How can I deal with being pressured by my department to pass students who failed?

Your department defers to you as the final authority on the student’s grade, and for a good reason: because you are the only person who sees the full picture of the student’s performance and the context in which it was assessed.
The department can give you high-level guidance and advice, but that is never a substitute for an instructor’s reasoned judgment taking into account the details of the situation.
The student, like all students everywhere, wants to pass, and like many (but not all) students will offer any excuse they can think of, no matter how feeble, for why they deserve lenient treatment. If the excuse rings hollow, ignore it.
Whatever your conscience dictates doing is the best course of action here. Making that final call is precisely what the department pays you to do and expects of you.


On MathJobs, what does "Faculty contacts in our dept?" means?

This is a really really important question, and it's really important that the correct answer is option 2.  Most graduate students interpret it to mean 1, and this puts them at a disadvantage.  You should list any people in the department who might be interested in serving a postdoc mentor for you.  You should always list someone.

There are two main reasons for this:

On mathjobs you can run a search for all applicants who listed a given faculty member as a contact.  I always look at the applicants who list me as a reference.  Along with sending an email, this is the best way to assure that at least one person looks at your file.
When I served on the postdoc hiring committee I was responsible for looking through 20% of the applicants.  We're only going to hire a postdoc if there's a good research match for them in the department who is interested in mentoring them.  If I see a good file, one of the most important things is to make it easy for me to know which faculty member to mention the file to.  Sometimes I can work that out myself, but it's not always obvious.  Listing someone as faculty contact immediately indicates who I should email.


Grad student overseeing (undergrad) student: how much to help?

This is focused on the educator aspect of it.

The goal should be to do as little as possible but help the student from getting stuck. Said another way, when asked for help, first try to figure out the crux of their problem and then give them enough of a hint (but not an answer) so that they can have an a-ha  moment and get some enlightenment. It isn't easy and it takes practice, but that is the goal.

Sometimes you answer a question with another question. Sometimes you "solve" a problem by giving them a simpler problem. Sometimes you just ask them to explain it to you as best they can. Sometimes you point them to a page in a book (or similar). If you give them answers they will start to depend on you rather than on themselves.

Listen, as they ask questions, to see if they have some misconception that underlies the current issue. If you can dispel those, there is a better chance that they can move forward on their own with more confidence.

So, if the student is to learn they need both reinforcement and feedback. Reinforcement implies repetition and should come from them. Feedback comes from you. But the work needs to be theirs. Answers have little learning value.

And yes, it is hard and takes practice.


How serious it is not to disclose full academic history in your grad school application?

I'd leave it alone, or disclose to your department, not the admissions office.

First, You got all your degrees at one university.  Presumably, the school you applied to was sent an official transcript, and that transcript would show all the degrees conferred by that school.  They have the info.

Second, the odd part about your application package is the MS in EE, given that you're applying for a second MS in EE.  Your new department knows this.  They wouldn't even bat an eye at the second BS.  Dual BS's are fairly common, and it wouldn't be a negative in your package.

Lastly, you gave them what they asked for, which was all universities you attended. You followed their instructions to the letter.


Asking recommender to avoid talking about a project that was abandoned

Generally, one only writes positive things in a letter of recommendation.  If you are writing a letter and cannot write positive things, do not write it.
Therefore, it is not necessary to ask that negative information be left out of a letter.
Should a reference letter for a student always be positive?


My student published a preprint of our published paper without me as an author

As far as I know, Google Scholar is entirely automated, and so those results will likely only change if the offending paper is updated or removed.

When you say the student 'uploaded' your paper - where did they do this? On a personal website? In a repository? Regardless, your first step is probably to contact the student and ask them to add your name or take the paper down. Bear Hanlon's Razor in mind: "never assume malice if incompetence would suffice".

If the student refuses, or ignores you, then (if applicable) you might contact whoever runs the website/repository, and ask them to amend/remove the paper. You might find that the editor/publisher of the original journal article is willing to support you here, as the republication may not be compatible with the licensing agreement originally signed.

Finally, since Google results are based on measures of how 'important' a website seems to be: you can cite, reference and advertise your original paper as much as possible, to promote it in search results.


Would a LaTeX glossary contain program function/method purposes/definitions?

A glossary is

a list of terms in a special subject, field, or area of usage, with
accompanying definitions.
such a list at the back of a book, explaining or defining difficult
or unusual words and expressions used in the text.

so the wrong place for extended descriptions of what your functions do.
Whether those descriptions belong in the text where the function is used or in a separate section with links from the text depends on more context than you can provide here. Imagine  the readers of your thesis, knowing what they know (but not what you know) and think about what would best help them follow your argument.
LaTeX can easily manage the cross referencing with a custom \newtheorem command.
Ask your advisor for advice.


Is it possible to get DOI from ISBN of a book?

DOI and ISBN are two different identification numbers and can not be translated into each other. A (digital) book need not have a DOI number, and e.g. a journal article that has a DOI need not have an ISBN number.

If you want to look up whether a book (or journal article, etc.) has a DOI, you can query it at http://www.crossref.org/guestquery


Is my university using TA's excessively?

Actually, I don't think it is excessive, though it may be a bit steep. It was a long time ago, but when I was a PhD student in mathematics at an R1 in the US, the "load" of a TA was about half that of the teaching load of a professor (1 course equivalent vs 2 for a professor). I don't see anything in your list that is really out of bounds, assuming #1 is occasional. In fact, all of it is good training for anyone wanting a career in academia. You need to practice all these things to get good at them.
I was thrilled (thrilled, I say) when, as an advanced TA, I was given complete responsibility for one section (of many) of an elementary course. The course was pretty standard so there wasn't much course design prep and the final exam was common to all sections, but, otherwise, the course was mine.


How to communicate college's financial problems to faculty candidates?

As a member of the search committee, and as a department in general, you want to aid the department in getting the best candidate possible. Misleading the candidate and losing them after the campus visit, or even after a few years, hurts the department. Doing the right thing may have long term benefits but might cause short term problems.

I would pass this off to a higher up. If you are not on the search, ask them how they are dealing with it. If you are on the search committee ask the chair of the search and/or the chair of the department. Once you get to the university level, they should be able to produce some numbers that presents the university in the best light. While this seems like it is deceiving, what you basically want to do is convince the candidate that whatever they have heard in the news, there is still a good reason to think the university will pull through the difficulties.


Writing a topical review paper with co-author(s)

Who does the actual "writing" (i.e. putting pen to paper or fingers to keys) is actually immaterial. I've published with half a dozen people where everything was "written" by one person, since he is (by far) the best writer in the group. He chose the words and the sentence structure.  But the ideas came primarily from two other people and the rest of us contributed ideas from our own experience. The "writer" synthesized all of that into a nice expressive form. But without the rest of us he wouldn't have been able to do it.
Authorship is (or should be) about intellectual contributions, not physical manipulations of keyboards or even of experimental equipment.
At the other end of the scale, I've written books with major publishers and worked with a copy_editor who helped with some of my (occasionally!!) awkward syntax. In no such case would anyone expect that their contributions were authorship.


Include proof in bsc thesis that I couldn't do fully myself

I don't see an issue here for an undergraduate thesis. If the "important paper" is new and the work overlapped with your own, you should be able to get credit for your work independently of the other. If it is a classic paper that you should have known about, but didn't, then you may have a more serious issue and a reason to re-write.

But citing the other work, just as in your example, seems right, including the main conclusions you draw from the paper.

But the professor to whom you are responsible (maybe not just the assistant) is the best source for an answer to this question.

If there is any serious issue raised by the professor, then you need, first, to think about what if anything is unique about your solution. It may be that a relatively minor re-write will do the trick if you just stress what is new/unique about it.

I'd also suggest some perspective. The fact that, as an undergraduate, you can "follow" but not "replicate" the work in another paper may be good or bad depending on the other paper. We normally expect that students at this level are students and thus can't know or do everything. Even experts can struggle with some deep ideas and intricate proofs.

I'll note that it would be a more serious issue for a doctoral dissertation. There is a fairly recent case, two people known to me, who had their doctorates delayed for a year because they each did a piece of nearly identical work without knowledge of the other. They didn't need to re-do any work, but it took a year for the (Computer Science) community to determine that this was just parallel work and no collusion nor plagiarism was involved. Sticky, but both are now highly regarded.


Options other than the NSF for PhD level grants?

A few government fellowships come to mind:

DoE Office of Science Graduate Student Research (SCGSR)
DoD National Defense Science and Engineering Graduate Fellowship (NDSEG)
DoD Science, Mathematics & Research for Transformation (SMART)

There are also many fellowships from industrial research labs that you could look into, depending on your field (Intel, IBM Research, Microsoft Research, Facebook, Nvidia, etc.)


What to do if you have a troubled relation with your postdoc supervisor?

From your comments it sounds like a Setup-to-fail syndrome. https://en.wikipedia.org/wiki/Setting_up_to_fail

The Wiki article is a bit iffy, but it basically means that he somewhat has low expectations of your performance after some incident. Thereby, when something happens he assumes is your fault because he has low expectations nevertheless.

Is usually a toxic relationship because is self fulfilling (you'll end up making mistakes, because he wants to) and self reinforcing (the mistake you just did helps him reinforce the idea that you'll make more).

Is a vicious circle that has to be addressed by both you and your boss (PI, manager, etc). But is usually a good idea to have some other people on your side.

Ultimately, if he is unwilling to change, it is better for you to leave for a less toxic environment.


PhD or MSc without undergraduate degree?

No, it is not possible. Your feeling that you "would not be held back by a lack of education" is inaccurate, and graduate programs will know that. They have plenty of qualified applicants who have more experience and background than you do; they have no reason to admit you.


Being overqualified as a barrier for getting a job

When they say you are overqualified, it probably means:

They are afraid that someone with a Ph. D. will demand a higher salary than they can afford to pay;
They are afraid that you will get bored with the job and quit after a few months because the work won't be challenging / intellectually stimulating for someone with a Ph. D.

So, in your cover letter, you have to tell a good story that addresses the above two items (i.e., tell them why you know you will love this job and not get bored with it). If you search around on google, you can find many articles / blog posts giving more detail.


Supervised a PhD to 90% of completion; take credit for 100%; what could go wrong?

On a generic CV, I would simply make a section of "Graduate students supervised and co-supervised", and include this student.  In this context it wouldn't be necessary to go into detail about whether the supervision was "to completion".

But for something like a promotion dossier, where you're asked to tick boxes, I would go to whoever is responsible for overseeing the evaluation process (department head, promotion committee chair, etc), explain the situation, and ask what you should do.  If at all possible, get an answer in writing. Then, when you fill out the form, attach a note saying something like:

  One student was supervised by me for about 90% of their thesis work (stages X, Y, Z), and then changed supervisors for the last 10%; I am officially listed as their deputy supervisor.  I spoke with Department Head Smith on October 24, 2018, and she advised that it was appropriate to include this student as "supervised to completion".

If Smith says "no, don't count it", then you attach a similar note saying "Smith said not to include this student, but I believe that this is a similar accomplishment to supervising a student to completion".

Since academic achievement is generally self-reported and "honor system", this means that any attempt to "cheat" is seen as a serious ethical offense.  If someone on the evaluation committee is hostile to you, they could use something like this as ammunition to wreck your entire promotion case.  ("Candidate says supervised to completion, but student's dissertation shows someone else as supervisor.  Clear-cut fraud.")  So that's what could go wrong.  But if you disclose the situation, and get someone else to pre-approve the way you're filling the form, you eliminate the possibility; maybe it won't be counted in your favor, but at least you can't be accused of fraud.


The concept of state of the art references in review of a paper

I think the statement is very clear. Wether your literature research was incomplete or the reviewer just wants two of his own papers cited once more, we cannot tell.

Make sure you can exclude the first possibility, then try guessing, and either be bold in your rebuttal letter, or cite some more.

(If the reviewer gave no hint to specific references, I'd suspect that you might have a somewhat grave problem: Either you paper is indeed crappy, or that reviewer just doesn't want it published, or wants it delayed, for his own good.)


PhD opportunities in Spring in US universities

Most PhD programs, and many master's programs, in the US only offer one admissions cycle per year, with programs starting in the fall. This is in part because of the PhD program encompassing classwork as well as research.

The main issue that speaks against spring admissions is that in most programs, the coursework begins in the fall semester, and any "sequences" (where course Y depends on course X) will often begin in the fall semester. Thus, starting in the spring semester may mean that your coursework phase will need to extend longer, so there's no real advantage between starting in the spring and waiting until the following fall.

Where there might be an advantage is if you are able to use some of the time for finding a research group (if that is necessary for a research thesis for the master's degree); in some cases, you could even get a head start on the thesis work, which could allow you to finish somewhat faster.


How to address my multiple undergrad transfers in graduate admissions?

On first appearance, this does seem like a significant negative of your application. I have a couple suggestions for you.

One, make sure you follow the graduate school's instructions on submitting previous school's transcripts. Some graduate applications may ask for only the receiving degree transcripts.  If some of the previous five schools' credits did not transfer and were not related to your degree, you might not have to mention those at all. Be careful though, as not including them when you are supposed to is considered a misrepresentation of yourself, and could invalidate your application (and even potentially your later graduation). On the other-hand, you may be asked to provide each and every full transcript from each of your previous schools.

If you do need to include the transcripts from each of the six schools (or they do all appear as transferred credits), I would highly recommend you include an explanation in your application.  Their biggest concerns will be if this number of school changes indicates an inability to commit, the tendency to give up rather than work hard to learn something difficult, and/or the presence of a serious level of indecision about your direction.  These are all serious issues for the successful completion of a PhD, in which you can expect long and difficult work on the same subject. You do not need to give much detail about your medical issues, but be sure that your explanation sufficiently explains the information given to them. For example, repeated withdrawals and restarts or a longer completion time makes clear sense in the context of a recurring medical problem, but why six schools and not one or two? Medical withdrawals and restarts at the same school would seem like a more reasonable option, which could lead them to doubt your justification.

Emphasizing your continued upwards gpa trend and your commitment to the area of psychology over the years will also help combat some of these concerns. Any out of class research will help you enormously as well as it shows you are willing to spend additional time on the subject, have the potential to succeed at PhD level research in general, and have experience to know you enjoy and are willing to commit to psychology research specifically.


Reviewing demo papers, poster papers or extended abstracts

IMO, the following guidelines might help:

Extent of novelty
Quality of the figures and tables
Dedication

Although the third point may seem a little fuzzy, it can be easily observed on sight, especially in the case of poster presentations.


Is it appropriate for my professor to include gender offensive material that is unrelated to the class subject matter in the course notes?

In economics a "sleeping beauty" is a company primed for takeover, often because it is under-valued. Asset valuation is quite a large topic in accounting, since it can have a huge impact on the final total value of the company.

Some authors are of the opinion that the (European) sovereign debt crisis created a mentality shift in accounting. That is, valuation tended towards more conservative methods, and in so doing, accountants created more sleeping beauties than before the crisis.

It is my guess that your professor did not have time to cover this topic in your course. Or perhaps it is used in another course? Why don't you ask him?

If you feel that there is hostile environment against women, then go right ahead and report it. You should not feel guilty in any way.

However, the professor could simply be trying to grab your attention with a small "shock", as asset valuation is considered by many students (that I have met) to be both mundane and boring.

We do not need more political correctness (PC) or micro aggression within higher education. So please ask yourself if he really ment to promote rape, or if you are simply taking this completely out of context. Again, what is stopping you e-mailing him? Write that you you do not see how it is related to the course, and ask for a clarification. His response should give you a clear indication of how to continue.


Can you do paid external work under a PhD contract in France?

It depends on the work you plan to do (see here, paragraph IX).

You are NOT allowed to do extra activities of the kind that could be part of your PhD contract (teaching, diffusing scientific information, expertise...). If you want to do this kind of work, it needs to be under your PhD contract.
For the other cases, you need to obtain an authorization from your employer. If your employer is the university, they will ask your advisor's opinion and evaluate whether the extra work risks compromizing your PhD before making a decision. I don't know if such authorizations are commonplace.


I'll answer your title question and sub-questions in three words (then add to that): Difficulty is relative.

Noam Elkies finished his PhD in math at the age of 20. The average graduate student would probably take anywhere from 4 - 5 years. That doesn't mean Noam was a god among graduate students when he was a graduate student, and that's the reason he was able to finish his thesis faster than Joe Schmoe (though he is quite exceptional) and Joe Schmoe should just give up. Far from it. The fact that you're doing well in your master's courses is a good indicator you're well qualified for the coursework part. Working on a PhD thesis means producing original research. Producing original research means dealing with not so cut-and-neat problems like ones you'd encounter in your homework or textbooks. It means working with problems that you're not sure are close-ended, open-ended, or neither. In other words, different skill sets are needed for research in addition to the problem-solving heuristics which you've already acquired from your coursework.

Since you've never wet your foot it seems to me you have no indication of your ability to do research . So what do you do? Just go for it! You only live once as far as we know, and it seems to me that your real problem is your self-imposed doubt. Get that out of your head. Research is about staring and thinking about a problem long enough then coming up with an answer which turns out to be completely wrong and in that, the process repeats until you get your "Eureka!" moment.

You should also stop worrying about others being ahead of you. There'll always be someone faster and better than you (unless your name is John Von Neumann :-) especially in academia. A good algebraic geometer from UGA by the name of Roy Smith didn't get his start in advanced mathematics until his late 20's, after working in industry as a meat lugger. He received his PhD at 35. Over 30 years later, he's still going strong. What you should learn from him is if passion calls for it, then there should be no stopping you. If you fail at a career, then that's that. It's not the end of the world. But if you never bother to even try, then you'll never know and you'll always have a "What if?" moment.

So just to sum all of this up: Apply to a PhD program and see what happens.

https://mathoverflow.net/questions/7120/too-old-for-advanced-mathematics/45644#45644 (if you're interested in Roy's post)


Can I affiliate with a university and use its IRB to do self-funded research part-time?

I will guess that this will be difficult to do in your early career. Universities have a lot of rules and a lot of lawyers worried about liability and such. If you teach part time, perhaps in the evening, then it would be a different situation. The pay is terrible, but it does establish the relationship you need.

But note that the IRB process isn't limited to universities. There are companies who are qualified to do it for a fee.

Anyone can do research and anyone can submit to conferences and journals. It is a way to build up your credentials. You don't need academic affiliation to do, or publish, research. Finding collaborators is a bit harder, but you can manage that as well, perhaps just by visiting a local institution and opening a dialog. Perhaps you would be permitted to join a research seminar or such. And joint publication with someone affiliated avoids some of the complications.

But, as you know, the best path is to get an academic job if it otherwise appeals to you.


Research opportunities (in machine learning) for undergraduate students at colleges without good research programs

One thing to consider is research experience for undergraduate (REU) placements over the summer. Many of these are actively built on affording research opportunities to students in schools that do not necessarily have their own research infrastructure.

Here is a list of those funded by the NSF, but this is by no means all of them: http://www.nsf.gov/crssprgm/reu/list_result.jsp?unitid=5049


Is it appropriate to 'build up' your findings in a paper?

Either way could be made to work, but consider:
If the proof methods of the three are essentially the same, then the first way would be boring (possibly).
But if the second builds on the first (etc) by using different insights and methodologies, then the first way might well be superior.
Don't just consider the progression of results but of the progression of proofs and, especially, insights, that get you to the final result.
And if the latter is the case, make sure you emphasize those insights. They might (and often do) lead to developing other ideas.


In Australia, possibility of transfer from a fixed-term Lecturer to a continuing appointment

Ask your head of school, but probably not.

Usually people switch from fixed-term to continuing within their university by

Attracting a large grant which requires that they be employed by the university.
Applying for an open position at their university.

It is not usually available as part of the promotion process.  I don't know every university in Australia, though.


Understanding an advisor’s refusal of an internship

If you consider the Master's assistant position from the perspective of a paid job, it would be unreasonable to expect an employer to grant what essentially amounts to a sabbatical. Professors and school teachers are often given sabbatical leave, but Master's students are in a very temporary position. It's not a common thing, and there are no long-term benefits to the employer to outweigh the inconvenience.

If it is feasible to do so within the bounds of the research project, then it would certainly be reasonable for the professor to grant the student's request. But I don't see that the professor has an ethical obligation to do so.

Funded research is commonly held to tight deadlines – once the timeline of a project has finished, any unspent money usually returns to the funding organization.

If the professor could do so, without a negative impact on the research, I am sure that any reasonable person would grant the request for leave. The simple answer is that it's quite likely that he or she simply cannot feasibly put the research "on hold".


What's involved in reviewing an article?

Reviewing peer articles is part of a researcher's job, it's good you get to review an article, the fact you built your master's thesis on it probably means you can have a relevant opinion.

A review typically takes half a day in my experience, could be more depending on how familiar you are with the material, and you were probably given this review by a senior colleague that is part of the PC and will read your review before it goes to the actual journal.

Just read it slowly, note your "small comments" on the fly (typos, language etc separately) and then try to give an overall view of whether you liked the paper (e.g. an easy way is to make a small 2/3 line summary of each section as you understood it) and the gist of it as you see it. A review isn't much more than that. Being constructive in criticisms is a good practice

So, imho this is part of the job, and you should take the time to do it. It is experience building to review other people's papers.


What should I do when the references are not replying?

People get loads of emails and it is very natural that some take a few days to reply. Also some emails may be missed or overlooked, so you can write again and say it's urgent. Normally such things should be done with a few weeks time if at all possible because answering to such requests is not the first thing on people's list.
If all else fails, try to contact somebody else. I'd avoid to give Professor X the list of names without having an answer from them. It doesn't look good to pass on such information without being authorised. You can ask Professor X for advice what to do without telling them names. Surely if Professor X is responsible for the tight time frame, they should have some understanding.


If, where and how to talk about personal problems during master in PhD application

I suggest you say very little in your application materials. Nothing more than "My completion was delayed by medical/(or whatever) considerations, now resolved."

Just that. If you get into a situation in which you need to say more, it will likely be with a small group and you can go into detail as you see best.

They will have some valid concern that the old issues won't cause a problem in the future, so be prepared to address that.

And who can say, even yourself, what contributed to the delay. Illness, family problems, lots of things can cause stress that reduce focus and make things harder. Don't make assumptions that you've done wrong, at least not in public.


Faculty advisor is leaving, any way to turn this into a good thing?

In my opinion your friend should talk to the director of studies or whoever is in charge of the PhD program. They should explain that their situation is far from ideal and ask for advice. The objectives of such a meeting would be to:

Appear on the institution radar as somebody who may have face difficulties due to these circumstances. This can help the institution anticipate problems if they can, and could make them more responsive in case of more serious problems at a later stage.
Take any advice that can be offered: this might include suggestions to work with a particular professor or any other kind of help.
If they already have an idea of somebody they would like to work with, make a case for it: the institution might encourage the academic to take them on.
Gauge the level of attention/care given to their problem: for example if it turns out to be difficult to even talk to the person in charge, it says something about how much the institution cares about their students.

In general it's a sign that your friend should not count too much on supervision in this institution. Maybe they can turn their attention and efforts towards collaborations with external researchers related to their topic. Depending on the institution response, maybe the positive perspective would be to embrace being autonomous and having more freedom to work with people they like.


Does marrying your PhD supervisor put doubts on your PhD?

Let us call the professor A, his advisor B. Let T be A's thesis.

If T was finished before the relationship, and the examination rules of the university were complied with, then there is neither a legal nor a moral issue. Don't worry, A writing T and then sleeping having a relationship with B is a non-issue. It's none of our business.

If the examination rules were complied with, but T was not finished at the time point the relationship started, then T lost some of its credibility, and all lost some of their reputation (to an extent which is difficult to quantify without knowing the details): A, B, and the university department.  One has a perfect right to doubt the credibility of T, the reputations of A and B, and the status of the university department. Prospective fresh students are right to raise such doubts. However, if nothing else has happened or will happen, the doubts must remain doubts and one should presume innocence.
To restore the reputation of A, of B and of the department and the credibility of T and remove the doubts, the department should evaluate T independently.
To evaluate the qualification of A, a prospective student should evaluate the quality (perhaps also the quantity) of the work of A outside A's collaboration with B.

If the examination rules regarding T were not complied with (e.g., B had a conflict of interest in a sense defined by the rules), one should insist on starting the standard procedure prescribed by the rules of the department.


It sounds as though your major contribution to expanding the extent of human knowledge is in showing how the new technique can be used to confirm results (X) which were obtained by the old technique. So when defending your thesis, you better be very sure that you show how this new technique enhances our understanding of X!!

If you are unsure how to best present this, talk to your advisor. In fact, even if you believe you know how best to present your contribution,  talk to your advisor! Take advantage of his/her experience and knowledge of the field to position yourself where your contribution can make the greatest possible impact.

You need to prove that you have expanded human knowledge, so focus on how this is better than the old technique, not on how you have gotten exactly the same results. Again, your advisor should best be able to show you how to do this.


Would I get into trouble if I give out "too many" A grades?

You won't get into trouble if all your students earn grades of A.  It has always been my hope that I'd have a class with all A grades, or even all A and B grades.  It has never happened.

If you "give out" all grades of A, someone, perhaps your department chair or the committee you mention, is going to ask you to explain yourself.

Your course (presumably) has a set of learning outcomes.  You should assess your students against those learning outcomes, at a level of difficulty suitable to the students' standing, e.g. a greater level of difficulty for seniors than for freshmen.  When you've done that, the grades will take care of themselves, and if everyone earns an A, you've done an outstanding job with the course!

Edit: based on the update to the question:  For the purpose of providing useful formative feedback, you need to assign a grade to each piece of work you assess.  Doing so has the added benefit of covering your posterior.  Such grades should be assigned according to a rubric that the students have seen before beginning work.  There is a brief example of developing such a rubric here.

Even in a course such as you describe, grades can be assigned granularly and with objectivity.  If you've done that, your students will thank you and your defense when questioned by chair or committee is that the students got the grades they earned and earned the grades they got.


In what circumstances do departments permit graduate students to complete their program off campus?

This is really something that will differ depending on where you are, what field, and even who your advisor is.

For example, at my previous institution, the rule was that you couldn't work on your dissertation remotely until after your proposal date (meaning you are fairly far into your program - proposals at that institution were 2-3 years in for many) and only with your committee's approval. Some chairs could, and did, refuse.

Others were extremely laid back, and probably wouldn't have objected to skirting that rule.


Should I include papers on a PhD application if I was not the primary author?

Yes, include it. It should be on your CV also. Tenth author can mean a lot or a little, but it is still an author. In my field, with your name, you would probably be listed near first, but if your family name was Waters, probably last.
But the important point is that you are an author of anything published under your name.
And certainly don't restrict it to primary author only, though you might want to highlight those in your CV.


How do people manage recommendation letters?

No it is not rude but there is a matter of fatigue in the end. the professor might just say "enough" at some point. Usually the letters will also be fairly similar so that each is largely composed of the same text but with smaller alterations tailored to the specific job application. Another trick is to ask the applicant to write a basic text covering what the applicant wishes the letter to cover. It is then easier to use that text and make modifications as one pleases.
Hopefully the applicant has more than one person to ask for references. Writing such letters is, at least in my sphere, something you are supposed to do, unless it inflicts severe effects on other activities. Yes, it is annoying at times,particularly if the request is such that one needs to complete the letter "yesterday". Hence providing some time will alleviate the discomfort.


I got an offer from my dream graduate school days after starting grad school somewhere else. What should I do?

To be honest, you will not be spared the moral decision. There will be a number of angry and/or unhappy people if you leave, there is no way around that.
The core question is: do you know the other supervisor? Will you be happy with them? Is the added value of the other topic/institution so much more than your current that this difficult and costly decision is worth it?
Because, yes, you will burn bridges. You have now to evaluate whether it is worth it. Do not look just at the institution, but also at the topic and supervisor. They are your key factors.
Should you find out it's not the right thing for you after all, that first institution is closed to you. I do not expect them to want to take you back; it would be unbelievably magnanimous (and lucky, namely that they would have a position and would re-offer it to you) from them to do it - and risky, too.
That being said, keep in mind that, they may be unhappy, but it is your life and your future at stake here.
In the end, nobody can make this decision for you. May your decision be the right one for you.


Should I ask for permission to write an expository post about someone else's research?

I don't think you strictly need permission, but I would recommend asking the speaker anyway, out of simple courtesy.  People are aware when they give a talk that they are making the information public, and that the audience members may share what they have learned, but putting it on the Internet may speed up that process more than the speaker is expecting.  Posting about the talk without the author's consent, or at least notifying them, isn't unethical, but it is sort of "bad manners".

If the speaker asks you to wait, I would suggest you honor that request: partly out of  general professional courtesy, and partly because it isn't good politics as a PhD student to get on the bad side of senior people, especially if you work in this area.  You may be applying for a postdoc with this person someday.  I would guess that at most, they might say something like "We plan to post a preprint in a few weeks; could you hold off until then?"

As a possible side benefit, when you contact the speaker to ask if it's okay with them, they might also volunteer some other information for you to use in your  writeup: copies of their slides, further details, a preprint, etc.

If they say it's okay, then as a further courtesy, you may want to send them a copy of your writeup before you post it, to see if they have any comments or notice any errors.  Or at least send them a link when you post it, and be ready to respond to any feedback they may have.


What is the most efficient way of deducing the culture of a lab during graduate recruitment days?

I second @ff524's comment about the "key questions". Not all of them are equally applicable to each person, so decide what fits your situation the best.

Plan ahead, and try to memorize a few questions you want to ask.

Here are a few tips:

Talk to the grads in that research group.
Talk to the faculty leading that research group.
Talk to the postdocs in that research group.
Talk to other faculty in that department (but in other research groups).
Try to observe interactions between grads and their advisors, if possible.

What you want to elucidate is the following:

What are the expectations in terms of balancing fun/health/classes/research? Does your potential advisor appreciate friends/family, or is he/she more work-oriented?
What's the expectation in terms of hours/week worked? Does that seem reasonable compared to other research groups?
Do people in the group seem to get along with each other? (If not, that's a sign that there could be drama.) Do you think you could get along with the people there?
Are people -- especially grads -- competing with each other for funding? This can put a strain on interpersonal relationships, unfortunately.
Are people -- especially the faculty and/or senior grads or postdocs -- looking out for their own interests or for those of others (particularly yours)? In other words, will they be on your side and look out for you?
Are people only interested in their own work, or do they show an interest in your abilities? Do they show an interest in you as a person -- beyond your academic capabilities?
Does your potential advisor seem to appreciate his/her students?

If you're feeling really gutsy, you could ask a few more direct questions, but be careful.


Degree program changed before attending graduate school

It's possible that a grad school would have an issue with this.

In my experience, admission to a graduate program is always contingent on successful completion of the undergraduate degree.  The grad program will require a final undergraduate transcript and reserves the right to rescind admission if they're not satisfied with it.  Presumably your application stated that you were working on a bioinformatics degree, and your admission was based on the assumption that you would complete it.

So it would be a good idea to contact the grad program and explain the situation.  You probably don't want them to first learn about it when they get your transcript, and have them trying to guess what happened.

Some relevant questions:

What was the requirement in question?  Is it some critical course that they might reasonably have expected every bioinformatics student to have?
Why didn't you complete it?  Was a course not offered at a time when you could take it?  Or did you fail a required course?
If (as your question seems to say) this was a new requirement, imposed after you started your degree, how recently was it imposed?  Could you reasonably have fulfilled it?
What does your undergraduate advisor say about all this?


How to measure engagement in uncommunicative class

One thing that I've heard suggested is a "one-minute assignment": at the end of each lecture, ask students to write down two things and turn it in:

A one-sentence description of what they thought was the most important point of the lecture, and
A one-sentence description of what was most unclear to them during the lecture.

These questions give you a sense of what the students thought of the lecture, and what didn't work.


I have a lot of extra room for classes. What should I take?

I am surprised not to see getting involved in research projects on your list. At many schools, you can get academic credit for research. It is often no good for satisfying requirements, but that sounds like that's not a problem for you.

Getting involved in research is an excellent way to further your dreams, especially in getting on the track for graduate school. It can also introduce you to lots of interesting material that you would never encounter in a class.


Is it possible to participate as a research assistant as a nondegree student?

This wouldn't work for me as an employer of research assistants. Undergraduates and random people off the street rarely have technical sophistication to be able to participate in my research projects. I'm pretty sure that in most cases I'm beholden to my NSF grant terms to pay a PhD, a postdoc, or a student to do the work, since this is what we said we'd do in the grant application budget. The people may be more or less interchangeable to the granting agencies as long as the work gets done, but I believe there's more to it than that.

I don't think a non-degree-seeking person can be a/an (graduate or undergraduate) research assistant under my university's HR rules either since they must be currently enrolled as an undergrad or graduate student to have either of those titles. Also, I'm basically not allowed to have an unpaid research assistant nor am I interested in such a person. First, it's probably illegal in the US, and second, it's a bit off-puting to me that you would come, do some research, and then leave once you've gotten the publication that you think will get you into grad school. I prefer to have a deeper, longer relationship with my research collaborators than what it takes to get one good publication out the door.


Can a PhD supervisor take unpublished ideas from a student's dissertation?

A PhD dissertation is published work, not a private document. It is publicly available to anyone with a library access (via interlibrary loan or via an appropriate dissertation vendor).

Of course, if anyone (including your former PhD supervisor) uses results from the dissertation, they must include an appropriate citation. That way you get a credit for your contribution.

If your contribution is considered valuable by the standards of your field, you can write it up and publish it in a refereed journal for better visibility (compared to the dissertation). You can also upload your thesis on an institutional repository or arXiv.

My advice: do not waste time arguing about ownership of ideas. It will not help your career. You had one idea that was good enough to interest people; make more!


Around what percentage of universities require(d) Ancient Greek and Latin for admissions?

I don't think any "major" or "top tier" universities in the USA have any language requirements other than English. Even then, you don't really have to speak English as much as be able to manage HW's and exams in English.

St. Johns would certainly appreciate it but most courses won't read classics in their native language.

My friend is finishing a PhD in classical history at an Ivy League program and he was unique in his knowledge of Latin from high school. I'm pretty sure 0 colleges require Latin or Greek.


When submitting PhD proposals in the humanities in the UK, are students expected to have already applied for funding?

The proposal and the funding are not, tightly, related. Funding status must often be determined, as the applicant has been admitted to the program, whereas the proposal preparation would be postponed up to the determination of the exact path of the research and desired denouements.

Most of the Ph.D. positions and the available vacancies in GB have been, considerably, defined under the aegis of the pre-planned funding. In the case of the engineering and industry-driven positions, the applicants could be sure about the financial support from either the department or supervisor's grant. The humanity-based programs would also be funded. The difference is the more restricted positions within the realm of humanity-driven program...

As the financial packages in GB would be presented by a wide range of resources with different policies (e.g. just for women, dedicated to the domestic students, defined for students of a specific country and so on), the admitted applicants are usually supposed to apply for the packages, does which fit them. However, there might be some universities with centralized system of scholarships that supporting policy for the Ph.D. candidates is always based on a fixed roster of the resources.

All in all, one might conclude that the close attention to the application procedure within the website of each program should be taken into account, case by case. Because even if a typical probabilistic standard procedure would be suggested, there might be some exceptions in your way, will which not be accounted by that standard and may lead to losing that case.


Letters of recommendation only from employers and managers

I have only been an admission committee member in the biomedical field so I cannot say too much about your field. For us, here are the concerns.

Generally, the pattern we have seen is applicants who returned to school after a long period working in industry face a harder time. A few factors include age difference (harder to find study partners), technology gap (unfamiliar with online learning platform or software), and anxiety related to assessment (examinations, tests, etc.)

While I understand it's a professional degree, a professional degree is still a degree given in an educational organization. There will be assignments, due dates, evaluation, course load management, study skill application, group work, etc. It will not be free of academic features. Admission committee would like to know if the applicants are ready for that.

If you have had a strong relationship with any professor I'd recommend go get his/her letter that would highlight your abilities as a student, but too bad you haven't had one or it may be too long a gap. This is not to say you should give up one strong co-worker's reference letter in favor of a weaker one from a former professor. Instead, a second best approach would be to ask one of your reference persons (preferably the one who trained you or someone who holds an adjunct professor title elsewhere) to highlight your good properties as a learner, and (if he/she also teaches) provide an estimation on your ability to thrive in an academic environment.

Another possible step to take is to ask the admission/recruitment staff. They can perhaps also let you know what the general patterns are and if your combination of reference letters would raise a red flag.

Good luck!


How to confront advisor about the expectation that I will support another student's project for extended period of time?

Has anyone had success confronting their advisor about this sort of thing without being too hostile?

Fundamentally, I wouldn't view it as a confrontation.  If someone is doing something unethical or abusive, then confronting them could be appropriate, but it's not clear that that's the case here.  Instead, I'd approach it from the perspective that you'd like to learn what your advisor expects, his/her reasoning and motivation, and how much flexibility there is.  Right now, you are unsure whether the amount of work required would be a month or a semester.  That's a very reasonable thing to seek clarification for, and there are plenty of other natural questions.  For example, how should you deal with any interruption to your primary work?  Is there flexibility if you're at a particularly crucial or delicate point in your current project?  Will your advisor help make sure it doesn't derail your work or delay your graduation?  You could also ask about the motivation.  If doing this doesn't seem valuable to you, instead of starting with complaints about that you could ask about structuring things to ensure you got valuable skills or experience out of it.

If you take this perspective, I don't think it will come across as hostile.  You're just asking reasonable questions about what's involved and how it can be handled smoothly and productively.  I hope the answers will be reassuring.

Of course this may be fruitless: your advisor could be a control freak or jerk who won't respond well to friendly questions.  However, if that's the case you've got worse problems than just this issue.  I certainly wouldn't start with the assumption that a confrontation is the first step.

It's also worth carefully thinking through why this arrangement seems unfair.  As a mathematician, I have no experience with this style of research, but it doesn't sound unreasonable for the sort of lab in which students are assigned projects.  You would be broadening your research experience, and your contributions would be recognized with authorship (but not first authorship since the senior student would have contributed much more to this paper, the same way you'll be first author on the paper that comes out of your main project).  This sounds potentially worthwhile, so you need to articulate more clearly what's wrong with the particular situation you face.

If this is far outside the norms of your field, then I hope you'll be able to convince your advisor to do things differently.  Otherwise, I'd just accept that you and your advisor don't agree about everything and, within the overall constraint of how the lab is run, focus on fine-tuning things to fit you better.

  In fact, I feel like by bringing it up I could only make things worse.

This is the part that bothers me the most.  Maybe you are just worrying too much, but it suggests something's wrong.  Perhaps with how you tend to bring things up, perhaps with how your advisor responds to reasonable concerns, perhaps with your overall relationship with your advisor.  Whatever the cause is, this is something worth trying to understand and fix.

In response to the "update" on the original question": I don't know enough about your research area to say how unusual or inappropriate that is, but it does sound worrisome. Do you have a mentor other than your advisor to discuss this with? That could be helpful for determining whether it's a major career danger or just a frustrating but manageable situation.


Writing a recommendation for highschool student

You're giving the student an extraordinary experience compared to her fellow applicants, so it's natural for her to ask you for a letter explaining that experience and your opinions of her work.  And I think it's very reasonable to provide one.


One of my student researchers is likely falsifying some results/data. What are the consequences?

You have suspicions, but the evidence, as you sketch it here, is circumstantial. You need hard proof. Then you can (and must) act.

Falsifying data is a capital crime in academia. It wastes time, possibly years of other people's work. Don't let it get through. This person, if they indeed falsified data and would come through with this, will taint anybody and anything they had to do with - you, your group, your department, your university. Their results will be worthless, and so will be the degree you bestow on them.

You would feel sorry for that person if expulsed; but how sorry would you feel for a person who for 2 years will try to reproduce this grad student's results and fail for no fault of their own? How about their life and career? An honest mistake is one thing, but faking data? You are feeling sorry for the wrong person here; you'll spare the guilty and will let the innocent being impaled? A grad student is sufficiently mature to know better than to produce "synthetic" data.

How about the person abetting such a fabrication? Frankly, if caught, depending on the power structure that person may get away with a milder penalty "for not knowing what was going on", but in principle they should get the same, if not a harsher penalty, because they certainly cannot claim they didn't know that this is wrong; and they know the repercussions.

How common is it? Hard to say, but there were a number of large scandals (Jan Hendrik Schoen comes to mind), there is probably a halo of minor such attempts. From my own anecdotal stock: I once heard the conspiracy theory that spectroscopists would intentionally introduce "innocent" wrong factors into published formulas that could be interpreted as honest mistakes to prevent competitors from progressing. I didn't believe it, however, once I had to use such a formula from a paper, and to be satisfied I rederived it and some of its "brothers" myself in a tortuous process taking several weeks; lo and behold: I found that one of them had an integer factor wrong. It goes without saying that I have no real reason to assume it was intentional, but the conspiracy theory still lodges in the back of the mind.

Bottom line: if he really fakes data, letting this happen is not an option; but the evidence must be carefully and (important for fairness to the accused) confidentially vetted to establish whether this is indeed the case.


What proportion of course material mastery should we consider is "passing?"

TL;DR: As much as a student would need to know in order to succeed in their career.

I think part of this answer will be subjective - does a student even need to master course material to pass, or do they need to be familiar enough with it to know how to re-learn it later in their career?  I come from a STEM background - I know how to do calculus, but if you asked me to come up with a Taylor polynomial right now off the top of my head, I'd give you a blank stare.

In my opinion, the goal of any class is to teach familiarity with the subject at hand.  No student will ever use 100% of what is taught in a given class - their career will dictate what they need to know.  As they spend more and more time working in a particular field, the knowledge that is important will stay with them, and the knowledge that isn't important will be set aside - not entirely forgotten, but not readily accessible without review.  The point is - they still know how to re-learn the material; they just don't know it off the top of their head.

With that in mind, I argue that the proportion of course material mastery that we should consider as "passing" is however much is needed to ensure that a student could, given a reasonable amount of preparation, re-learn the material at any point later in their career.  That amount will vary from class to class, and it's worth remembering that some skills will carry over and be reinforced from class to class.  To my mind, this means that fundamental skills - calculus, introductory classes, writing courses - need to be held to a higher standard.

As for incentives for professors - there's a variety.  For one, if you want to work at a high-caliber institution, you're going to want high-caliber students.  This means pushing them to learn and master more of the material than perhaps a professor at a not-so-high-caliber institution might care.  For another, there's an element of peer pressure involved: if I teach my students poorly, and don't require them to learn enough of the material, then my peers will have to pick up the slack in later courses.  That reflects poorly on my teaching, and it means that I may have to do the same thing with these students in later courses that I teach.

So what proportion of course material mastery should we consider is "passing?"  Whatever is necessary for a student to (1) be able to relearn the material in a reasonable amount of time and (2) be able to retain the core concepts for use in later courses.


In general, I would treat software documentation depending on how it's distributed.

If it's published in book form, then it should be cited as a book. The version number goes where you would put the edition, and the company that manufactures the software is the "publisher."
If the manual is distributed electronically, then you should cite the website from which it is obtained as the "source."
An exception to this is if you are asked in the documentation to reference a specific work (for instance, a research article, or a website) when citing a code. Then you should follow the specific guidance provided.


Correct form to tell and write the degrees I hold

If this is for formal use then state it exactly as it appears from your university and give any translation that is logically correct. But BS in Physics or BSc (Physics) or Bachelor of Science (Physics) or similar would all be universally recognized in the English speaking world.

For informal usage (i.e. no legal implications whatever) then either of your suggestions would be fine or something such as I wrote above.

For extremely formal situations, use what the university uses and let the reader translate it. Probably name the university, as well.


How to look past the fact that I probably have chosen the wrong research area?

Don't think of yourself as stuck in a research area. You are starting to gain some independence and can also start to morph your research into any area you choose. Over your career you might do this multiple times, actually.
Use the post doc to start to explore the areas you'd rather work in as much as you can.
Staying with your doctoral advisor might not be your best move, though with coronavirus it may be necessary in the short term as you note.
Your PI for the post doc might be able to give you some freedom here. But even if not, increasing your reputation in one area can lead to more freedom to move and change your direction.
Your career needn't be an arrow.


Asking for a letter of recommendation after only some days of collaboration

The outcome of such things is unpredictable, but you might do well with this. But you can have a conversation first with this professor to see what they think of the idea.
Letters of recommendation are best when they make a positive prediction about your future success. It may be that this professor has already formed such an opinion and would be willing to express it formally.
You can ask, of course, but have a conversation first, getting their opinion on your future and how you can optimize it. A letter can flow from such a conversation.
Note that this is a US perspective and a personal one.


Can I change my academic affiliation after a conference paper is accepted but before submitting the camera ready version?

According to your comment, you are asking whether the conference will allow you to change your listed affiliation between acceptance and submission of the camera-ready version.

In my experience, the answer is yes. I have done this several times without issue. If there's no way to do this by yourself in the paper submission site, you can email the chair and ask him/her to update your information.

Whether you should use your new institution as your affiliation just to get them  to pay for your expenses is another issue entirely, which you have already asked about in another question.


Is solving all of the exercises in a textbook a good idea?

It depends enormously on your personal objectives, apart from your personal predilections. For example, if a significant goal is to advance your understanding of mathematics, then obsessing over exercises (many of which are contrived busywork in undergrad textbooks, and sometimes in grad-level textbooks in the U.S.) is a dubious investment of your personal resources.

For one thing, apart from the articiality of some of the exercises, many of them will be semi-incomprehensible if you've just read the chapter they appear after... but obvious after you've read further! A significant reason for this is that mathematics has developed with various goals in mind, so that the most important enduring concepts and facts refer to important phenomena... not just to some artificial choice of linear logical development as is the common style in textbooks.

On another hand, if you do not aim to be a professional mathematician, or if somehow you have a lot of spare time, sure, why not do whatever you want? Indeed, another common trap of studying mathematics is being too obedient about following some syllabus or textbook, as opposed to following one's own curiosity and interests. It is subtler to parse the situation that your impulse is to do all the exercises... :)

Another practical point is that, at some point, probably soon, unless you severely restrict what books you look at, there's no way you'll have time to do all the exercises in detail, even if you are a whiz-kid. There are too many, and sometimes they are prankish. For example, the "exercises" in Atiyah-MacDonald's "Commutative Algebra" (a misleadingly slim volume) are mostly "theorems" one would find in other books on the same topic.

And, then, there's the point that novices' "solutions" to difficult exercises are often severely suboptimal, even if "successful". Sure, it's good to think about issues, but, at the same time, you'll be able to approach those questions far more wisely later (if you still care, and the things haven't become completely obvious anyway!).

But certainly no one is "required" to do all the exercises, despite some propaganda on the internet. For that matter, it is probably not optimal for most peoples' circumstances and goals. Still, taking an extreme stance, maybe the world will end tomorrow, and if you want to spend the evening doing exercises that you find enchanting, I'd be the last one to try to discourage you. :)


Change grad school and get accepted. Worry that no prof in the new university wants to work with me

Your admission to the new school was decided upon by members of the faculty of the department to which you applied. So it's unlikely that you'd have been admitted without there being at least one or two people in the new department who think you'd fit in and would therefore be interested in working with you.

If you still have doubts, there is an easy way to answer the question. Just ask the professors you're interested in working with if they are likely to have positions available when you arrive, and if they'd be willing to consider you for them.


For an undergrad, which is more important? LoR or publication

In the US, good letters of recommendation are a must. Research experience, especially resulting in publication is definitely a plus, but since it is still a bit rare, you are probably already ahead of the curve there.
The "problem" with undergrad research is that, given the time (and maybe money) constraints it is hard to reach a conclusion on anything that is very significant. In research, you don't know the answers when you start and you are looking at the unknown. There is no schedule that you can apply to actually reach finality unless the problems are rather straightforward. The time between writing the paper and publishing it can also be long and indeterminate if the journal is reputable. Conference publication is a bit more time predictable, since the conference will be held on a certain date, but if you miss a deadline, the next opportunity might be a year away.
If you are doing something hard, then my recommendation would be to keep at it. People will, I think, reward you for that even if you don't reach a conclusion, provided that the advisor can praise your efforts and predict your future success.
I think you are already in a good position on this point, though doctoral admission is dependent on many things beyond the two you mention. But, in the US, letters are essential.


Optimizing conference paper solution to be eligible for Journal article

Let the editors and/or reviewers decide whether the new contribution is sufficient. Mention that you extend previous work. It may be wise to be explicit about the novelties with regards to the previous work in the cover letter.

In case the original paper was published in conference proceedings (e.g. not just a talk), it is very important that you cite it. When you do that, there can be no claim that you are attempting to recycle existing material without anyone noticing (self-plagiarism).


I don't think it's so much that universities want their grad students to have attended other schools for undergrad, it's more about achieving a broader experience for yourself which will be especially helpful after grad school.

In my experience, professors (and departments and universities) generally want to attract the best students they can for grad school. The top students in an undergraduate program may be heavily recruited for graduate programs at the same university, especially if they have been participating in research with a professor and he/she is impressed with their work. It can be difficult to judge applicants' grad school potential based solely on application materials and a professor having personal (positive) experience with a student can lead to very strong recommendations and near-certain acceptance.

On the other hand, if you should choose to go to graduate school, it is in your best interest to choose the best (for some definition of best) situation for you. I think this is where it's often beneficial to change institutions. Attending multiple universities broadens your contact base, exposes you to new resources and ways of doing things, gives you perspective on multiple departments, and better prepares you for future moves to new locations/institutions/etc. I think that the importance of developing a broad network of contacts for your postgraduate career is incredibly important and changing institutions for different degrees is almost guaranteed to help you there.

In your case, where you've done an internship at the school you're considering, I would not worry much about potential negatives if you decide to apply there for graduate school. I think an internship is a great way to get a feel for the institution and the professor. It's also a potential way to get yourself a very strong recommendation and an "in" to the department.


Would it be better for Ph.D. graduate school admissions to compress my undergraduate years for a Master's Degree?

There is no rush.

Admissions won't give you bonus points for finishing early, so you're having to compete with people who took more time on the same amount of classes.

From my personal experience, I rushed and completed my undergrad a year early and my masters a semester early, but it didn't gain me much. In fact, my GPA took a beating.

Also, I wouldn't call it late if you're completing the masters in one additional semester, that would still be one semester early since it sounds like a 5 year program (4 + 1).

If you want the best chances of getting into a top school: take your time. Either graduate with your bachelors or spend the two additional semesters getting your masters while attempting to get good letters, some research experience, and maybe even a publication. Trying to rush it further isn't going to help and gives you less time to do the important stuff for admissions (e.g., research and letters).


Should you include your collaborations in your CV?

For the main question, you may to include the list of collaborations in your CV. Although it could be inferred from your publications, not all collaborations have the need to be published, especially in the case of classified projects such as the ones funded by your nation's defense research department.

From the arguments from the comments, it is clear that co-authors are considered to be collaborators. In some cases, all of your co-authors may not hold considerable contribution and certain collaborators you wish to show are not in the list of co-authors of your papers. Hence, you may include a Major Collaborators list in your CV and cover those whom you think are important collaborators you have worked with.


As a Ph.D. student, should I spend time reviewing papers?

An important part of an academic career/CV is service. Reviewing, editing, hosting conferences, ... falls under this category. So yes, it is important.

You seem to consider it to be a potential waste of your precious time. This is false. Depending on your field, reviewers have earlier access to new work than others which is always beneficial.


Can political issues between Iran and USA affect me?

I think that as far as paperwork goes, your Australian citizenship will ensure you have very little trouble.

Regarding racism, I think the point that Boaty made above was that your explanation about your being Iranian but Bahai will really not change people's attitude or conduct towards you. Reason does not work with racists or bigots.

On the positive side, you will find many people (especially in academic contexts) who will be welcoming and non-judgmental.

The extent and frequency of the racism that you experience will partly be a function of how identifiable you are as a minority. If you have a skin color that lets you "pass", do not have a beard and so on, you will attract less of it.

Similarly, geography is an important variable too: If you are in a small town in the middle of Idaho, you are obviously more likely to be treated with suspicion and hostility than in Berkeley, CA.

Overall, my advice would be to not worry about it and have a great time.


Professor not responding to LOR email after initially agreeing

I'm not sure if I'm reading too much into it.

I think you are.

My guess is that Professor #2 received your email, saw that it contained information for your letter, remembered that he had already told you he would write the letter, and set the email aside, planning to read it in detail when he got around to actually writing the letter.  He probably didn't read far enough to see the part where you asked him to acknowledge the email.

So, if you're concerned, simply send a second email:

  Dear Dr, #2,

  I just wanted to make sure you had received my email of August XX with the information for my letter of recommendation.  Please let me know if it looks okay, or if there is anything else you need.  As a reminder, the deadline to submit the letter is October XX.

  Thanks very much for writing a letter for me!

  Sincerely,

  Lily

As to your other question:

  I accidentally called this second professor "Professor" in my email even though he's technically a lecturer so I always address him as "Dr. So-and-so" in my emails.

Don't worry about that.  It happens all the time and most professors eventually just stop noticing.  It's certainly not the kind of thing that would offend someone so much as to affect their decision to write a letter.


Citing (or not) a flawed or incomprehensible paper or preprint

in what follows, I'm assuming you're correct in your assessment of the flaw.

The first step is to communicate with the authors. If you mutually resolve the flaw (they accept the mistake, and/or redo the proof), then you either cite the corrected version or mention when citing the paper that it has a flaw and cite your discussion with them as a personal communication.

If the conversation with the authors stall (they're nonresponsive or shift the goalposts), then you can cite the paper and briefly outline the flaw in an appendix (or if you're space constrained, post a brief link to a document available elsewhere). I'm not entirely happy with this last idea, but I can't think of anything better in a space-constrained scenario.

I don't think that incomprehensibility is a good reason for not citing, or citing negatively. You'd have to narrow down the incomprehensibility to something in particular that the authors are not clear on (a definition, a set of cases, or something like that). Again, this should be a last resort if the authors are not responsive to contact - ideally, matters of lack of understanding should be resolved between the authors without it making it into the paper.

post-caveat: my answer deals mostly with theoretical papers. In more applied works, it might be trickier to determine whether something is "known to be incorrect" or "not known to be correct".


What should I write in the experience section of CV?

In the experience section of the CV, there should be (relatively) relevant experience to the job/internship you are applying to.
It is not clear what you want to write in the experience section. Of course, you shouldn't have a section labelled "experience" and then nothing in it. I would also advise against putting irrelevant experience in this section (e.g. babysitting 5 years ago) which would have the same effect to me.
Writing "internship in [place] on [topic] cancelled because of coronavirus" would not feel right to me neither, especially if this is the only item in "experience".
Keep the CV short and simple and then address in your cover letter the fact that you didn't do an internship at the end of your Bsc degree because of the coronavirus.


What do I do if a professor at a foreign university doesn't respond to my emails?

Professors directly teaching might have some obligation to answer your email (some university have quality of service policies, ensuring that students receive feedback within a given number of working days), if it's related to their teaching.

Professors from partner universities might fall under the same obligations, if there is a mutual agreement. However, professors from other university have no obligation whatsoever to answer you.

Professors are usually very busy, among other things dealing with their own students, they might not have the time to deal with other students. If you are asking about a proposal and you do not receive an answer, you should assume by default that they are not interested. There is no much you can do, apart from contacting other professors, or asking your own professors to contact them.


Copied from this question per Franck's request: the NIH recently examined where people with a biomedical Ph.D. ended up. The results of their survey are discussed here.


Definitely, but, as a CS grad, then later, an MBA grad, I do have to say that the MBA degree won't help in the tech world, at all, unless you're looking at management opportunities or starting your own business. Getting a Master's degree part-time does impress most employers, however. Since it sounds as though your enjoy academic challenges, go ahead and give it a try, especially if there's reimbursement for tuition. But frankly, you would just be doing this for your own personal development; there's just not much out there right now for MBA's, unless you go full-time to a national top-20 program.

I've found that a Master's in CS is no better than a Bachelor's, so if you're thinking about a CS part-time Master's degree, while you're working full-time in tech, skip it. I once worked for an medium-to-large tech employer (about 2,500 tech staff) who was dead-set against MSCS grads, even at the same pay, since they were afraid that the MSCS grads would expect faster promotions (and frankly, be much smarter than their boss). So, it seems that, in recent years, one has to step up to the PhD level in CS to get a big career boost.

Anyway, with your ASBA, you will not likely have to complete any prerequisites, which are just UG survey courses in Accounting, BA, Finance, Econ, etc. I'll say that if you have a CS BA, you've got the math chops, also, you have the BFA, so you can communicate well (extremely important in B-School...watch old reruns of the TV show "Paper Chase" to get an idea of the MBA classroom, since it's similar to a law school class), so you will likely do very well. I would caution, though, to try to attend the best program in your area. No one hires or promotes from weak programs, though you can get into a B-School PhD program from one, from what I've heard.


Do I need to do revision on my accepted paper?

I would interpret "accepted" as "accepted in its current form", i.e. you do not have to make any changes.  But in order to be sure, ask the editor or program committee.

If you want to make changes based on the reviewer's comments, that is most likely possible; but again, you should ask the editor to make sure it is okay, and to find out when those changes would be due.


Optimal reference letter writers for permanent positions: Senior experts or younger, more active researchers?

Which one can write a recommendation that is specific about your qualifications and abilities?

A brief anecdote: I was on a search committee where someone had a recommendation from a big-name person in their field, someone widely known outside of their field. At first glance, the candidate's personal connection to this person was impressive. However, the letter body was a single paragraph and light on detail. OK. We had to read the other letters to get the detail we wanted.

A big-name recommendation may get the attention of the hiring committee reading your applications. However, because they're ultimately evaluating you, the level of detail in that letter will matter more to many evaluators than the name at the bottom. Someone still up-and-coming may not initially grab the attention, but if they write a more specific letter, that may ultimately be to your benefit. So if you have two open slots for recommenders, include both! If you're choosing between one or the other, it comes down to weighing relative risk, since not every hiring committee will respond in the same way to your set of recommenders.

To give an idea of a typical balance of letters, I defer to Karen Kelsky, who runs the advice site The Professor Is In. To someone who asks about the mix of recommenders three years post-graduation, she says:

  In the end, a balanced roster of letters at three years out will include your advisor, a well-known person who knows you as a colleague or collaborator, a senior colleague from your department who will provide a detailed teaching reference, and—assuming you have space for four letters—one of your other Ph.D. committee members who has also stayed up-to-date on your post-grad-school life.

Note the mix. "A well-known person" may well be one of your "big names," but could also be someone up-and-coming. A "senior colleague" may be a "younger, more hot-shot researcher" in your department, or a "big name" approaching retirement. As long as these people are a mix of people familiar with your work, debating the relative stature of the "well-known person" or the "senior colleague" is small change.


How can I apply to be an adjunct faculty?

What are common steps required to become an adjunct faculty?

Ask your department chair.

Where can I find additional information (e.g. would a university-wide policy be given at the university website?)

Ask your department chair.

Assuming I speak with the department chair, what should I say?

"I'm interested in becoming adjunct faculty.  What's the hiring process?  Why yes, I do happen to have my CV with me."

How could I sell my case, other than my (demonstrated) ability to obtain funding and (undemonstrated) ability to be an advisor?

Ask your department chair.


Does choosing not to submit GRE scores look bad (particularly for CS PhD programs)?

I would assume, but can't guarantee, that if they have a policy that GRE scores are optional then the policy would preclude assumptions about missing scores. So, in that sense you are probably safe.
But, you can hardly control for what an individual committee member might have in the back of their mind.
It might even be possible to learn more about the policies used and how interpretations are made in such cases.
Since some places now make them optional, some students choose not to take them, I also assume. And in the US, at least, admission is based on a wide variety of things, of which test scores are only one.


What can a student who is already studying hard do to improve low grades?

Don't panic. The fact that you're still enthusiastic about your studies suggests to me that you can likely fix the problem, whatever it is.

If you're having trouble with just one or two of your subjects, then there's probably a gap in your background knowledge. Try to figure out where that gap is. Right now it may feel like everything in those subjects is difficult, but I suspect if you look hard, you'll find out there's just one or two small gaps in your knowledge, and that's something you can remedy. Perhaps you can take a lighter course load next semester to give you time to focus on the areas you're having difficulty. Once you figure out what the gaps are, you could either take the appropriate course, or teach yourself. This strategy may delay your graduation by a semester, but it could be worth it.

If you're having trouble with most of your subjects, then I suspect you're not studying very efficiently. You may be working hard, but not using your time well. Unfortunately, I don't have specific advice on how to improve your study habits, but there are lots of resources available for this kind of thing, and others here may be able to point you to those resources. Again, it might be worthwhile to take a lighter course load while you practice your new study habits.

Talk to your student advisor about your problem. If you think it's a gap in your foundational knowledge, t may be worthwhile to pick one problem that you found particularly difficult, and ask the instructor (during office hours, not in class) to go through it in gory detail with you to help you figure out where your knowledge gaps are.

Also, there is probably a student centre or something like that at your school, where you can get advice on how to improve your study habits.


What to do when you notice that a value in your paper is wrong, once it is accepted but before it is published?

This is not a major revision. Just change the value in the final version. (And explain to the editor in the cover letter that you are correcting a typo. A misplaced decimal point is essentially a typo.)

You are not misrepresenting yourself in any way. Because you're explaining the change in the cover letter, you are giving the editor the chance to reject the paper if they deem the changes are big enough to count as a "major revision". However, any editor that rejects the paper for that reason would have to be totally insane. Typos get fixed in the final version of papers all the time.


Just graduated bachelors comp sci. Didn't get into MS. Confused what to do

Get a job. You write that you have really low confidence, are really bad with interviews, are socially awkward, etc. These are not reasons to not get a job. The point is that even if you had been admitted, you will still have to get a job after you finish your MS degree. Since you will have to face these demons eventually, you might as well do it now. These things may be scary, but they can also be conquered (see Workplace.SE for more advice). It can even be a blessing in disguise - you might decide that you'd rather keep working than go to graduate school. Remember also that the longer you wait, the less employable you become.

You could take a gap year also and do all the stuff you mentioned, but you would be spending money without earning it. That is not sustainable. Unless you are independently wealthy, you would be burdening your caregivers for an extra year. Your caregivers are likely much older than you (i.e. they need to think about their own retirement). Meanwhile you'd be spending one of the best years of your life on things with uncertain long-term benefits. Is that responsible behavior to you?

You can't postpone growing up forever. Get a job.


What criteria should be used to shorten the list of references?

Reference limits aren't typically literally there to limit the number of references, they are there to limit the length and breadth of the Introduction and Discussion.
Rather than targeting specific references, look whether there are intro/discussion (I'd start with the intro) sections that aren't really needed, or can be consolidated to a brief statement and citation of a review. Probably if you are going as far as citing news articles you have too wide a view in the introduction.


You should do whatever you or your institution would ordinarily do for a student who brought a doctor's note after missing an exam. You are not the student's doctor and the cause of the student's illness is completely irrelevant.


Submit other people's code together with a paper

I don't think the fundamental issue here is how to submit the code, but rather how to give credit in the paper.

How did you describe the code in your paper?  If your experiments use other people's code, then you need to indicate this explicitly and give them credit.  Even if the author is anonymous, it's important to indicate that you are not taking credit for it yourself, as well as to indicate where readers can obtain the code.

If you have already dealt with this in the paper, then you have no problem when it comes time to upload the code for review, since the reviewers will already know exactly what to expect.

If you haven't dealt with this in the paper, then you have a problem and will need to revise the paper ASAP.

As for whether it's from an untrusted source, you'll need to be upfront about this.  If you can justify why this is a reasonable choice (for example, you've checked the code reasonably carefully), then you should do so.  If you can't justify it in a way that reviewers will accept, then you have a problem, but you shouldn't try to cover it up.


I would reach out to the instructors of the classes you enjoyed the most and put a good effort into, regardless of grade.

As an instructor myself, I have written recommendations for students who have and who haven't received straight A's - my main requirement for writing a recommendation is can I see this person succeeding in the position I am recommending them for? If not, I let the student know that I am not the right person to write the recommendation for them.

I say reach out to your instructors - the worst they are going to tell you is no.


At the beginning of PhD research, how to balance independence with satisfying my advisor's expectations?

Is this concern a normal feeling?

YES.

  For the purpose of this literature review, should I just follow where the research takes me or should I change the focus of it and just try to please my advisor?

The correct answer is neither.

Given that this is the beginning of your PhD research, you haven't yet developed much of a collaborative relationship with your advisor. This is the time to start.

Consider your advisor's initial suggestions as you would any advice from someone more experienced than you. (Even if your advisor is not an expert in machine learning, he/she does have more experience than you in developing promising research ideas that are suitable in scope for a qualifying exam - don't underestimate that expertise.)

That means you should definitely start out along the path your advisor set out for you. (Unless you hate it - in which case, go set up a meeting with him RIGHT NOW and tell him your concerns.)

But, that doesn't mean you need to follow his instructions to the letter. If, somewhere along the way, you are inspired to follow up on a particular idea, don't reject it just because it's not exactly what your advisor told you to do. Part of what's expected of you is to come up with ideas of your own.

If you have an idea you'd like to follow up on, do a little bit of work to verify that it's not a complete waste of time, and then bring it to your advisor and ask for his advice. He/she may explain to you why it's not advisable to pursue it (e.g., maybe it's not appropriate in scope), or suggest pursuing it further after your qualifying exam, or maybe your advisor will be as excited about it as you are.

Whatever the end result, make sure to communicate honestly and often with your advisor. Especially at this early stage, it's a good idea to check in now and then with your progress and make sure you're on a path that's heading somewhere good.


Is it okay for the author field to contain names of research labs?

I have seen labs signing papers in cases of very big collaborations. If that is how it is cited in the journal, you should adjust your bib file like so (thanks to Federico Poloni for the fix):

Author = "White, R. R. and {West College Child Development Laboratory}"


Can research breadth be a downside when applying for doctoral positions?

You could say something like:

"I've done a pretty wide range of different things, trying to find out where my true passion lies. Getting multiple masters degrees shows that I'm not a dilettante, I get stuff done. And it's been an enriching experience, letting me see the connections between different fields. But after long consideration I've decided pure math is what I want to settle down on."

And it has the virtue of being true (from what I read in your question).

Consider what a professor might think, while reviewing two candidates, one pure math straight up, and you who's tried several different things and finished them.

The pure math student might have a lead on you in pure math.
You've demonstrated persistence and an ability to get things done. Likely, you will also get a PhD done.
You've shown that you're mentally flexible enough to master multiple different subject fields.
The math student might at some point decide he's not seen enough of the rest of the world and worry if staying cocooned in pure math is really what he wants. You on the other hand have tasted the various forbidden fruits and decided this is really the one you want.

Just on the surface like that, you look like a candidate worth interviewing.


How to stop hopping the learning chain and actually begin somewhere?

Dan's answer is very good, and I want to add one more point:

Accept that on the first pass you will not be able to fully understand the topic. Appreciate that there are decades and sometimes centuries (for the math, at least) of research supporting the topic you're learning. Thinking you can "get to the bottom" of it in a few months, let alone a week or two, is not realistic. Choose a topic and try to understand that as much as possible. Keep notes on other interesting topics along the way, but don't get distracted by them; just accept them as assumptions as this point and move on. You can get back to them later.


In CV, mentioning of a report that summarizes the postdoc research without publications?

I doesn't sound to me like it should go on the CV. I'd say that if you're applying for jobs you'll probably get to recycle some of that material for your research statement, but it seems weird to put that piece on your CV.


Length of Supporting Statement to Faculty Position application

I would not refer to what you are writing as a statement. I would say it is a response. Responses should be as long as they need to be, but not longer.

If they have given you a person specification with 15 points, and ask you address every point, then, yes, your response is going to be long. There should be no need to guess on this. They have asked you to be thorough so you should be thorough.

While it is common for companies to use person specifications to ensure they find a proper match for a position it is rare for me to see someone use it in the manner you describe. However, it does not sound crazy, just like they want to really be sure that they are getting all the information they need, and they clearly want to be thorough. In the end, the goal of the person specification is to make sure you eliminate, as early as possible, those people who are very likely to be a poor match for the position/organization. If you can respond appropriately to each point, then you are much more likely to be called for an interview. So don't leave anything out that answers their questions.


How to handle rude and distracting fellow graduate student who sits in the same office?

A friend once told me that people take from you exactly what you choose to give them. In other words, this person manages to distract you because you let them. Similarly they manage to annoy you with their rude behaviour because you let their insults get to you. Therefore, I am going to suggest you a nice change of approach, rather than a change of office.

IMHO the best way to tackle distractions is to ignore them. My experience shows that a large pair of noise-cancelling headphones coupled with a focused look that never leaves whatever it is you are doing, work miracles in this case.

Whenever I need to focus and lock myself in the zone, I gear up and ignore everything that happens around me. If people ask me questions, and I actually manage to hear/see them, I tell them, swiftly and politely, that I'll be with them once I finish whatever it is I am doing. Your body language is extremely important while doing so. You want to make sure that you show that you won't be leaving what you are doing to deal with them, because you deem that what you are doing is more important. For example, I don't remove my headphones to answer, and go back to my task straight away. In addition, once you adopt this technique, be democratic and use it with anyone and not just this particular person who distracts you.

Make sure that you show that you are actually focusing on work rather than on leisure. Human psychology 101 suggests that if someone sees that you appear super-concentrated whilst in reality you are browsing social media they will feel allowed to disturb since they will think that you're not actually working. You have the right to not be disturbed whilst you are on a break, however the fact that you are taking a break implicitly says that you are free and can be disturbed.

Interestingly enough, the ignoring technique also works for rude behaviour and insults. Nothing clips one's wings more than instantly getting the feeling that one's behaviour has little or no effect. For your own sake, I'd suggest you begin by ignoring the rude comments that hurt you. This will not be easy at first, but you'll feel the benefits as you get better at it.

Now, nobody should be forced to feel like you do. What you describe is prototypical bullying. Bullying should have no place in life, let alone academia. The steps I would follow would be to begin by talking to this person telling them you would like them to stop with their rude behaviour. Although they might be joking you can't seem to tell whether that is the case, and think that the problem will be solved if they stop whatever it is they are doing.

After talking to them, wait some time. If the behaviour persists then escalate the complaint to your supervisor, the team/department head, or whomever you think has the authority to deal with this. The important thing is that you remain calm and polite during your interactions with your colleagues. Last thing you want is for others to accuse you of being rude.