Low Undergrad GPA but 2 years Lab experience since graduating, How do I know where to apply?

I've been working as a research assistant at a fairly reputable lab for about 1.5 years

This is great, you've got actual experience working in a lab.

  By graduation I managed to raise my GPA to a 2.85

And this is going to be a major stumbling block for an admissions committee.

So far, you've done all the right things to get your academic career back on track.  The question is, what is the best strategy to overcome a 2.85 GPA.

Step 1: Make sure your GRE scores are stellar.  This would be a good idea anyway, but for you, this is likely essential.  With a bad GPA, your GRE scores will provide some evidence you've overcome your very bad academic start.

Step 2: Research more than one school.  Most schools have unpublished GPA cut-offs.  If your GPA is below that, a human likely won't even see your application.  There are ways around this.  One way is to have a professor at your current university contact professors at the university you'd like to attend and advocate for you.  Some schools may be able to special case your application if you have a professor already on your side.  Some schools won't budge on this.

Step 3: Make sure all of your letters of recommendation are from professors you've worked with and will be glowing.  Have them address how you've overcome your bad start.

Step 4: In your statement of purpose, address the low GPA and explain how you have committed to changes that have raised your GPA substantially from where it was.

Step 5: Bet on several schools.  Even people with great applications shouldn't assume they'll be accepted.  Apply to several schools, and ask your current professor to help you choose some that will overlook your GPA.  Talk with the person who runs your lab, and get their opinion of where your application would have the best chance of being accepted.  You may be best served by a smaller up-and-coming school or a school with a new-ish department.

Finally: Make sure that every school you apply to is one you feel you'd be happy to attend.  Everyone applying to grad-school needs to do a gut check like this.  You're committing the next 4-7 years of your life to this school.


Professor put me in cc when sending recommendation letter to college I am applying to?

It is becoming more widely accepted that people have the right to be aware which information is kept on them by various organisations, to request access to this information and in some cases to request this information to be deleted (see e.g. FOI for UK, GDPR for EU). So by cc'ing you in, you professor acknowledged your right to access the same information about yourself that (s)he is sharing with the third party.

No, it does not reduce your chances — it is perfectly reasonable for professor  to show the recommendation letter to the candidate, if they wanted to, and in some places it is even required.


How to find tools that are presented in the papers?

The tools you state are prototypes developed by the authors. They may not always have enough rank to be easily Googled, so the best place to search for them would be the respective institution sites and author sites.

For instance,

MAPO can be found in the corresponding author Tao Xie's website (although you might need his consent to access it).
MICA is available in GitHub with copyright by Carnegie Mellon University.

If that doesn't work, the best thing to do would be to mail the corresponding author requesting the required access to the software.


Refusing for turning on a zoom camera during an exam?

It sounds like your professor plans to monitor video to prevent cheating. Since the exam is open note/open book, this would primarily be to make sure students are not collaborating between each other.

I think there are reasons this situation is unfortunate from the students' side: could students be penalized if their video freezes? (mine does all the time on Zoom calls despite a good internet connection and despite good incoming/outgoing audio throughout...) is it fair to give your class a view into your personal living situation?

It's also quite a difficult time from the professor's side: they're trying to make sure they can administer fair and honest exams while knowing that given sufficient leeway some fraction of students will use that to their advantage.

I think it's reasonable to ask your professor for flexibility, but you should have your reasons/concerns in mind and express those rather than only your solution (opting out of video). If you come at it as trying to work between your concerns and those of your instructor, you are more likely to be able to come to some intermediate arrangement.

However, depending on the time until the exam, size of the class, etc, they may not be able to make any allowances in the sake of fairness unless there is a real serious concern. Having your classmates able to see you is probably not going to be sufficient, since they would normally see you in-person as well, unless you already have some disability considerations related to that. They'll all be focused on their own exams anyways and probably won't even have you on-screen.

OP's logic suggesting that because past exams didn't have video this exam doesn't need video (paraphrased) doesn't make much sense to me. Maybe this is a particularly important exam (a final?), or maybe the professor has some circumstantial evidence that cheating happened previously that is insufficient to act on, like certain students having very similar answers. There might not be much they can do about the exams they've already given, but they are probably hoping for a better result for the next one.


How to disclose a major change in scope from orignal F31 submission

No, it's not a stain, no it doesn't matter. Not at the "F" level, not at the "R" level. All that's really important is the overall output of the project: whether you able to eventually publish papers using the funding given to you by the end of the project.
You have to complete the progress report (I believe if you do not your funding will be suspended; probably you can get the funds released if you complete it late but I don't know the details of that situation), and I would not suggest reporting that any funds have been used illegally or that you participated in research misconduct. Otherwise...it really doesn't matter for either your reputation or for you continuing to get the funds. There's a statutory requirement to submit these, and I'd suggest being truthful, but they're not going through a peer review process or anything. It's normal for projects to change, and a global pandemic is probably one of the most unassailable reasons for this.


I did master (M.Sc) in Germany with Mathematical Modelling of Complex System, can I call myself Diplom-Mathematiker?

(Note: The answer is primarily referring to the question in the title, which is not quite the same as the one in the text.)
No. Why would you think so?
Diplom-XXX is a title which is, mostly, not awarded any more.  The "Diplom" system has been replaced with the BSc/MSc-system. But this does not mean they are equivalent (it is a rather different system), and you certainly cannot call yourself Dipl.-Math..
From a more pragmatic point of view, I would consider it a more or less equivalent degree. But again, this does not mean you can call yourself "Diplom-Mathematiker" if you got an MSc in Maths.


Double blind peer review when paper cites author's GitHub repo for code

Censor out the repo's name, and provide code to the referees as an auxiliary file.


Why does a post-doc fellowship application ask where else do I apply?

It's hard to say about any specific fellowship (especially without knowing which one), but I've served on graduate admissions committees where we've asked applicants a similar question.  I don't recall any case in which I thought someone's answer changed whether they would be accepted, so I don't think you should worry much about this.  I see three ways in which the information is relevant.  I'll phrase everything in terms of my experience with graduate admissions, but the same reasoning probably applies for fellowships.

Sometimes we learn a little more about the applicant from where they decided to apply, since we learn which sorts of departments interest them the most.  The main case in which this could signal weakness is "reach schools": if you apply to a top department and tell them the only other schools you are applying to are much lower-ranked, then it amounts to saying you don't expect to be admitted.  I'd be wary of answering in that case, but I wouldn't worry about it otherwise.
Knowing where else a student has applied can help in recruiting, since it means we can take into account other offers or deadlines they may face and can make a pitch based on what we expect their other options might be.  (One way this plays out in practice is it helps us guess who might benefit from extra encouragement since they may have received an offer from Department X this week.)
Departments are interested in this sort of information for statistical reasons, so they can keep track of which other departments applicants consider similar to or competitive with them.  This reason has nothing to do with evaluating applications or recruiting students, and it could be satisfied with an anonymous questionnaire, but that's more work to administer than simply adding a question to the application (and it might get a lower response rate).


What are the potential benefits and pitfalls of leaving tenth grade early to pursue an internship at a prominent research lab?

I'd like to offer a counterpoint to Anonymous Physicist. I started school early because I was on the border of the birthday cutoff date, and then skipped my senior year of high school. So I left for college at 15.

It was too early for me.

Not academically. I passed all of my classes, and found a number of them still a bit boring. But going to college isn't entirely about classes. For most people, it is their first time living life on their own terms. You make your own schedule, make your own food, wash your own clothes, make your own decisions with no immediate consequence.

In short, you're learning how to be an adult. And in that, I floundered a bit. It took time for me to build a work ethic. It took a bit of failure for me to figure out how to maintain my own motivation and discipline. Enough for me to lose my scholarships and eventually drop out.

And that was with a bunch of other early entry students to provide social support. If you're going to be unique in that environment, that will provide it's own challenges. And then there's the culture shock of going from being the best at your school to being just another person among the best in the world.

So I would caution this approach. The things that led to my failure were things I didn't even think to consider at the time. The grass isn't always greener on the other side of the fence.


Changing mind after rejecting a job offer

People change their minds. This is a reality.

It would not hurt you to ask if the position is still open. Explain the situation and ask if they would still be interested in hiring you for a post-doc. Be warned that it is very possible that they will just write back and tell you that they are no longer interested or that the position has been filled.

Be prepared to explain why you suddenly want to pursue the post-doc that you previously turned down. Be careful to avoid sounding like you have issues with commitment. Do not speak ill of your industry work.

In the end, even if the professor rejects you for the post-doc, I highly doubt that it would cause you further issues. It is not like the professor would write to all of his/her colleagues and inform them that you are looking for a post-doc, and that they should blacklist you.

One last thing I will add: Maybe do not quit your job in industry quite yet. It is much easier to apply for post-docs when you have a steady pay check than when you are unemployed. This will allow you to make decisions without having to consider immediate money concerns quite as much.


Citation of a book chapter that was put online

I would cite this as a book section, including the DOI (because that's where you found it/how others will be able to find it) but not including "date accessed", because that is intended for more volatile resources like web pages. (If a reference has a DOI you can usually treat it as non-volatile.)
Sticking as precisely as you can to a reference format is important, but the most important thing is to make sure that the information is present that allows readers to (1) attribute credit appropriately and (2) re-locate the original source.

(1) Carver, A.; Gallicchio, V. S. Heavy Metals and Cancer. In Cancer Causing Substances; Atroshi, F., Ed.; 2018. https://doi.org/10.5772/intechopen.68247.


If I have a list of abbreviation at the beginning of a paper, do I still need to give the full word when I first mention the term in paper?

I agree with Buffy 100% that it is not strictly necessary.  However, the question is raising a red flag for me.

The purpose of academic writing is to communicate ideas as clearly as possible to other human beings.  If you include the full words, does it increase the clarity of the sentence?  If you're unsure, ask a colleague to read over a bit of the paper.  My strong suspicion is that they will prefer to see the word written out the first time, and will want to use the key only secondarily (if they forget an abbreviation.)

Always keep the four C's in mind when you write: Clarity, Clarity, Clarity, and Clarity.  All else is just formatting.1

1 - And as De Novo observed, formatting is also clarity. ;)


How to efficiently find citations for quotations after writing?

Presumably you have an idea of which references you made the most use of, and can skim through them again. If you really have no idea, the most efficient way to find the source I can think of is Google (or your search engine of preference). Simply copy and paste (a text part of) a quotation, put quotation marks around it, and search for it. Then correlate the findings with your set of sources. Alternatively, if you have say PDFs of all/most of your sources, you can use advanced search features to search for a quotation in multiple files at the same time. Sometimes PDFs are scanned and non-searchable, so googling can be more capable.

Now, since you mention mathematics, let me also say that these techniques obviously don't work as well for equations. For those you can try searching for related terms/names, but it can be difficult to find the exact source that way. It's probably more efficient to skim through your sources for this, which works well except for in-text equations. The latter tend to require careful reading.

Overall though, consider this a lesson to cite as you write. Do this even for notes only you will see - if it's a useful source, you'll want to remember it later!


Copyright-related advice for graphic designer creating content for academic publications

If the authors of a paper do not specify otherwise, when they transfer copyright of a paper to a publisher, that includes its images. That's what most people do.

But, during the copyright transfer process, an author can specify

if there are original images of independent value that they'd like to retain copyright to, or
if there are images whose copyright is held by a third party, which they have a license to reuse.

See for example this ACM copyright transfer form.

If you are creating images for papers on which you are not an author, you can retain copyright of your images and just give a license to use in the paper. The authors will have to specify on submission that they are using third party images, and show that they have permission from you to use them.

If you are creating images for your own paper, you may be able to claim them as an "artistic" image and retain the copyright, depending on the publisher.


When do the application reviewers contact my references (PhD application)?

Admissions committees may contact you references at any time, or not at all. Usually they will look through all applications, then choose a subset to contact references, and a subset of those to invite for interviews. It is also possible that they video interview a subset of applicants then contact their references afterwards.


How common is mandatory attendance-taking in college courses in US?

In the US there are actually some federal rules governing attendance keeping. Colleges must account somehow for students receiving federal aid, for example. That is a lot of students, as it likely includes those with government backed loans. While the rule doesn't seem to require that instructors keep a formal log, they are required to know who is attending and who is not.

For example, Here is a sample page from a large US state university: https://uc.uiowa.edu/faculty/teaching-instructional-policies/student-attendance-absences.

Some states will, themselves, impose additional rules, as will some individual privately funded colleges and universities.

There are a variety of reasons for such rules, including liability. If a student "disappears", especially one who is not technically an adult, the powers that be will want to know.

Beyond such rules, some instructors count attendance in the grading rubric, but I don't think that is especially common post-secondary. But non-attendance can be a symptom of other problems and so instructors are expected in general to know who is there and who is not - especially when missing class or other activities is repeated frequently.

So, while I don't know what percentage of colleges require this, my guess is that it is fairly high, based on the need to keep records. But it is also my guess that the rules aren't strictly honored in a lot of places.


Is there a code of ethics for Ph.D. supervisors?

There is nothing commonly accepted. And you are right that nobody receives formal training in how to supervise a Ph.D. Academia is really still very much in a medieval mode here, where you learn from your master (your own supervisor), potentially work under other masters (changing labs) and then are deemed worthy to have apprentices of your own, who you will treat roughly as your master treated you.

However, if you Google for "Betreuungsvertrag Promotion" or "Doktoranden-Betreuungsvertrag", you will find quite a few templates for formal agreements the supervisor needs to sign in some German universities. The key word being "needs to" - this is compulsory for the supervisors.

Unfortunately, these agreements only cover things like regular meetings between the candidate and the supervisor, and that the supervisor will give good advice and in general ensure that the Ph.D. can be attained within n years. This is all very nice, and any decent human being should already be doing all that is in there, but it's all rather vague. In addition, I seriously doubt that anything like this would be taken seriously in a potential lawsuit.

Bottom line: the good supervisors already do everything that's in these agreements, and the bad ones won't start once they have signed this.


Tattoos that can be easily concealed in sensitive times (during interviewing, etc.) should never be a problem. Further, academia is in general a pretty tolerant place when it comes to looks. As Suresh says, we are used to much weirder things in terms of look than a small tattoo. You'll be fine.


How do you go about asking your advisor/research assistant supervisor for a week off?

Your contract should include some official vacation time. Doesn't it?

So, it should be your right to take those days off, and your supervisor shouldn't be able to say no, unless it interferes with your work, such as lectures, lab schedules, ...

But it is still nice to keep it cool and ask politely, better in person.


Every paragraph has a purpose. The answer to your question depends on the purpose of your paragraph.

Clarity in academic writing is always good, but you should weigh whether being explicit is clarifying or obscuring the important points. "For recent reviews see {cite bunch of reviews}," may be fine if you want to direct the reader's attention to the existence of those reviews. Perhaps you're doing a metareview, or for some other reason want to track development of the literature.

But the terser version is cleaner if the existence of reviews is tangential to your point. The reader can investigate further if she wishes--hopefully the titles of your cited works make their purpose clear, so she's not digging around to figure out what they're about!--but she can also breeze past the citations to your main point. Extreme concision in citations is widely accepted. I've seen citations to my work (broadly, in interdisciplinary social science) where I was not entirely sure why the authors thought it was relevant!

So what is your paragraph trying to accomplish?


Can you apply for a faculty position via a recruiting agency?

I have never, ever, encountered a faculty search - or indeed a postdoc search - handled by an agency.

Nor have I ever been contacted by an agency looking to handle recruitments as a potential candidate, despite getting ads on sites like LinkedIn that suggest I've been accurately categorized as faculty.

In the vast universe of possibilities, I'm sure there are exceptions, but my best guess is that this is boiler-plate language that goes in all job ads from that institution.


What is the current industry standard for online course exam proctoring

One possible solution is a timed online quiz or exam with new questions, not available in any book or course notes, designed to make students think about and apply the material or process to be assessed.

Some students always say this is « too hard » others say it is fine... So can’t win...


English certifications: which ones are recognized overseas?

From what I've heard, the TOEFL is well recognised.

That being said, once you get your PhD, I don't think people ask for some English certifications (at least, I've never been asked to, and I'm not a native speaker). I guess your publications and the interview in English should be enough to see if you're able to communicate in English.

EDIT List of who accepts the TOEFL.


Should considerations be made if half of a project group drops the course?

I've seen this happen before. What ended up happening was that Mr. Doe ended up being allowed to do an individual assignment on par with the level of effort as a member the group assignment.

Losing members does not change deadlines. The same result is expected, i.e. a paper is due on a deadline. That shouldn't change, even though your group has changed. Half a group doesn't mean you can get twice as long to work on it, mostly because deadlines rarely move as a result of group changes, and practically because the schedule won't account for it.

What has changed is the amount of work you can realistically accomplish. Instead of having four person-units to work with, you have two person-units to work with. You will not be able to make the same effort as four people, but I highly doubt the professor will expect you to be able to meet that level of effort, simply because asking a human to fill in as two humans rarely ever works in the real world, at least not for long before that human breaks down.

Do not expect to change your deadline. Expect to change how much work you will complete by that deadline. Talk with your professor about how much effort the two of you will need to apply to meet his expectations, as opposed to whether or not you will meet his deadlines. Does he expect you to perform as much work as four students will do, or just meet the same timeline?

If he also wants you to do twice as much work as other students, then I'd have issue, but if he only wants you to meet deadlines, and will take into account that you're short 50% of a normal group, then I wouldn't find any real merit to saying the deadline is unreasonable.


Obvious authorship and “blind” peer peview

I have reviewed papers, where some of the references are blinded as well. So that is one way of doing it, and that certainly happens. Sometimes the authors and the journal are more lax. There are pros and cons to blind reviewing, but if a journal chooses to use blind reviewing, then I would prefer it be done consistently. However, if, after carefully reading the materials for the authors, you are still unsure what to do, then you can always contact the editor about this.


Should a speaker attend a conference where he/she is required to pay their own registration fee?

Most international conferences are paid for by the registration fees of the attendees.  The higher the ratio of attendees to speakers, the more registrations the conference can afford to comp (give for free).  When a large fraction of the attendees are also speakers, as is the case with a lot of peer-review-centric conferences, then it's often the case that only the keynote speakers have compensated registration and/or travel.  If the conference is close on its budget, even the organizers are expected to pay their own way and their own registration fees.  The smaller the conference, the more likely this is to be the case, but even very big ones often expect everybody but the keynote speakers to pay their own way.

In short: yes, this isn't unusual at all.


What is the difference between project and thesis?

It differs by school. Technically, a thesis is a claim that can be proven or disproven, but, in practice, the term "thesis" is often used for a project (for undergraduate or Master's degrees). On the other hand, a PhD thesis is not just a project; it should advance the state of knowledge in a field in a way that can only be done by someone knowledgeable in the field.

My department is considering renaming our Master's thesis requirement to Master's project, to acknowledge that it need not be a research contribution.

Of course, even a project can entail publishable work or advance the state of the art, but it need not.


Finding high quality copyright free icons for computer diagrams in IEEE or ACM submission

The quoted part means that you don’t have to follow the license if you are allowed to use the icon anyway (without the license).

This could be the case if the icon is in the public domain, if its use would be allowed by something like fair use, the right to quote, or similar.

In other words: the license can’t restrict you from doing something which you are allowed to do according to copyright (and other relevant) laws. Copyright licenses (like CC BY) give additional permissions (under certain conditions), not additional restrictions.

If you don’t know for sure that the icon is in the public domain, or that your use would be legally allowed, better assume that you have to follow the license.

Most licenses require attribution. All of Creative Commons’s licenses do (as they all have the "BY" component).

If you really don’t want to attribute your icons (the attribution doesn’t have to appear next to the diagram, if that’s what you are concerned about), you have three options:

Use icons that are published under a license that doesn’t require attribution. It doesn’t have to be a known copyright license, it could also be stated in the terms of a service of the icon site.
Use icons that are in the public domain. The author would have to state this somehow (e.g., by saying "public domain", or by using the public domain dedication CC0 1.0, or one of the other public domain equivalent licenses), or you would have to know that the intellectual property rights have expired.
Use icons that don’t meet the threshold of originality. Of course it’s not easily possible to know if that’s the case. Better be safe than sorry and assume that all except the most simple icons are eligible for copyright protection.


What generally happens if a department is unable to attract students?

As comments already indicate, this is hugely dependent on the country and university.

When I was in the Netherlands funding of the university was directly related to the number of students and the number of students who finished. This dependency was passed on by the universities to the departments. Typically, there was some sort of delay build in, so the budget would not become too unpredictable.

Usually fluctuations are not as dramatic as in your scenario, and smaller decreases can usually be covered by reducing the budget for conference visits, inviting speakers, etc.

However if the number of students halfs then cuts in personel are pretty much unavoidable, as personel is by far the largest post in the budget. However, firing people on a permanent contract is hard. It is much much easier to not prolong a temporary contract. The department usualy consisted of a small number of professors (on permanent contract) plus a larger number of lecturers (some on a permanent contract and some on a temporary contract). So the professors and lecturers on a permament contract are safe, but they will have a smaller department.

So this is a case where there was an explicit policy to add such a feedback. However, this description is specific to the Netherlands (and may not even be current). Other countries are organized differently. Even within countries there can be a difference between universities or types of universities.


In which case does PLOS ONE use a third reviewer?

I'm not certain what PLoS ONE's exact criteria are for number of reviewers (and there is likely to be some discretion allowed for individual editors as well), but in most venues that I have encountered, there is a preference for having at least 3-4 reviews to increase both the breadth of opinions and the likelihood of "consensus" on a paper, and often a required minimum of 3 reviews.  So most likely 3 reviewers were invited from the beginning.

Moreover, the asynchrony of journal reviewing means that it is very easy to end up waiting for a final review.  The typically process for managing journal reviewing is something along the lines of:

Invite a set of reviewers, who have 1-2 weeks to respond to the invitation.
If some reviewers decline or fail to respond, invite more reviewers and iterate until a sufficient set accept.
Once reviewers accept, they have 2-6 weeks to return the review.  Many reviewers put off responding to the last minute, and some ask for extensions.
One or more reviewers may fail to return a review at all, at which point the editor puts a black mark on them in the system and has to start all over again inviting a new reviewer.

You can see how this can quickly add up to 10 weeks or more, and it can stretch even further if the editor isn't acting immediately upon events in the reviewing process (as often happens).

So take a deep breath and don't worry yet: there is nothing you can really predict about your paper based on the current timing, since you're well within the normal range of journal review time (unlike the request for revisions I got today for a paper submitted 14 months ago).


Personal Life Dealbreakers for Academic Jobs

I am not a lawyer, so take this with a grain of salt.

In the US it is illegal to take information about a candidate's membership in a protected class as a basis for hiring or firing, except in circumstances where that information concerns what the law calls a "bonafide occupational qualification."

The idea is that certain kinds of employers get to discriminate in ways that would otherwise be illegal because of their status as private entities dedicated to a particular mission. For instance, a Jewish synagogue can discriminate against non-Jewish applicants when it is hiring a rabbi. If the state prosecuted synagogues for religious discrimination because they only considered Jewish candidates, this would effectively be the state saying that Jewish Synagogues can't exist.

So, in certain kinds of religiously affiliated schools, it is legal for the school to hire only members of a certain religion based on the same principle. But this only holds if membership in the religion is an explicit, advertised condition of the job, i.e. if the school is dedicated to being a school exclusively consisting of members of that particular religion.

Most religious schools in the US are not actually like this--for instance there are dozens of catholic schools in the US which are open to students and faculty of any religious tradition, or no religion at all. Schools like that are not allowed to discriminate on the basis of religion, because clearly at such schools membership in the religion isn't a "bonafide occupational qualification".


Students change advisors all the time for all sorts of reasons. While it is important that advisors and advisees have to recognize that they are supposed to work on improving their relationships and fight through tension, sometimes it just doesn't work out or will not work out in the long term. I've changed advisors and during that process, I found several other students who have gone through the same experience.

It is important to recognize that this does happen for better or for worse and it is important for you to do what is necessary to do what is best for you. Despite what you would think, people (even academics) don't really put much weight on seeing someone change careers or direction so you shouldn't worry about such things being regarded as suspicious.

The first step would be to find a set of people that you can rely on for rational advice since this will likely be an emotional transition. Parents and close friends come to mind but also finding an older student, administrative staff, and understanding professors will be key. In my case, my co-advisor and one of my committee members were resources in addition to several senior graduate students who had changed advisors.

The second would be to start to find a new advisor. If you get along with your current advisor, he would make good suggestions, if you're switching behind his back, probably not so much. As you a mid-PhD student, you now have a much better understanding of what type of advisor/mentee relationship you want and you can narrow down advisors based on that reputation. During my search, I got in touch with senior students first asking them able advising styles (and availability of funding). Only after that initial conversation did I meet with the advisor themselves. Despite what you would think, advisors actually like picking up/stealing veteran graduate students from other advisors due to the expertise that they may add to the discussion.

Finally is the administrative side. You chair will have to know about this and your committee will likely be restructured. People don't have to know the reason why you've changed (my current advisor still doesn't know). If possible, try not to burn any bridges since you will likely need his (his/her for other people reading this) signature at somepoint on your thesis. Try to keep things professional since this really is a career based move rather than something personal although it really is.

The best news is that everyone I've known who have changed advisors are/were really happy about their new sitatuion. It's just a very stressful transition but it really wasn't as stressful as I was expecting.

(edit) I've noticed this about eykanal's answer regarding the timing. Yes, it is inevitably that you will lose some time especially if you're in the thesis writing stage of your career. However, if you're an earlier student in the dissertation/research phase (I was in my 3rd year), I didn't feel like I lost much time. Most of the first years of grad school are "wasted" relearning learning and taking classes. Especially in the sciences, most of the early years is developing various soft-skills and competence which isn't lost when you change advisors/research projects. Furthermore, spending an extra year to reconfigure a PhD is probably better than falling into ABD purgatory.


How should I email dissertation to committee?

If you are obliged to send them the two documents, simply do so. Keep the cover letter as simple as possible. Just remember to address each of them separately, it looks better.

  Dear Prof. Smith,

  I'm sending you, as you are a member of my PhD committee, the PDF version of my thesis together with my CV. In case you had any questions, feel free to contact me at any time.

  I'm looking forward to meeting you.

  Best Regards,

  capadocia

As Bill Barth points out, make sure the people know when the defence is. In most places, university staff sends the official invitation, but if you know the dates, you can include them:

  I'm looking forward to meeting you on October 15 at the defence.


I don't think there are many journals that currently use public peer review, so it's unlikely that there's a list of them. The most well-known journal that does this, I think, is F1000Research, which also powers Wellcome Open Research and Gates Open Research.


What is the difference between "request for proposals" and "call for proposals" in the context of applying for funding?

Different funding agencies use different language for essentially the same thing---and also the same language for very different processes!

In the United States, at least, every different agency has a different process, customized to its mission and to the community that it is trying to interact with.  Moreover, even within agencies there are often radically different processes behind the same names.  For example:

With NSF, applying through the Program Solicitation for "Expeditions in Computing" is an entirely different (and much lengthier) process than for a standard NSF small/medium/large like the CCF core programs.
With DARPA, every Broad Agency Announcement has its own individual customized process, which is typically explained at the associated "proposer's day" meeting.

You really need to get to know the particular agencies that you are interested in.  A good way to do this is to meet program manager or listen to the talks that they give: program managers often attend major conferences in the fields that they fund, and in particularly organized fields, they will sometimes have a workshop at the conference in which program managers give "how to get funding from me" talks.  Another good way is to talk with colleagues who have worked with the agency before and know the ropes, or to become a partner in a collaboration with them.


Informal vs Formal Acceptance (Graduate)

"Pending funding decisions" usually means that they are awaiting the results of grant and fellowship applications.

If you're applying to a university that does department-wide admissions, then they are probably trying to figure out the funding situation for the entire class before sending out the formal letters, since the formal letters normally specify the funding source as part of the statement.

If you're applying to a university where individual faculty members handle their own hiring, then they might be trying to figure out which funding source they will be using to pay your salary or stipend.

But usually a faculty member is not going to tell you "you've been admitted!" if they're not sure they'll be able to pay for you, so you shouldn't feel guilty about celebrating a little.


For an industry position this typically means you have worked on and completed a project that involved X. Ideally you should also have some way of presenting verification of this if challenged, but generally confidentiality agreements may prevent specific details. In the academic sense, this effectively means the same thing, but you should have some sort of publication to verify your involvement in X.


Is writing a research paper on Overleaf risky for plagiarism?

Overleaf is unlikely to be a problem
To plagiarize your work, someone would have to

find it very valuable
hack your Overleaf account (and know it is there they need to hack) or that of your coauthors or you would have to have shared it publicly
finish the research before you do, which typically means they would have to have superior or in any case solid knowledge in the field,
publish it before you do
have more credibility than you do in the academic community, so that you can't just say that it was actually your work they are plagiarizing

Of all these factors the second one is the only one that has anything to do with Overleaf. In order for it to be the crucial issue, you already need to have a competent and well-connected researcher out to plagiarize you. While it could happen, it feels unlikely, and you probably know if you are in this situation or not.
If you do happen to be in a position that requires extreme information security (governmental research, dual purpose research, authoritarian regime, a powerful enemy out to get you), then it is a good rule of thumb to not use Overleaf or other cloud services. But in this case you really should seek help that is a lot more competent and specific than the answers here.


If I 'publish' something online -as a blog article, or pdf- will it be less attractive to publishers?

Yes, it will be less attractive to (most) publishers.

Most publishers operate as businesses and seek to maximise profits [citation needed]. The availability of an earlier edition on the Internet will reduce the demand for the publisher's version and thus the potential revenue that could be gained from publishing your book.

The extent to which your self-published version could impact on a publisher's revenue (and therefore their willingness to publish) will relate to how readily available it is and how similar it is to the version that the publisher would produce. If it is stored in a dark corner of the Internet and only loosely resembles the newer version then it may have little influence on their willingness to publish.

However, there are some publishers that operate on a not-for-profit basis; for example Open Book Publishers. These kinds of publishers probably would not mind the reduced profitability of your book due to previous publication.


How to ensure proper peer-review for a self-published book?

In mathematics, traditionally, and I think currently, very few books are reviewed at all in any serious sense. One possible sense would be "critical appraisal", and this is rare: a handful of books is given serious reviews in the Amer. Math. Soc.'s "Bulletin". The other possible sense of "peer review" is in a sense adding something to one's CV for jobs, tenure, promotion, grants. Almost by definition, this never happens. That is, "refereeing" is done for the conventional journals, whether paper or electronic, and referees are solicited by the editors, for papers submitted to that journal. The "valuation" of books is typically done not via "reviews", but by the status of the publishing house, and the status gain from publishing a book is probably less than a small paper in a medium-status journal. Thus, in particular, self-publication confers none of that cachet. And I'd wager that self-publication would compromise "review" in the sense of appraisal, as well, because other publications would have higher priority for the reason of status.

(I do hope things improve, but I do think this is the current state, in mathematics.)

Edit: As examples of "self-publication", disregarding the "peer review" idea entirely, a certain number of relatively senior (and not only!) people put book-like items on-line at their web-sites, often at universities. I heartily endorse this (and have been doing it myself for quite a while!) However (?), this appears to confer even less status than "books" published in physical hard-cover, I presume because there has been no hurdle of sufficiently-impressing publishers (who do ask opinions before "consenting" to publish).

The more legitimate issue of "(peer?) review" to ascertain correctness, or helpfulness, etc., I think has so few precedents that little is happening. First, Math Reviews has no procedure in place to review such things, and it doesn't happen. Second, there appears to be considerable reticence to cite such things, even in stable situations, for a variety of (not entirely sensible) reasons. Third, while one might imagine that on-line, thus, dynamic, documents could be more reliable, by virtue of being correctible (indefinitely!), this actually disturbs/perturbs many people... Further, third(b), disappointingly to me, very, very few people have ever given me any feeback/corrections about my on-line stuff, or even asked for clarification (in some cases leading to correction or, anyway, better writing). I can imagine that some of this is politeness, or respect, which is understandable.

But, I might claim, the real "problem" is lack of precedent. The "refereed journal" model is 150+ years old, and itself depended upon evolution beyond the "reading before the Academy" 200+ years ago when printing itself was a non-trivial matter, etc.

Thus, rethinking the action-oriented sense of the original question: since "self-published" ought mean nothing, really, in today's context, apart from the fact that it doesn't have a "prior" approval from status-conferring entities... to "get an expert opinion" one ("gosh, let's just try to think clearly for a sec!" :) would send th'thing to (web-obtained?) experts, asking very politely whether they'd be so kind as to offer critical remarks... and as a very polite secondary question, whether they'd be willing to be quoted in such remarks.

(This has led me to thinking that the difficulty in quantifying "civility" and "politness", especially between different generations (if only in convention and usage), potentially causes substantial difficulties in on-line forums, and/or "stack-exchanges", and or . Not that I think high-status entities have a "moral" superiority, which is the stereotypical exaggeration-to-disqualify, and which is a popular (mis-) interpretation of that elite, but that experience can be worth something, and that something is not easily acquired by any other means.)


Is there Visiting Administrator in academia?

The term you might be looking for is secondment.

To quote one example university (Macquarie University policy):

  Secondment: an arrangement made with the mutual consent of the
  supervisor and staff member, where a staff member is released under
  specific agreed arrangements to work in another area within the
  University or with another organisation for a specific period of time.

  A secondment arrangement may be made in the following circumstances:

  within the University (internal secondment)
  to an external organisation (external secondment)
  from an external organisation (external secondment)

Thus, you may want to search your university for a similar policy.


How should I credit a plagiarized paper in open source code?

I suggest you to be very careful to label the first paper a plagiarism, unless you are 100% sure that there are areas of a word-for-word equivalence with the original paper(s) without credit for original authors. Having said that, I noticed that the first paper's author cite the second one (authored by Beasley and Chu) - and another one by the same authors - as well as clearly state that the same (or similar) approach has already been used by Beasley and Chu (references #22 and #23), so it seems that some credit has been given (which is not to say that some is enough).

In regard to which paper(s) to reference, I would say that it depends on the following two aspects: 1) if the second paper is indeed a case of plagiarism, then it certainly doesn't make sense to cite it; 2) if it is not, then the decision should be made, based on whether there are distinctly different sets of ideas in both papers and whether you have used both sets or one.


I believe fellow TAs are giving students answers and inflating their tutorial average, what should I do?

Is it possible that the other TAs, by having done the course before, have a better overview of the kind of questions asked in the exam (based on those of previous years), and therefore are better able to train students for those exams? That would explain the facts as well, without anybody consciously in the wrong (and it is always worth to explore such possibilities).

I can also understand that your professor is not actively doing anything about it as long as the difference is not too big. Some TAs are better than others, some groups are better than others, there is always noise and some differences between groups are to be expected. I was a TA for several math courses where we would grade weekly assignments of our own groups (that counted for 10% of the final grade, next to a 90% final exam). I would grade harsher than other TAs and my group's average of the homework would be lower than that of other groups. However, my group tended to do better at the final exam, I believe in part because they were pushed harder to make an effort. What I mean to say is that worse intermediate test results don't say everything.

Unless you have hard evidence that your fellow TAs are 'gaming the system' I would be hesitant to attach too much meaning to the present facts. If, besides this, their manners are unpleasant or the group atmosphere isn't right, the easiest solution would definitely be to avoid them by not TAing the same course next year.


Hi thanks for all the comments!

I asked the author on Twitter and it turns out the he uses Keynote to make those diagrams, and not some obscure library written in python or TeX.


Recommendation letter by significant other if you worked with them professionally?

No. If she discloses your relationship in the letter, the reviewer will likely disregard the letter completely, and may question your judgment for having asked her for a letter. If she does not disclose your relationship in the letter, that is a serious enough omission that it could have consequences for you later on (I can't quite tell where you are in your career, but the more senior you are, the more severe these consequences could be).


Do the authors have to cite or make comparisons against works on domains such as arXiv?

I think this question is ultimately about standards within particular fields and societies. In math, where arxiv has been central for decades, it would be odd to overlook highly related examples, and using your language it's reasonable to assume authors would be obligated to check. In psychology, where I work, preprint repositories are still fairly unusual, and authors are not expected to review these sources.


Is it acceptable to publish student names with the label 'stupid question', on a publicly-visible website?

No. This is completely unacceptable. Sometimes faculty rant on social media and email lists where they do not think students will see the comments. Even this is frowned upon if the student could realize it is them being made fun of. It is completely inappropriate to make fun of students on a public website with students names.


Opinions on when to submit things to arXiv vary both between and within fields.  See

To Post or Not to Post: Publishing to the arXiv Before Acceptance
How to use arXiv?

for lots of opinions.  You should talk to your advisor/colleagues who can give you a better sense of how people in your field think about this.


Answering Ambiguous or Outright Preposterous Questions

Easy.  Maximize your grade.

You'll have plenty of opportunities in life to influence people and try to reduce the total stupidity in the world.

This is not such an opportunity.

Maximize your grade, if for no other reason than as an interesting puzzle, where you put yourself in the shoes of the idiot who wrote the question, and try to reverse-engineer the question.

You may still not hit the "correct" answer, but you might as well try to solve the puzzle....  Why not?


Diverging coauthor opinions - publish anonymously or don't publish at all?

Rather than knowing that some opinions expressed are contrary to my own views, you could present both views and clearly label them as such. For instance, you could open by explaining:

The authors opinions differ significantly and each author presents their own opinion below:

Followed by each opinion:

Author Name A: ...
Author Name B: ...


Is it considered ethical to sign yourself with name followed by PhD when in fact your doctorate was a DTech?

Ethically, you should portray yourself accurately. So don't say PhD unless that is your degree. It might even be considered, by some, as an attempt to defraud.

If the DTech degree stands on its own, then there is no issue with using it. But if some consider it a "lesser" degree then they would interpret saying PhD as an attempt to give yourself a promotion.

So, not only an ethical issue, but a practical one.

Note that the US NSF has definitions of which degrees it considers "research doctorates" and hence "equivalent" to a PhD. But not that they are PhDs.

Of course, for usage outside the US, there are different conventions. If the country in which the degree was earned considers the degree to be equivalent then it is, but it still is not a PhD. Be accurate. When it matters, you can, of course, explain the background.

However, DTech is a bit tricky since it can be a higher level (than PhD) degree from some UK institutions, but a lesser level degree from others. Higher-level degrees normally require a doctorate be earned previously.


Is it appropriate to call a professor for a recommendation on the weekend?

No -- it's totally inappropriate.

Seriously. Think about it. Unless you're at a school where profs phone grad students at their home on weekends to inquire about a late paper, it's totally inappropriate.

Note: Many grant agencies / admissions committees know that we (the faculty) are thorough flakes and couldn't be trusted to tie our own shoelaces in the morning. They usually give a few days of extra time for faculty references to come in after the deadline.  Others, however, are very strict on deadlines and thus faculty need to be properly shepherded into getting their materials in time.


What software license allows me to have GPL for academic use and paid use by industry for my open-source project?

Your license is not the GPL if you add additional restrictions, and your restrictions may turn out to be incompatible with the GPL in subtle ways. Consult an IP attorney.

Fortunately for you, even if your code is GPL, many companies might not want to use it because they might worry about it infecting their product. So, you might be able to charge them for a proprietary licensed version. That being said, if your work came in under a US grant from the NSF or similar agency, its terms may require you to open source the work period. Additionally, your university is likely to have an Office of Technology Commercialization or similar body that is responsible for software licensing to industry. At mine, the Board of Regents retains the rights to all software and commercially licenses it with the "inventor" getting half and the university getting half, typically, unless it is open sourced.

You should check with your university and the grant terms that funded your work. Corporations are typically tax payers in their local jurisdictions, so it's not necessarily wrong for them to benefit much as another researcher would from your work (i.e., for free).


Is it OK to submit a paper without asking your former supervisor?

You should never submit a paper without the active consent of the co-authors.  If your advisor is a co-author (and they probably will be for work based on your Masters thesis), then you definitely must have their consent to submit.  You can do most of the writing yourself, if you want, since you probably have more time to devote to this than your advisor, but you should talk with your advisor about your intent early in the process and must determine authorship.

Addressing the follow-on question in your edit: new research conducted independently from any work done during your Masters, however, need not have your advisor as a co-author.


University making unreasonable demands with regards to external undergraduate research opportunity

You need to sell this as an exception to their policy in terms of benefiting the college and it’s students. Be as positive as possible with all of this. Talk about the great opportunity you found and how it will benefit your education, further learning and your career. Make a big list of pros for why this opportunity is great for your education and for you but don’t mention cons. Not for the opportunity or for the college research. Don’t make a direct comparison. “Aboard is better because [reasons the college research sucks].” will not go over will. Stick to the positive moral high ground. Think in terms of this is right thing to do and tell them why.

Now that you have a better opportunity, you need to convince them to allow it. Try to find anything unique to your situation that can be used as grounds to make a case for an exception. Sounds like research opportunities are scarce at the college in your field. Push that point or anything else unique. What would happen if the college research opportunity fell through or was delayed? It’s understandable to cultivate options to not miss anything in terms of your education. An exception in your case doesn't make it something that needs to be repeated for other students. Stress that point. You are presenting a unique, one time exception. Letting you go aboard allows them to build up better research opportunities while not having improvise opportunities as the need arises.

You mentioned being in niche-field. It’s difficult for the college to give the same level of focus much less research opportunities as a more mainstream career. This makes it harder for you to find an opportunity at the college or aboard. Letting you go can benefit other students. By letting you go aboard another student has a college research opportunity.

Reach out to your professor first. If they support you, it will be much easier with him/her on board.


There’s one obvious way: to send a signal that lab presence is important, the research group leader and permanent staff must be more present in the lab. Most students are looking for opportunities to increase interaction with professors and advisers, thus by being “accessible” in the lab for discussions, you will increase lab presence. In addition to inciting students to come, that will be a even greater stride toward “cooperation and discussion among lab members”.

This also works with post-doc and the more experienced grad students: you need to avoid the idea that “lab presence” is only for the newbies, while the grown ups get out of there as often as they dare!


Why would a revised manuscript following very minor revisions appear as "under review" in the journal management system?

It is not uncommon after minor revisions that the paper is indeed send back to (usually the same) reviewers. In most cases another round of revisions is not needed and they will simply accept the paper, but this is of course not guaranteed.

For some journals, as a reviewer, you can indicate whether you want to see the paper again after minor revisions, I do not know whether this is an option for Elsevier journals.


Is it appropriate to submit a co-authored writing sample to PhD applications?

I suggest that you don't submit a sample that was written jointly. It would defeat the purpose of the request. The reader doesn't know how you write. I suspect that it would be rejected by many (most?) places.
There are a lot of possibilities for what you might submit. An old assignment, perhaps. Or write up something specifically for this purpose. Perhaps you could write a proposal for some specific research that interests you, showing that you have done some background reading and are looking ahead.


How should a PhD student deal with an unprofessional and unhelpful advisor, who misses most scheduled meetings?

If you want me to take you at face value, it's not even worth completing the Ph.D. under your current advisor. You won't get a good problem, you won't get good guidance, you'll get stuck and won't get help, and you won't get a good rec letter for your next position.

That being said, a round of basic people skills may be helpful here. Have you tried asking your advisor such basic questions as how do they think your research is going? how can it be improved? You can even ask why they're frequently late. You can ask when would be better to meet, for instance.

That failing, the standard solution is to switch advisors, even though this is costly.

No, you can't really "go above" a tenured professor in any meaningful way, and even if you could, it wouldn't help you get sincerely better advising or a strong rec letter. Please research who else you can talk to though - another professor you trust who can advise you with some safety, resources through the grad school, etc.


It sounds like you've been admitted to a US PhD program in computer science without guaranteed funding.
While you will have to decide for yourself what to do, to me this seems like an unusual circumstance. As Buffy's answer mentions, it's common for students to not have an advisor right away in US PhD programs. However, it is not common to be completely unfunded.
I don't know what led you to being in this position, maybe there was a miscommunication between you and the program you applied to. Did they think you would have some sort of funding from your home country? Did they think an advisor had already committed to taking you on (in my grad program this would have been referred to as a 'direct admit' student)? Did you not have any conversations about funding during the application process?
I would not recommend moving to another country for an unfunded PhD unless you are independently wealthy and the cost is no concern. If you can arrange for a TA or RA position before the semester starts then that's fine. It seems like you're out of luck for now on the RA front, so find out from your program what the steps are to get a TAship.


Is sharing research progress and ideas on blog acceptable?

Blogging is very common and appreciated in mathematics. For example, here are some blogs maintained by well-known mathematicians: Terry Tao, Quomodocumque, Tim Gowers. None of these blogs are devoted exclusively to mathematics, although each of them contains plenty of math. Each of these links to tons of other math blogs, so you can see many more examples.

I think that what you propose is a very good idea, subject to some caution. As Alexandros suggests, I would only discuss other people's ideas if you get their permission. (Or, perhaps, if you are discussing something publicly available. In mathematics this is certainly considered okay but you should check with someone in your discipline.)

Most importantly, I would suggest waiting to blog about your work until after you have completed it and made your results publicly available. (In math it is typical to post a preprint to the arXiv at approximately the same time that you submit your paper for publication, and at this point your work is considered public. But in some disciplines a paper is not considered "public" until it is formally published.) There are several reasons for doing this. One is that you avoid the risk of being scooped. Another is that, by waiting, you get to advertise your finished work. Typically, math blogs contain links to PDF copies of the papers they discuss. When I get interested, I often want to click through and read the paper!


From my experience, whether you are outgoing or talkative is not that important. Myself and my former PhD supervisor would notice good students based off the academic merit even when they struggled with English as a second language or if they were a bit introverted. It is not necessarily about your ability to become friends but more your ability to produce quality research when you get trained. A good PhD supervisor will be able to recognise that.

That being said, depending on the culture of course, my approach was to first send an email outlining your interests and request either a brief discussion, or a coffee when they get a moment.

I don’t think it is awkward at all to knock on a professors door and say hi and tell them your intentions to become a researcher.

I am not familiar with how it works in India but in Australia, if someone knocked on my door and was interested in doing some research, I’d buy them a coffee and have a chat if I was free. Otherwise, tell them to come back another time.


ZbMath is like Math Reviews in concept. It publishes summaries of already published articles, to help those perusing the literature to find articles of interest. These summaries are, generally speaking, not evaluative, rather informative (in some cases the published reviews are simply quotations from the article's abstract) and they are signed. Since there is no evaluation, there is not much likelihood of conflict of interest. A reviewer could downplay an important paper by writing a short succinct review, or exaggerate the importance of a minor paper by writing a long review, and one perhaps occasionally encounters things like this, but neither really does much damage, except perhaps to deflate or inflate an ego.


Sending a second follow-up email for a potential PhD position

It's typical to apply for multiple (10+) PhD positions simultaneously, rather than sequentially. Don't wait to hear back from this place, just send your other applications now. It's fine to ask again about your application, but this time ask for the date by which you can expect to have a decision.
Here's a suggestion for how to formulate the email (you can modify it according to the specific details of your situation):

Dear Prof. X,
Last month I applied for a PhD position in your department. Do you
have any further news about my application, or an idea of when you
might make a decision? I am really excited about this opportunity and
look forward to hearing from you soon.
Best wishes,
MDG1999


Is this an experimental or observational study?

This is not an experiment, as you do not have experimental control (the ability to manipulate an independent variable, or to randomly assign participants to different manipulations). The point of an experiment is to demonstrate causality: that the independent variable determines (at least in part) the dependent or outcome variable. In your case, there is not even a question of causality to be addressed: the participants’ judgements can’t affect the algorithmic rating, and vice versa. What you are seeking to demonstrate is whether there is nonetheless an association between the judgments. ie For a given location, are the answers similar to each other?
So yes, this is simply an observational study, designed to test whether two variables are associated with each other. As there is no causal relationship between them, the terms “independent” and “dependent” variables aren’t ideal. In your case, it might be best to say that you are seeking to determine whether your automated rating is a predictor of the outcome variable, which is the participant judgments. But you could just as validly phrase this in the other direction, and see if the algorithmic ratings differ systematically across values of the human ratings.
Don’t worry that your study can’t be described as an experiment. Entire scientific disciplines (eg a lot of astronomy, anthropology, archaeology) are largely non-experimental.


To the best of my knowledge there is no way to get MDPI to notify you of upcoming special issues without knowing about everything else they publish.

If you're looking to submit to those special issues, I recommend looking for subject-specific communities (e.g. mailing lists or similar) that people might advertise calls for papers to.

If you're simply looking to read them, I suggest setting up some good Google Scholar alerts around the subjects; if you get these right then as well as giving you interesting articles from all over the place, they will tend to show up multiple articles from the same special issues.


How would the UK leaving the EU affect academia and PhD admission?

The following are opinion, not fact, as AFAIK nobody has a clue what a potential post-Brexit academic situation would look like:

It's standard for qualitative features in regulations and costs to remain fixed for students over the lifetime of their studies. So I would guess that the fees won't change halfway through: you'll know the approximate costs at the start. It wouldn't surprise me if in two years fees for EU students would remain the same, especially if (as your question seems to imply) you've been normally resident in the UK for 3 years.
I would always expect a PhD studentship to cover fees. I would be very wary of one that didn't guarantee this. The risk of higher fees should be on the studentship, not on you personally. (Of course, you may self-fund, which is a different issue)
In the current UK climate I would be more worried about visas to study. With the current arguments around net migration, and the crazy situation where students are counted as immigrants, I would expect student visas from the EU to become a problem.


When publishing, should every author officially sign off on the final work?

It's rude and obnoxious, but it's not illegal and depends on your relationship with the offender whether you want to try to do anything about it. I have a paper that I never saw before submission and whose conclusion I would have qualified in a different way than what was submitted and accepted for publication. I keep my eye on that group of people now so that it doesn't happen again. I never complained because I wanted to keep the relationship on decent terms.

It's not ethical, but calling the publisher and asking for a retraction is probably your only defense now that the article is published. That's not really great for you, and it will probably destroy any relationship you have with this person. Saying something about future papers can probably be done tactfully, but I'd still be careful.

What I don't see is how this demotivates you. Papers are being published with your contributions in them which will still contribute your value to future employers. If you had an expectation of author order, that should have happened before the writing was started, and really before the research was begun. That's a conversation that can still be had before other research continues.


You could use the
principle of maximum entropy.

Thus, the first submission should be accepted about 50% of the time. When the first is rejected, next the second submission should be accepted about 50% of the time and so on.

This way you "make every time count": you maximize the amount of information (in the sense of information theory) that you receive from each decision.


Is it common for a published paper to have some small mistakes?

I can tell you with absolute certainty that almost every published paper contains at least one minor mistake. At the very least, I know that every single one of my papers has at least one typo that survived several rounds of reviews and revisions, and I can always find an error or two in every paper that I read carefully.
If the error is not a substantial one, i.e. one that significantly impacts the validity of the main results, then you shouldn't worry about it too much.
If you realize that your methodology is broken, your data is wrong, your theoretical analysis has logical flaws, your conclusions contradict known results or something of the sort, then it is worth considering taking some immediate action. The ethical thing to do would be to contact the journal's editor before the paper is published and have it retracted (as painful as that may be), and resubmit it if/when you manage to fix the problem.
For fixable mistakes found after the fact, some journals publish errata - appendices to the published paper that resolve issues found post publication.
If it's just a typo (missing comma/missing word/use of antonym) then don't stress too much. If you feel like the decrease/increase typo is in a key sentence describing your results (say, the intro/abstract, or in the sentence describing the key findings), it may be worthwhile to contact the editor and ask to resubmit a correction.


Is there a term for "PhD at a department" vs "PhD at an (independent) research institute"?

I'm involved, as adviser, in a PhD program that falls exactly in your second category. The program, which is briefly presented here and here, is jointly run by my university (POLITO) and by the Italian national metrology institute (INRIM), which is a governement institute. Half of the available positions are paid by POLITO and half by INRIM. Frequently students are co-advised by advisers from both entities (this is not mandatory, but it's useful; and the student list on both sites is not up-to-date for what concerns co-advising information).

However, the degree is awarded by the university only, and there is no formal distinction between the students that get their PhD from the above program and those who get their PhD from a program associated to a single department within the university. I'm aware of a couple of other similar programs in my field around Europe (here one in Germany), but I've never heard of any specific term distinguishing them.

Different is the case of a double degree which is awarded by two universities.


Paper submitted by co-author without authorization

Ask the editor - with coordination with B and C - to fix these minor "slips" (as you will say).

Incorrect statements need to be fixed, and missing references to be amended, that's an objective thing that does not need discussion.

I would stay polite to B, even if you plan not to work with them in the future. You are angry, but you are not going to change them. Hopefully, you are going to be able to fix this paper, and that's what you should concentrate upon.


Rules for notifying co-authors about re-presenting a project at a conference

From what you've said this sounds like a honest mistake made in good faith, and if I was your supervisor I'd accept your apology and move on. At your stage it's to be expected that you're still learning some of the norms of the culture, and they're not always clear.

That said, I do get particular about authorship. Let me tell you a story from my previous career...

I was a young PhD researcher, working in collaboration with several other staff and the head of my research institute. Let's call him Toby.

I came to feel that Toby had a significant conflict of interest related to our work, one which was not being properly handled. I felt that my boss was trying to pressure me to accept methods and interpretations that weren't scientifically justifiable, but which just happened to lead to results that were favourable to our institute's funding. Another co-worker felt the same way.

We refused to accept these methods, and soon after we were both fired. While we were serving out our four weeks' notice, we learned that Toby had gone to an international conference and presented these results in a talk and poster, and that he had listed us both as co-authors in this work.

If he'd attempted to do this in a journal publication, we would've been asked for consent to be listed as authors (and would've declined). But because talks and posters don't have quite as rigorous processes, he was able to slip this through. We ended up having to contact the organising body and request that our co-author credits be removed from the published proceedings.

(Toby was furious. Toby also had right of veto over any reference that anybody in the organisation might write for us as we looked for new jobs. It was not a very enjoyable time in my life.)

As my experience illustrates, crediting somebody as a co-author isn't automatically a positive. When my name appears on a paper, I share responsibility for the contents of that paper, so it's very important that I have the opportunity to give or withhold consent for that to happen.

Two important things about consent: it's conditional, and it can be revoked. If your supervisor only agreed to the first poster, then you didn't have her consent for the second. You might think it's almost certain that she'll agree to the second one, but you still have to ask.

(I know my friend will happily lend me $20 if I ask, but it's still not okay to borrow it from his wallet without asking!)

There are reasons why somebody might say "yes" to one request and "no" to another. It might be that they have issues with the conference or its sponsors, or that in the time between one request and another their thinking has evolved and they no longer want to endorse material that previously seemed okay. Regardless of why... it's best to ask.

Moving forwards, my advice would be to say something along the lines of:

  As I've said previously, I'm sorry for resubmitting this presentation
  without your consent - I misunderstood expectations for how this sort
  of thing should be handled. I've withdrawn the poster, but I get the
  impression that you still have concerns about this issue. Is there
  anything else that you'd like me to do to remedy this?


Passionate about a PhD in math, but unsure how to explain my chaotic transcript due to mental illness

You need to focus. Why do you think you need a PhD in mathematics? If you plan to be a serious researcher, how do you plan to balance that with working in your under-performing school district? What specific area of math is your intended focus? Are you trying to get into a top 5 program or any program? That also makes a difference. If you can show that you are focused today and have doable plans with a PhD, telling your story won't be as difficult as explaining a low grade in an entry-level math course such as differential calculus. You will have a hard time living that one down. Figure out why you earned a D and how that changed your approach to understanding math. You might want to consider applying to a MS mathematics program and state your intention to seek the PhD at that institution.


How to write a brief author biography for a journal article?

Can't you look at author biographies from other papers in that journal?


What are the roles and responsibilities of an adjunct faculty?

There's a wide range of people called adjunct faculty.  For example, it may include working professionals in the field who serve as part-time faculty (this is common in law and architecture, and I've seen it with industrial researchers in computer science).  Depending on the circumstances, this sort of adjunct may be treated much like the other faculty in the department, except for being part time.  However, I assume you are talking about the most common use of the term "adjunct", at least in the US, namely low-paid, low-status faculty typically teaching part time on temporary contracts.  (They may be working full time overall, but only part time at any given institution, so the universities can avoid paying benefits.)

For this sort of adjunct, it really depends on the details of the contract, and it may vary between universities, as well as depending on issues such as whether any of the courses are online.  A typical arrangement will include some amount of course design (at least at the level of creating a syllabus), lecturing, grading, and office hours.  Typically there is no committee work or other service and no research duties.


How can I find out which universities allow a sandwich (stapler) PhD thesis?

The department where you are going to submit the thesis probably has a document of PhD/thesis regulations that specify if such a thesis is allowed. For example, my department's regulations have the following statement:

  [...] Scientific publications may form a part of a doctoral thesis. If the doctoral thesis consists of several scientific papers, a presentation of the guidelines of the papers submitted has to be added in an appropriate extent. [...]

i.e. a sandwich thesis is possible here. So you should find out if your favored departments have similar regulations and have a look in there.


Course requiring students to use Examity

Yet it has been 2 days since this email has gone out and my professor has not retracted the statement on the course website that we will be using Examity.

I think your concerns are reasonable.  But I think you should give your professor a few more days to react.  Keep in mind that professors may get thousands of emails.
You could write at a later date:

Dear Prof.,
I appreciate your efforts to promote exam integrity, but I prefer not to use Examity because I am concerned this company might take my private data.  Dean Whatsit said using Examity is discouraged.  May I take the exam without this software?
Sincerely,


Is there a tool to visualize the citation network which works with Google Scholar?

To my knowledge, at the time of writing, Google Scholar does not define an API to access data, so presumably no software exists. Beyond Google Scholar and the tools you've already mentioned, you could try  https://www.semanticscholar.org or https://aminer.org. (I'm a little unsure what you mean by citation network, so perhaps they don't satisfy your needs.)


Physics PhD switching fields after short career break?

I spent my whole life studying to be a professor of History. I did my AA, BA, MA, and part of my PhD in various sub-fields of History. I was enthusiastic about the career for the majority of that time, but while in graduate school I began to get the sinking feeling that I was not as interested in the field as I'd thought. I also kept getting the unshakable feeling that I was wasting my life. My other friends were out in the workforce, getting married, buying homes, and I was still hobbling around a library writing papers in the wee hours that would ultimately never be read by...anyone.

I left my PhD after realizing that while I probably had the ability to finish it, I did not want to pay the expense of 3-4 additional years of virtually unpaid labor. The likelihood of landing a professorship was low anyway because of the state of my field and of academia in general.

Three years later, I am now a junior software engineer. My job is challenging, rewarding, and a source of pride. It pays me a livable wage. And it's a tremendously good investment for my future. I shudder to think of what might have happened to me had I stayed in academia: cobbling together a living in "adjunct hell" or moving to some Nebraskan cornfield for a tenure-track position at a community college. No thanks.

To be sure, Physics PhDs have more career options - but not as many as you'd think. You'd have to slide your way into a hard-skill position somewhere and lean on your math skill set heavily, in the event that you could not land a professorship or a research position in aerospace (or wherever your interests lie).

However, learning to code is a great idea regardless of whether you stay in Physics, because it is a highly employable hard-skill, even among scientists. I'd look into Python specifically for its role in data science and its usefulness in science research careers. You literally cannot waste your time (as it relates to money or career goals) by learning to code.

Leaving the PhD might not harm your future applications to PhD programs, but it certainly does not do you any favors and you'll need to explicitly address/justify this choice in your new application. The first question they're going to ask is, "Should we invest in this applicant, knowing s/he already left one program?" There are even a few folks in academia who snobbishly refer to leaving the program as "washing out." These people are urchins, but some of them hold clout and occupy positions of power in your target school/program.

You also need to consider how exactly to explain your decision to leave the program. The wording is critical. If you make any indication whatsoever that your decision was informed by whimsy, they might ball up your application and practice half-court shots with it into the trash can. Your decision to leave the program needs to be part of a thoroughly strategic plot to further your career goal: "As I proceeded through my program, I found myself gravitating more and more towards climate science [specific reasons/examples etc etc]." You decided to return to the private sector, brush up on your ancillary skill sets, and then move into a program that better suited your interests. And you loved your former program, advisor, and colleagues. You need to appear that you've got a plan and you've got yourself and your goals all buttoned up.

The "unrelated" job doesn't have to be unrelated if you can weave it into the larger tapestry of your career goal. If coding is relevant whatsoever to jobs in climate science (hint: it is), then you can swing that experience like a truncheon in your application. Plus, having any "real-life" professional-level work experience is a great thing on any PhD application because it indicates that you can work on a team, follow orders, and complete complex tasks. My university (in the US) would rarely accept PhD applicants from recent bachelor's grads because they had not yet had any professional work experience and basically had never "adulted."

One last thing to consider is the fact that you are being offered a job that will allow you to develop a critical skill: coding. That in itself can turn into an incredibly rewarding and lucrative career, if you cultivate it properly. You'll be making money immediately and your job options will open up over time. If you return to academia, you will spend years making very little money, with no real guarantee of a lucrative career afterwards (this point is controversial but the debate over whether PhDs have a good return on investment is something you should absolutely read about).

I mention this last bit only because I think a new career has presented itself to you and you might not have realized it yet.


Copying my comment:

I don't think you should. I can't recall ever seeing test scores listed on a CV. Nobody really cares about GRE scores except graduate admissions committees, and they get the scores straight from ETS anyway.


Reviewers had differing opinion on my manuscript

If the editor said which reviewer to follow, obviously do that. If the editor didn't say anything, then my experience is that he or she just wants to see what you think. For example if you think it's better to improve the graph than to remove it, improve it, and then write your reasons for doing so and / or a rebuttal to the first reviewer in the response to reviewers.


Is it fine to ask a collaborator to give me a recommendation letter directly or should I ask my adviser to do so?

It's always better to ask a person directly for the letter of recommendation. That way you can judge the person's enthusiasm and interest in writing a letter. They will also be able to give you more direct information than working through the "middleman" of your advisor.

If you feel uncomfortable approaching your collaborator for a letter, that's probably a sign that you might not get the quality of letter you want.

But you should also mention to your advisor that you are asking your collaborator for a letter, regardless of which path you pursue.


Is it a good idea to combine the glossary and the list of notations in a mathematical PhD thesis?

Have your definitions in line rather than in a glossary, it improves the readability of the entire manuscript (whether or not those definitions are actually necessary). People rarely go through glossaries anyway, since it would involve spending twice the amount of time just to switch pages back and forth. Inline definitions, instead, help the reader to flow on without dismissing the attention on the context.


Assessing quality of research groups within math departments as a prospective PhD student?

For both your questions, I will posit that the key factor is whether the group in question is doing "high impact" work. For example, are their papers interesting and often cited? Are they working in very "popular" areas? Do the respected researchers in your (sub)field know the names of the senior group members?

To your questions:

I am not a mathematician, but I do know that the rankings will be at the level of the "department average", where faculty hires will be based on the "group" or even the individual. So, a high-power group in a third-tier school is better than a lower-power group in a higher-ranked school.
The factors listed above are perhaps the "true" criteria -- but, as an undergraduate, you are probably not in a position to judge your prospective advisors' work. This is why the rankings are so useful. If you have anyone at your current institution that you trust to be well-informed as to the state-of-the-art in your (sub)field, you may want to ask that person for some advice as well.


The point of a survey paper of the type you are discussion (as distinct from a systematic review), is to provide an organized view of the current state of the field.  As such, you should not be attempting to cite every paper, but only the ones that are significant (which will still be an awful lot).

Writing a good survey paper is hard, and there really aren't any good shortcuts: you do need to become familiar with the content of a very large number of papers, in order to make sure that the view you are presenting is sane.

My suggestion, based on my own experience in this area, is to use the following iterative process:

Begin by collecting a large pile of papers to survey.
Based on your experience and a few initial readings, hypothesize an organization schema for the field.
Start reading (mostly skimming) and organizing your collection of papers you read using this schema, including noting which ones are most important and which do not fit the schema well.
As you find significant numbers of papers that do not fit the schema well, adjust the schema to better fit what you are actually finding and shift the organization of your collection to match.
Add new papers to the "to be read" collection based on the adjusted schema, then return to reading and organizing.

When the process converges to a stable schema and an empty to-be-read pile, you will have a well-developed view of the current state of the field and be in a good position to write a survey.  Note, however, that this may take a number of months...


Confidentiality of thesis data: PhD with industrial partner

The standard for a Ph.D. thesis is simple and universal: it must make a contribution to the sum of human knowledge.

As such, all results in a thesis should be public and presented in enough details to allow another researcher with sufficient background to reproduce them.

It's fine for some of the work that you are doing to not be public, just so long as enough of the material is public to make up a Ph.D. thesis.  For example, if you have figures scaled to unknown values or missing geometry information, then you need to ask: is there significant scientific value even without this information?  For example, if the proprietary figure is an example of how a method was applied, that's probably OK as long as there are other forms of verification elsewhere.  If the proprietary figure is the verification, however, and it's missing critical information, then that is not OK.


How to handle unprofessional negative reviews from a journal?

It appears that the editor gave more weight to the first review, or at least gave you the "benefit of the doubt". Since you have the chance to re-submit, and you decided to do so, you should have to respond point-by-point to every comment that both reviewers made. Now "respond" is a deliciously diplomatic word that includes all the spectrum of reactions: from, say, "I did exactly what you asked" to, say, "go find a hole to hide and die, you stupid ignorant".

The main advise I have to give is : keep your judgements to yourself (about which review was helpful to you, whether the one appears sloppy etc), don't differentiate between the two reviews in your response, and don't be more aggressive in your writing style when you respond to the points made by the second.

For example, Don't defend not comparing your work to concept X because "it is completely out of date". Defend your choice because, say, "concept X, valuable indeed when it first appeared in the literature, has been succeeded by etc see reference 1, reference 2, reference 3". You get the spirit. If the "outofdateness" is your opinion and the field does not agree with you,then, you have another paper in the making, one where you will try to convince the other scholars of your field that concept X is indeed outdated.

If you do that correctly, the editor will certainly get the message (and well corroborated) about what you think of the quality of the two reviews, and why, even though nowhere in your response such an evaluation will explicitly appear.


Asking a High School Teacher for a Letter of Recommendation

Don't ask the high school teacher unless that's the only way you can get an enthusiastic letter.  First, asking someone from high school looks like an admission of weakness or decline, like you haven't impressed anyone in college as much as you did in high school, and that's not a good message to send.  Second, a high school teacher will have less perspective on how you compare with undergraduate and graduate students, which is the primary issue.  Finally, it's really hard to judge graduate school potential on the basis of high school performance.  For example, the math team experience you mention can be misleading.  Contest problems differ systematically from research in that they are guaranteed to have short, elegant solutions and they have strict limitations on what sort of background might be required.  These constraints are often comforting to students, and I've known people who loved math contests and were great at them but didn't enjoy or weren't particularly successful at research.

I'd recommend talking with your machine learning professor to see whether he thinks he's in a position to write a compelling letter.  If so, then go with that.  If he is reluctant, then you should choose someone else.  That could include the high school teacher if necessary (better a recommendation from a high school teacher than from someone unsupportive), or other options you haven't mentioned.


What is the best practice to mention "conference presentations" in CV

I would try to avoid having the same information twice or referring to another section in your CV, that makes it complicated to read.

What I would do, but this is of course something subjective, is having one section for "journal papers", one for "conference papers", depending on your field they might be worth as much as journal papers, if that's the case then just one section, for example "peer reviewed articles". And one for "oral contributions including conference papers". I guess there's a better name for that but I would put the presentation and the paper into one entry:

  How to write a CV

  DSVA, Some else, another person

  presented at some conference, 01.01.1971, the internet

  published in: Me, et al., "the title 1", venue, pp., 20XX,

If the authors are the same I would leave out the second line.

The alternative would be just adding the information about the talk to the paper section by adding:

  Presented by DSVA in an oral communication at some conference, date

Since the conference paper and the presentation seem to be very tied together this would make a lot of sense.


This is a little bit shaky, but let's give it a try. Apart from a programmatic solution where you would have to write your own web-scraping scripts which would construct appropriate URLs for each authors and extract their publication statistics, there might be another, though still quite tedious and technically involved approach.

Harzing's Publish or Perish program (PoP) has a feature called "Multi-query center". It allows you to create a set of queries and then generate publication/citation statistics for each of them in bulk. It is meant to periodically re-generate the citation statistics for a set of queries so that you do not have to laboriously write the queries again and again. Now the technical steps towards your solutions would be the following:

produce a set of queries corresponding to the list of authors you are interested in;
update all these queries at once by a single button click;
save the statistics for all the queries e.g., into a CSV file; and
extract the numbers you are interested in in your favorite spreadsheet program.

The most technically involved step is to produce a set of queries corresponding to the list of authors you have. If the list is not too long (e.g., up to 50), the easiest method would be to enter the queries manually. In the case you have a very long list of authors (several hundreds), then I would try to generate the set of queries programatically. The PoP program stores the queries you enter in it in a file Queries3.xml in the corresponding Program Files folder. The queries are organised into folders, the XML is easy to read. Producing a correct XML file with the queries is a little bit try-error process, but you can easily succeed when you create an empty query with an authors and then using a small script (or you favourite text editor/spreadsheet) copy the query entry and only change the Author attribute of the PoPQuery element.

Good Luck!


Is it OK to mention dreams and future plans for a specific company in my SOP when applying for master's degree?

Unlike the other existing answer, I would advise you to tread carefully.

Maybe this is different for a Master's in game development, but generally speaking, "I like to play computer games" qualifies as the #1 worst reason we get to hear about why students are interested in computer science. One of the reasons why this is such a bad motivation is because it shows a certain level of misunderstanding about what computer science is, and I would argue that this is even true for a master in game development.
Even great computer game developers are, to the best of my knowledge, not only interested in gaming, but also in AI, computer graphics and animation, HCI, physical simulation, distributed systems, optimization, etc. Not all of them at the same time, but being "just" interested in building cool games seems rather weak, to be honest. I think it can be pretty much implied that you are interested in games if you apply for game development. Show and discuss your interests in other related areas that sets you apart from all the other applying gamers.
Also, having working at Blizzard as your dream job does not show determination. Many people have this as their dream job, and still do not follow through. Determination is doing something to make your dream a reality despite problematic circumstances, not having a dream in the first place. You should explain what you did, not what you hope to achieve.