorial standards, as determined by our selection criteria, published content may be removed from Web of Science. Timeframes for completing a re-evaluation will depend on the particular circumstances of each case.

Will this status "on hold" affect the impact factor for the journal (it is Q1 currently), and how long it will be "on hold"? What should I do with my paper?

Can you explain why you care what "clarivate.com" thinks about this journal? They are a for-profit multi-billion-dollar corporation...

You haven't named the journal, nor its publisher. It would be a problem if the journal is predatory.

Predatory journals will publish just about anything if you pay their fees. They are not reputable or reliable. Bealle's List may be too old to completely rely on, but it is a place to start. Sharing the name of the journal here shouldn't cause any problems.

The only people who can tell you how that would be interpreted in context of your departmental regulations live in your department.  Talk with your chair about it.

If the journal is in the first quartile (Q1) then it is unlikely to be de-classified for academic reasons.  Clarivate may be trying to pry some concessions from the publisher.

If I read this right, then you published in Journal of X for which later on Clarivate and their indexing products decided that they don't trust Journal of X any more. There is nothing you can do about this: The dispute is between Journal of X and Clarivate, and you are not party of the dispute; you are just an innocent bystander.
If your department requires you to publish in journals that are indexed by Clarivate, then the truth is that you are likely out of luck. You can't force Clarivate to index (or continue to index) Journal of X. You can of course discuss with your department head whether they still accept your publication for their purposes, and maybe they will if you explain that at the time you submitted the publication, the Journal of X was still indexed.
Going forward, you will want to make sure that (i) you keep doing good work by international standards, and (ii) choose journals to publish in that are of high quality and high ethical standards, and consequently will continue to be indexed in the future.

Actually, I read it that the article was accepted, not published. There may be something that can be done.

what is the expected time that I should know the result of the re-evaluation process, please?

Does this evaluation mean that the journal isn't good or will be removed? or it is just a routine procedure

@user20133451 The status text which you included in your question states: "Concerns have been raised about the quality of the content published in this journal" - why would you think they mean anything different than what they've said directly?

cause there is a probability for "remain covered if it continues to meet the quality criteria" as the status text included so i'm asking for what is the expected time for the re-evaluation process and does that a routine procedure for some journals in this duration

The time frame is also covered in the text you quote: "Timeframes for completing a re-evaluation will depend on the particular circumstances of each case." In other words, it is what it is. There is nothing you can do but wait.

And yes, in all likelihood the journal you choose isn't any good.

@WolfgangBangerth - that is a little unfair, since (1) their advisor may have had a hand in the selection, and (2) it was indexed before, so met the criteria. Only in retrospect might it be a bad move.

@JonCuster I didn't say the choice was bad. I said that the journal was bad.


text:
Authorship decisions after data collection and analysis
I am a graduate student in a STEM field. I collected and analyzed data for another graduate student (different PI) and they are now refusing to include me as an author on a research paper. I optimized conditions/parameters, characterized a new material with a specific instrument/technique, and processed/analyzed data.
Can I prevent the data from being used if I’m not included as an author? What I have in mind is saying "I'm not OK with this data/analysis being used if I am not included as an author".

You say that you "took" data for another graduate student. Do you mean that you collected data for them? Did you have an agreement with the other student about how they would use the data that you have given them? What is it that you want to be included as an author on? Their PhD dissertation ?!?! A conference proceeding? A research publication? Additionally, how would you propose to "prevent" them from using the data? Any sensible answer to your question is likely to depend on you describing the situation more fully.

I suggest that you now go back and heavily edit your original question. Add in the additional information that you have included in the comments. Don't do this as a series of "additions"; integrate the material from your comment into the question. That is the way to attract an answer!

People asking for clarification here are trying to help you. If you don't treat them respectfully, what does that suggest? It's totally understandable that this is a stressful situation, but it's important that everything is clear so that you don't get the wrong advice. Things that may seem obvious to you might not be obvious to another asker.

Before getting to a solution to your problem, you should take this as a useful lesson for future work: always negotiate authorship up-front before commencing work on a project.  That is a useful lesson to learn and it will prevent you from getting into these types of situations in the future.
As to the present project, I would recommend that you first seek to resolve the matter through negotiation with this other student, and if that fails, arrange to have the matter reviewed and have a determination made by an appropriate third-party expert in the university (e.g., an experienced academic in the ethics office or in another department).  Before negotiating the matter or raising it for review, first read some guidelines and academic literature on authorship for statisticians/data analysts (see this related answer to get you started) to get an idea of the principles used for determining when data analysis is enough to warrant authorship.  Your description of your work sounds substantial to me, so it is likely that it will be enough to warrant inclusion as a co-author according to relevant guidelines/literature.
I recommend against withholding your analysis, except perhaps temporarily while the issue of authorship is reviewed and considered.  If you are unable to come to an agreement with this other student, the best course of action would be for you both to agree to a binding determination being made by an appropriate third-party expert in the university.  If you are both willing to agree to this then a decision on authorship will be made and you can both proceed accordingly.  (Even without agreement, the university has mechanisms relating to research ethics that can allow it to investigate and make a binding determination for its employees.)  In the event that the decision is against you, I recommend you accept that, supply your analysis without any impediment, and just take this experience as a lesson in pre-negotiation of authorship.

Your summary might be framed this way.
I was handed a set of samples by a colleague. I characterized the samples in a specialized instrument, analyzed the data, and generated a report on the results. The only inputs that were given to me were the samples and the types of results desired. I worked independently using these inputs and turned over the report at the end. I did not consult with the colleague to decide why certain approaches in the characterization and analysis should or should not be taken. I did not enter into discussions about the interpretation of the results within themselves or in context to other findings from my colleague. Can I now claim right to co-authorship on a publication that includes the results from my report?
In the above frame, the most direct answer is no. First, the hard reason. You did not negotiate a contract on your duties and rewards before the fact. The party that got your report is under no a priori contractual (legal) obligation to award you co-authorship. Not simply written, not even verbal. This is not a happy situation to reach. As might be said also by others, at best, this finding can serve you as a lesson for next time.
The second reason for an answer "no" concerns the answer to the question of whether your colleague has any ethical responsibilities to include you as co-author. As you briefly framed your case, and as I have reframed it in greater detail, you served primarily if not exclusively as a service provider for the work done. You took in samples, took in a description of what was desired as the output, ran a specialized instrument over the samples, and provided the desired output result using the given inputs. Some consider the level of work just described as not being worthy of co-authorship on a publication. Some will instead consider it more responsible to be recognized only in the acknowledgement section of the publication.
The extent that the work you did deviated from the above description must be considered. Did you provide "original ideas" during your discussions, for example by suggesting different approaches to the characterization or analysis to obtain results that provided greater insights in their own right or in the larger context to the entire work itself. In addition, you will have to consider the extent that the other party carries your same ethics about co-authorship roles and perhaps even the extent that the journal enforces standards on when to acknowledge contributors to its publications. All these factors, which you have left rather unclear in your post, will dictate how much room you may have to negotiate for co-authorship or acknowledgement on the paper. If you do go down this path, you will benefit by having someone with a deeper background in your case to advise you on the best professional approach to take. Ultimately, you may find the effort so overwhelming that you simply have to allow even this level to pass as a lesson this time.
In summary, given that you have no a priori contract, and presuming that the ethical frame does not deviate significantly from the above, you may face insurmountable hurdles in pushing any further for co-authorship. At best, you should ask for recognition in the acknowledgement section. You should certainly do so in consultation with someone who has insights and experience to support your case. Finally, the scale to define what level of involvement leads to what reward in a publication, from being left off to being acknowledged to being a co-author, is not linear, standardized, or always agreed-upon by all parties involved. You likely have some further discovery to make beyond asking here for an affirmation.
Finally, with regards to the last part about discovery and consultation, implicitly understood in your posting is that you are working with a (different) PI. What advice does your PI give you about this situation? Was your PI in agreement with your decision to do characterization and analysis work for someone on a different project and then simply hand out the results from that work without some up-front agreement? What does your PI say to your attempts now to try to take back or block those results from publication? Your next step should be to answer these questions and follow the commensurate advice from you PI.

I think this answer makes a number of assumptions regarding the relationship between OP and the other parties, and the amount/type of contribution that OP provided to the project, that are not necessarily supported by OP's post. Specifically saying that "you contributed only to the extent that a comparably trained machine or function or robot could do an equivalent job" is a significant leap.

@academiaTA I have removed the bluntness. Also as modified, the OP has ambiguities about the true depth of involvement. Further consultation is advised.

I think there is simply not enough information about the field or the tasks performed to just conclude "no." This is on the OP, not you, of course. My interpretation from a different field than you was "probably should be."

I think that there are really three different questions, or possibly four. I'll begin with the very hypothetical fourth!

Is it likely that other people in your situation would feel that they had been treated unfairly by the other graduate-student/PI pair? Quite likely, but frequently when you (i.e., many people) invest in another person without expecting any great return for either of you, and then the other person gets a great reward (e.g., authorship), you might feel cheated. To highlight an analogue situation, consider that you've spent one dollar on a lottery ticket for your friend, and then they win really big! Many people in this situation are likely to feel as if they've been treated unfairly when the winnings aren't shared with them. It's human, but the feeling is driven largely by a (completely hypothetical) notion of what you yourself would do in the reverse situation.

Is it unethical for the other graduate student/PI to refuse you authorship? I don't think this has an answer with which everyone would agree! You indicate in your comments that you wouldn't anticipate being included as an author on other student's PhD thesis ( ... a completely bizarre outcome that I suggested merely to test the limits of what, and why, you feel unfairly treated). But you do feel that you should be included on a research paper, as indeed I would in a similar situation. Yet I've also been in the situation of (i) having my name mentioned only as an "also-ran" in the acknowledgements (as indeed you might hope for a mention in the student's PhD thesis); or (ii) not mentioned anywhere at all despite the significant contribution I felt I had made.

Can you really prevent publication if your name is not included? There are such ways, but most methods of truly preventing the publication entail enlisting the help of third parties: lawyers, university research review boards, journal editors, etc. You (wisely!) show no inclination to do any of those things, and instead say that you would "prohibit" the publication by expression your verbal prohibition to the authors, and hoping that they attend to you.

What is good advice for a person in your situation? There are two things. First, see what you can gain by negotiation. Second, learn the hard hard lesson and move on. If there is the slightest chance in future that you would want to be included in the list of authors on a way-in-the-future publication, then set aside your feelings of friendship and loyalty, and ask for a written statement to that effect.

I think that the effort of negotiating is worthwhile. Try to meet with the PI (definitely) and student and be prepared with some evidence of the facts of the input you had into the substance of the paper. Definitely stress your unhappiness at not being included as an author given your input. Be prepared to lose ... but also be prepared to graciously (yes, it's hard!) accept an acknowledgement in the paper that outlines your contribution.