Which publication information should be mentioned in CV : Online first, or volume(issue)?

It's really up to you how you list your references, what I do is to list it with the updated information on the CV, due to:

This reflects the actual state of the article which will come up in searches.
The later date of the full publication shows that the article is one of the 'latest' in the field.
The article often has the published online date anyway, alongside the other important dates, at the beginning of the article.

I have always taken the CV as being a way of 'showcasing' the latest state of the researcher's work.


Writing an expository piece is not a research activity. Research activity in general refers to original research with things like systematic reviews and meta analysis falling into a gray area.


Would it be unethical to claim affiliation when it was not made official yet?

Affiliation should indicate the institution with which you were affiliated while doing the work and writing the paper.  If the paper was already finished before you started at an institution, then don't list it; use your previous affiliation instead (or "none" if you weren't affiliated with any institution).

If you end up making significant revisions to the paper after enrolling at the new institution, then you could consider listing both it and your previous institution.

If it matters, I wouldn't necessarily use the "official enrollment" date to decide when affiliation starts, but rather the date when you actually started attending classes, using the institution's facilities, etc.


Re-write paper to make it truly double blind

Check out double-blind peer review policies from the venue you'll be publishing in. Here's an example from Elsevier. In a nutshell, you want to prevent any reader from immediately connecting the paper to your identity by e.g. not listing your affiliation, anonymizing self-references, removing funding sources, and so on; but you're not aiming to "beat Google".


Confused between applying immediately to graduate school and taking a break for research experience

First and foremost you need to research specific graduate programs -- focus on the program and the specific research topics and opportunities. If and when you find one that really excites you, apply now. If you don't get accepted, or change your mind in the meantime, identify what would most interest you next. Maybe this will be your "Option 2". If so, and after a year there you still want to get in to the original graduate program, apply again. Frankly, if this is the way it works out, you'll be better off, as you'll have much more perspective.

Don't fixate on a higher degree in a specific field per se. Depending what country you are talking about, you could be working at the degree for several years. It better be something that you're obsessed about, in adepartment with a pleasant and helpful culture, in a liveable town/city. The odds are that the expectations you've build up in your mind will not resemble the reality for very long, so the reality better be workable.

I worked in industry for almost five years before going to graduate school, and during that time I flatly rejected suggestions that I should consider it. Ultimately I realized I did indeed want to go deeper, and applied. One bit of advice I got was "if the thought that you should be going to graduate school isn't the first thought on your mind when you wake up in the morning, don't go." By the time I applied, that was true. I had a fantastic time in the early years, but was very frustrated by an uncooperative advisor by the end. I finished, and tried to make academia work for another ~12 years. I quit a year and a half ago, as I realized the university was no place for somebody with my priorities and level of integrity. The PhD per se is of no consequence to me now; in fact it renders me overqualified for just about everything. My specific areas of study are of no consequence either. I'm not sorry I did it, but if I'm honest, there was fair bit of waste involved.

If I had to do it over again, I would (1) get myself organized and leave industry for graduate school after 3.7 years instead of 4.7 years, (2) switch labs when I first started thinking about it (after about 3 years into the degree), and (3) quit the academic charade when I first started doubting it, about 7 yrs post-PhD, rather than sticking it out for another 5. If I could redo things, I'd be in just about the same place I am now, but with 8 more years up my sleeve, and I'd be far less disaffected.


Is it a good idea for an applicant to a graduate program to call a potential supervisor, if he does not answer emails?

Do not phone.  You should not have emailed.  There is a standard process for acceptance into graduate programs, and contacting the professor is not part of it.

In the US, at least, and in the fields I'm familiar with, professors with any kind of international profile are inundated with applications to work in their lab/graduate program, even though in most cases, the professor has little or no control over whether students are accepted into the graduate program, since that is run by a graduate committee.  Accordingly, emails to a professor asking to be taken as a member of their lab, before the student is accepted into the graduate program, are worse than useless; they are pestering a busy person with irrelevant requests.  Such emails are typically deleted as soon as the professor reads the first sentence, or at best -- if the professor is extremely generous -- forwarded to the appropriate person.

This is multiplied by ten if the email sender doesn't have a good grasp of English, because (fairly or not) such emails are often perceived as simply carpet-bombing, spammed to scores of people on the off-chance of a hit. Again, professors may receive dozens of such poorly-written begging letters per week, almost all from completely unqualified candidates. (The question here, while far better written than many such letters, is far enough from standard English that it would likely hit this barrier.)

It is multiplied by a thousand for a phone call.  It's quite likely that if you did make phone contact with the professor, the act of phoning would add you to the "Do not touch this person with a ten-foot pole" list, even if you were accepted to the graduate program.

If you are interested in working with this person, there is probably little point in contacting her directly. Go through the standard graduate student application procedure and then once you're accepted, contact the person and make it clear that you are already in the program.

The exception would be a potential graduate student who is truly exceptional.  This does not mean an overlap of interests; it means an overlap of interests plus a very strong skill set, meaning pretty significant work in the field already, or some other really out of the ordinary ability -- not grades, not a prestigious university, but actual demonstrated skills.  And this would not, typically, be communicated by the prospective student, but by someone associated with the student whose judgement would be more reliable, like a professor or industry expert.  So even in this case, the student should not be pestering the professor with emails or phone calls.

There may be individual exceptions, who welcome this sort of thing, but the odds are very much against you.


Is it appropriate to request letters of recommendation from professors a second time?

Yes.

Writing recommendation letters is part of our job as professors.  It is perfectly ethical to request that we do our job.

Conveying desperation in your request is neither necessary nor productive.  You have nothing to be ashamed of or to apologize for.

On the other hand, anyone can (and should!) turn down your request in good conscience if they feel that they cannot write you a strong recommendation letter.  If someone says that they can't write you a strong letter, believe them and ask someone else.  You really don't want a weak letter in your file.


How common is it for a student to finish a Master's degree at a school and to be rejected for a PhD at the same school?

One very obvious thing would be availability. My department has around 100 masters students each year, but will only have 7 PhD places. We pretty much take as many masters students as we can (because they pay). As you can imagine, this is not always popular with the people that have to supervise them for their dissertations.
Master degrees are funded by the student (either directly, or via a loan). PhD positions are funded by external funding bodies or scholarships.


In what order should existing inter-related research be cited in a journal paper?

I think you should cite them in the order how they appear in your text and not the year which it was published.


Getting a Masters in computer science but I am without any undergraduate degree

What You study in the bachelor in computer science is different from what you do in a working environment. In the bachelor's degree they teach you the basis to achieve a master's degree, like math, science and other subjects that probably you've never studied from an academic point of view.
I live in europe and I believe all the european universities require a bachelor's degree in order to be admitted to the master programme.


To ask for a PostDoc position in the university X, is better to do it by myself or to ask to my supervisor?

Put yourself in the shoes of the professor: what would they like best in a candidate? Contacting them yourself demonstrates more commitment than having your advisor do it for you. There may be cases where an introduction by a third party is best, but it seems to me it's better to use that only if really needed: guy is a superstar, your introductee knows him very well, or you are just trying to strategically probe whether a candidature would be well-received without actually getting involved yourself.

Also, you can get your advisor to follow up if you don't receive an answer, or just to help you when/if they are contacted as a reference.


In Australia, "PI" means partner investigator.  This is someone who is involved in a grant application but is not eligible for funding.  For example, they might be an international collaborator.

A grant applicant is a "Chief Investigator" or "CI."

Reference:  http://www.arc.gov.au/eligibility-matters


Any chance for an overseas student to pursue online courses and get a degree?

In mathematics, some graduate degrees are offered online, but you should be careful.  There are real advantages to doing it in person, and most of the schools offering online degrees are not well respected, so if you select a program based on internet advertising, you will probably waste your money without learning very much or ending up with a valuable credential.  (It's depressing how many businesspeople view distance education as just a money making opportunity, without any serious commitment to doing a good job.  When you investigate online education, please keep in mind that many web sites are trying to sell you something of questionable value.)

One respectable example is the University of Washington, which offers an online M.S. in applied mathematics, and there are some others like this.  They could be viable options if attending in person is impossible.  I do not know of any well respected math graduate program from a 100% distance education university in the US, so you should be very suspicious of such programs, although perhaps they exist in other countries (Open University?).

There is no worthwhile online Ph.D. program in mathematics.  If your only goal is to get the degree itself, for example to move up in a salary scale for a job you already have, then it might be possible, but you would have to look carefully to make sure the program is accredited, and even so it won't be an impressive addition to your CV.  If you are hoping for a career in academia or industrial research, don't even think about an online Ph.D.  If an institution offers an online Ph.D. in mathematics, and presents it as being just as good and respected as a traditional Ph.D., then you should be extremely suspicious of the entire institution.

As for computer science, I don't know as much about online master's programs, but the issues are similar and I imagine the conclusions are as well.  The online Ph.D. situation is definitely the same as in math.


Multidisciplinary Science & Engineering - Too overwhelming for industry/ academics?

I think that this is easier to accomplish for a senior researcher than a relatively new one. Academia tends to value specialization in research, so at the beginning of a career you may need to focus your efforts, and your applications, on some specialized area.

But many of the big questions can only be answered by taking a broader look, so it is a mistake to think that a multidisciplinary approach isn't valued. But it may be harder for a new researcher to convince people that you can do serious work in more than one area, or that you have sufficiently deep understanding that you can bring those multiple threads of thought together in a coherent way.

The trick is to get a good position (tenure) so that you have the freedom to work to your own muse. Once you have some sort of reputation, people will defer to your ideas more than they will for a new, and possibly misguided, free spirit.

Our education system seems to start out broad, then go narrow and deep. Then you can freely broaden it again from a solid base.

Note that there isn't anything right or wrong here, but it does seem to be a common conception.


Can publicly available datasets which are hosted in Github be used in research papers?

I can think of at least a couple issues.

Is the data actually available for use? Just because it is on Github does not necessarily mean that you can legally use it. You still need to determine how the data is licensed (easy if a license is published with the data, possibly difficult otherwise). I'm not exactly sure how data on Github is treated, but code published on Github is "All Rights Reserved" by default and I assume data is similar.
How do you know you can trust the data? One reason you cite the owner or original creator of data is to assert that it is reliable. If the data you're using is not from the source, you'll also want to cite where you obtained it and hope that it's a trustworthy source.


Is doing a research internship during MSc. studies worth exceeding the standard period of study?

This is a matter of balancing trade-offs and can be viewed in a variety of ways. While I won't go into all of the many ways, here are two ways that taking the internship could be perceived:

1) You were not able to commit to something you agreed to commit to at the start. Your leaving for a better opportunity may be interpreted by potential PhD supervisors as an inability to stick with a program.

2) You found an opportunity to build a new network of collaborators, gain new knowledge, experience, and perspective. You will also be making money, which can be used to make your life easier later on.

There are infinite ways to view the trade-offs, but only you can make that distinction.


Should I accept this unfunded offer from my dream school or wait for funded offers?

Unless you are independently wealthy, you should never take an unfunded offer for graduate school in mathematics.
Even before the pandemic, some people with a dozen good papers after two successful postdocs - a well above average publication rate - were failing to find jobs.
When I was last broadly applying for academic jobs 10 years ago, the general advice was to send 80-100 applications to jobs you were competitive for in order to have reasonable certainty of getting at least one offer.  Even before the pandemic, there weren't that many jobs in total to apply for, and each job gets more applicants than they did 10 years ago.  (This year is brutal; the only people getting research-oriented jobs will be AMS Sectional plenary lecture candidates (there are roughly 40 per year, total - that's less than the number of Berkeley+Stanford PhDs per year) or better.)
There are even fewer jobs in industry for which a math PhD is a better qualification than several years of experience.
For a more teaching-oriented academic job, the funded position at a lower-ranked graduate school is actually better preparation, because you will be teaching for your funding, and because the undergraduate population at a lower-ranked school is generally more similar to the undergraduate population at most universities than the undergraduate population at a highly-ranked school.
If you borrow money for graduate school, you could end up in a situation where you are unemployed with no means of paying back your loans.  Don't forget education loans cannot be discharged via bankruptcy.
Going to graduate school in math with funding is already a costly decision from the financial point of view, though it's fine if getting to spend a few years doing math is worth it for you (as it was for me).  Going to graduate school in math unfunded is potentially ruinous.


I feel burned out after finishing my master. Should I take year off before the PhD?

I would definitely advise taking a year off if you indeed feel as you've described. Burnouts are common and costly, and you might want to prevent one at all costs. There is nothing wrong with taking a break. Even though in academia it's sort of subliminally assumed that you're going to sacrifice your life, sanity and your unborn children to research, there really is nothing bad to say "hey, I need some time to myself." And no one is going to care, least of all admissions committees. You can even turn this break to your advantage by doing some volunteer work, or part-time research work. Seriously.

Personally, I spent 5 years doing undergrad in psych, then 2 years doing a Master's and by the time I finished my first year of PhD in clinical psychology I was so burned out after 8 years of post-secondary education and 5 years of constant academic research that I crashed & burned and dropped out of the PhD. Periods of rest are conducive to general sanity. Best of luck.


Paper ending: conclusion vs. conclusions

According to the Little, Brown Compact Handbook, in MLA style the final section is called the "Conclusion", while in APA style the final section will be labeled "Discussion". When using either citation style (and I would assume this holds no matter what citation style you are using), this section will contain your summary/interpretation, the conclusions (plural) that you wish the reader to take away from the paper, and perhaps a call to action or an outline of future work. So you are right,

  conclusions [are] things to take away from a paper, and a conclusion [is] the end of something...

though not necessarily the end of a book; a conclusion can be the end of a paper, article, etc.


Posting to ArXiv a longer version of a submitted journal paper

It's not extremely common, but you can find significantly extended versions of published papers out there on arXiv, authors' websites, and the like. And at least in my filed of research it doesn't seem like that big of a problem to post an extended version after publication if there is a merit and clear reason to do so instead of cramming everything in one place or writing a weak paper out of what is left out.

For example, this paper on arXiv is an extended version of a paper published in the IEEE Transactions on Information Theory and explicitly states when it was first submitted to the journal, when a revised version was submitted, and when the extended version was uploaded to arXiv (which was after submitting the revised version to the journal but before it got accepted for publication). There is a slightly updated version of the extended one on the personal webpage of one of the authors as well.

In any case, I think it's generally a good idea to respect the editor's opinion unless you have a strong reason not to follow their suggestion. But you may also want to ask the editor if the journal has online-only storage for supplementary materials to officially attach what they asked you to cut out and/or if the journal is ok with uploading the originally submitted, longer version to arXiv. If arXiv is common in your field, I highly doubt they say no to posting the longer manuscript online; if it's not allowed to post a preprint you submit to a journal, how on earth can we use arXiv as a preprint server anyway? What would they do if you had already posted the longer manuscript on arXiv before submission to the journal, for example?

My feeling is that as long as you don't abuse the system, it's ok to post an extended, fuller version online (with a clear note that it is an extended version of a shorter paper). So, for example, if the editor is not happy about a lengthy, marginal part which you think is helpful and of interest to some but perhaps not all readers, I don't see any reason not to upload your original manuscript to arXiv. You should check the journal's policy and the norm in your field first, though.


How are reference letters for postdocs submitted?

Postdocs in mathematics in the US are universally* handled through MathJobs, which was commissioned by the American Mathematical Society for this purpose. Recommenders submit a single letter, which can then be attached by the applicant to any number of applications, without ever giving the applicant access to the letter. Recommenders can also send a more specific letter to particular schools if desired.

This system has been so successful that it has been made available to other fields as AcademicJobsOnline by the Duke University Mathematics Department, who originally created MathJobs.

I do not know whether positions in Eastern Europe use MathJobs, however.

*If anyone knows of a postdoc in math in the US that does not use MathJobs, I'd be interested to know; it's been a few years since I last heard of one.


In your circumstances, your best bet is likely to study in your home country. Many EU countries have stipends or student loan schemes targeted at qualifying local students that could otherwise not afford higher education. If you are willing to work next to studying, the world is basically your oyster anyway - many/most institutions in Europe allow students to work next to their studies even if the program is nominally full-time (of course the university does not look for a job for you, that would have to be your responsibility).

In your circumstances, moving to a different country to study will be a lot more challenging. Student loan schemes and stipends are often not available to foreign students, and funded study places basically only exist for the PhD level.


Self-plagiarism: Copy part of thesis for blog posts?

You should do two things:
1) Discuss this with your advisor. He/she will know the regulations better than we do.
2) Make it clear on the blog that you the blog-writer and you the thesis-writer are the same person, e.g. by using your real name.

Another issue, that you didn't yet consider but that surely needs consideration is the copyright for your thesis. At some universities, the department/university library wants at least some rights on your thesis. If they then find parts of said thesis copied verbatim to an online platform, you might get into trouble. It might well be that this is not the case at your university or that they don't care as long as you cite your thesis, but this is something you need to clarify before posting stuff.


Importance of degree and publication vs. degree alone

A tangible advantage can only be measured for an agreed upon measure (or "utility function" if you prefer).  This is a classic misstep in attempts at persuasion.  I can't convince you to do anything (or appreciate anything) if I don't know your core values and phrase my arguments in terms of those values.  Unfortunately, the phrase "future job prospects" is rather vague, so I will guess a bit at what you're hoping to pursue and accomplish.

First suppose that you're considering getting a PhD in the future.  This one is easy.  If you do go for a PhD, a large chunk of your time will be spent on research and publishing.  What exactly this looks like varies significantly even within math, depending on how applied your subfield is.  However, if you stick with the same subfield (or even one nearby), then publishing a paper during your masters will often give you a reasonable sense of what you'll be doing during your PhD.  This will help you to know whether you want to get a PhD or not.  Having published a paper during your masters will also help convince the admissions committee that you are likely to succeed in a PhD program, and improve your chance of being admitted to a PhD program.

Suppose instead that you plan to pursue a job that requires technical writing skills.  This one is pretty obvious too.  Writing (as with most things) is a skill that you acquire only by doing.  Many (most?) journals require a higher quality of writing than is typically needed in your masters thesis.  They also require you to write in a certain style, to a certain audience, etc.  Being forced to do this will make your writing better.

Finally, suppose that you want to convince someone that you take initiative or that you conceive a project and see it through.  In either case, having published a paper can serve as good evidence.  Like most things, after you've published multiple papers, the process will get faster (though not likely fast).
But the first time you do it, you'll invest a lot of time, and often not know quite what is needed.  This can be frustrating, but also rewarding when you succeed.  The ability to teach yourself new skills is far more marketable than anything you will learn in grad school.


What should I focus on to get admission in a Masters programme in the US?

Please keep in mind that only a small percentage of Master students get funded.

It's less competitive to get into a Master program than a PhD, mostly because the students pay their own way.

If your grades are not the best you should try to get high GRE, good reccomendation letters, and possibly to some research during your Bachelor.

Are any particular reasons why you chose the US? There are many other school around the world that would cost you less and get a good education as well.


Potential advisor ask for a paper review as a part of interview process, any difference between journal and conference paper?

Actually, in CS, conference papers are treated with great respect. Much more so than in some other fields. In CS, most new results are presented in conferences and the proceedings are very important.

So, contrary to your worry, picking a conference paper would probably be preferred.


How can I approach my professor when he is sending me indirect messages with another person?

Have you contacted the second supervisor about this problem? If yes what does he think about this problem? Is he able to contact the first supervisor?

If you haven't contacted the second supervisor about this problem I would do so ASAP


I occasionally participate in answering academic questions in online forums when I hit a block with getting on with my thesis.

No worries, we all procrastinate (ehm... cough cough).

  I often cite a particular large and well-known academic source in my answers. I have my own copy of this book.

You really don't need to own a copy of a book to cite it: many, if not most, academics borrow the books needed for their work from the libraries. Moreover, its cost is irrelevant to your question.

  I am wondering whether it would be academically unethical of me to link directly to this resource in my answers, given the questionable copyright status of archive.org.

If the archived copy is legal (e.g., the publisher might have released the copyright because they no longer print it), it is certainly ethical to link it. However, I'd avoid referring to the copy if it's legality cannot be reasonably established. In addition, should the copy be removed due to copyright infringement, you would end up with a series of broken links.

It is worth noting that links to books are seldom seen on academic papers, unless a book is exclusively available online. Therefore, the issue is more related to whether or not posting the link online.


Are virtual machines good for reproducibility and open science?

I like to think of VMs, containers, and the like as allowing repeatable research. I don't consider it reproducible if the results can only be repeated by having exactly the specified VM/container used by the original researcher.

That doesn't mean VMs or containers are not useful for open science; they do provide a means for people to rapidly disseminate the computing environment within which the results were produced. They also provide a point of reference should software used change at a later date which causes repeatability issues. If open source software is used it would be possible to track down what changed and why this affected the particular results.

At the very least, VMs and containers provide a good means with which to document the computing environment used to generate the published results.


Thomson Reuters does that for all fields: http://highlycited.com/.


Why do some academic journals requires a separate "summary" paragraph in addition to an abstract?

They serve slightly different purposes.

Specifically, the abstract is what you'd tell your coworkers; the significance statement is more like something you'd tell your mom.

The abstract is meant to quickly summarize this particular paper. A good abstract will provide a little bit of context or background, lest readers wonder why you're studying gene X or brain area Y, but the bulk of the abstract is approach and results. "Here, we show...." The significance statement is meant to put your work in a broader context and explain/justify why your article is worth publishing. (I suspect these are also helpful in attracting media attention, if that is of interest).

For example, suppose your paper investigates an antibiotic resistance gene. The abstract might look somethng like this one from MacMahon et al. (2009):

  The ardA gene, found in many prokaryotes including important
  pathogenic species, allows associated mobile genetic elements to evade
  the ubiquitous Type I DNA restriction systems and thereby assist the
  spread of resistance genes in bacterial populations. As such, ardA
  contributes to a major healthcare problem. We have solved the
  structure of the ArdA protein from the conjugative transposon Tn916
  and find that it has a novel extremely elongated curved cylindrical
  structure with defined helical grooves....

This briefly hits on the context, but doesn't really delve into it. A significance statement would talk more about this healthcare problem (e.g., X patients have multidrug resistant infections) and how this paper helps solve it (target for co-treatments or whatever?).

Edit: take a look at the PLoS Computational Biology guidelines and examples (linked therein) that @cheersmate found for some more direct comparisons.


How to avoid plagiarism when reciting a list of technical terms word-for-word from another article?

If you enclose the text in quotation marks and cite the original source, it is not plagiarism.  If it is a list, a quotation makes more sense than paraphrasing.


Should I mention the number of followers of my blog in my SOP for grad school?

(a) There is not harm in mentioning it. Of course, how they interpret it is up to the department. In my cohort (social sciences), there was one student with a blog that he runs that generates quite some views. I am sure he included that (views) in his application.

(b) I would imagine it can only have a positive effect on your application.


Transferring Master to Master, different country/ LOR issue

Imagine for a moment that you are a trailing spouse.  You have fallen in love with someone with a job in City X, and s/he is not in a position to relocate.  Transfers in this case happen all the time, and there would be very little difficulty in asking for a letter of recommendation (LOR).

I suggest you say to your supervisor, "I love the coursework here and I love working with you, but it's become necessary for me to transfer to City X for personal reasons.  Would you be comfortable writing me a letter of recommendation for University X?"

If you have a close relationship with your supervisor, and s/he asks you what the personal reasons are, AND IF YOU WANT TO REVEAL MORE INFORMATION, then you can add, "the culture and surroundings here are just torturing me."  But probably it would be best to leave this out, especially if you are not 100% certain your supervisor will not spread your comments around.

Bravo to you for taking care of yourself.


To avoid plagiarism you need to cite most things that you use (exceptions below). It isn't a question of paraphrasing or not. If you use it cite it. Sometimes it is better to quote than paraphrase, but using other people's actual words is more a question of copyright than plagiarism. Plagiarism is making it seem like the work of others is actually your own.

The main exception is "common knowledge". You don't need to cite the fact that the Earth is roughly spherical and not flat (Sorry, Terry Pratchett, RIP). You don't need to cite the definition of the derivative in math. But if you get something out of a paper, it is most likely that it needs citation.

And, citation requires more than just the name of the original source. A reader of your work needs to be able to go back to the original and see the complete context of the idea, including the paper it came from and any references that appear there. A chain of evidence is vital to scholarly work.


Is it good to label papers as Part I, Part II?

You can do that, though a better approach may be to title them something like

  Hypersingular monoids in graph theory. Part I: Definitions and basic properties

and then

  Hypersingular monoids in graph theory. Part II: Applications to semiregular smoothness theory of spiked stars

This way, you're a bit more expressive than just part 1 and 2.

The downside of this approach is that good journals will ask you to make sure that either "Part I" is already self-contained and of independent interest (which is probably difficult to achieve if you are currently splitting up something you've already written), or that you submit the two parts together (so that the combined oeuvre can be reviewed as a whole). The latter, of course defeats the purpose of splitting it in the first place.

Long papers are a hassle all around. It's difficult to get them through the review process, and much depends on what concretely you have in the paper(s). As a consequence, there is little that can be said in terms of specific advice in your situation without knowing the details of the paper. Talk to some of the experienced people in your field about the situation and ask them how they would suggest you handle it!


I would suggest that you include the work you have read, as well as the works that the other papers mention. The purpose of the literature review in a paper is to describe related pieces of work, and showcase how your work complements, surpasses and stands out. This strengthens the narrative of your research and helps the reader understand what makes your paper valuable, compared to other approaches. In order to achieve that and build a more complete image, you need to include as many related papers as you can find and study in the literature review part.


Are there US universities that do not need GRE and TOEFL score for admission in PhD in Mathematics?

The truth of the matter is that while you may find many schools that do not require the GRE, virtually every US school is going to require either the TOEFL or a similar test such as the IELTS.

The reason for this is that one of the important criteria for admission to most US graduate programs is the ability to do coursework and interact with fellow graduate students and faculty in their lingua franca, which in the US is English. Consequently, schools need to ensure that the students they accept have a certain level of proficiency in English before they enroll. (A number of grad school admissions officers have mentioned that they blacklisted candidates from certain countries because of problems related to fraud—candidates would hire other people to conduct telephone interviews with universities in the US, and the actual candidate would come with hardly any English whatsoever.)

So, for most schools, you will find it a requirement to be able to speak the dominant language of instruction—and not just in the United States. (For instance, all students at our university must show the ability to speak either German or English, depending on the program to which they apply.)


Is teaching a graduate course with 30 students an unreasonable expectation for a PhD student with a TA contract?

It is incredibly common for the number of hours devoted to teaching be woefully inadequate to deliver good instruction except possibly for highly seasoned instructors teaching the exact same course multiple times.

Unfortunately, I don't know any fair solution to this.  You'll probably spend two or three times longer than the expected number of hours in order to do even an adequate job.  From what I observe, people cope either by working far more than they're supposed to, or by delivering not-very-good instruction.  It's a difficult spot to be in.  (Alas, not the only difficult spot in academia.)

The bright side is that if you're really interested in teaching and put in way more time than you're "supposed" to, next time it won't be as bad (you'll only have to put in somewhat more than you're supposed to), and if you do well you will both help your students and be known as someone who is a good teacher (good if you want to do more teaching).


Emailing supervisor after applying for phd to discuss about research problem and funding

Hope you are well.
Okay so since you have already applied to the program as per your supervisor - You can reach out to him through email to let him know that you have applied to the program and you will be keeping him in the loop in case of any updates. Along with this you can then ask regarding the research question and its specifics - Make sure the email is not too long though.
Also, and you may find different people with different opinions on this - I would advise not to bring up the funding question in the first email - if he replies to your email you will be sending after admission submission - only after that you can go for the funding question.
Saying this because certain times supervisors do not have funding readily available and are always looking for students that are self-funding because that is in their favor ofcourse.
Hope it helps - Let me know if you need help with something.
Thanks.


Math/stat postdoc: how important it is to be a 'named' postdoc?

Very few postdoc positions are endowed, and most of those are at universities that are already very good. As a consequence, the practical implications of being on such a position are relatively small: If you get one, you're pretty much by definition already at a good university, and the delta in prestige is pretty negligible.

What matters are (i) your publication record, (ii) which institutions you've been at, (iii) your letters of recommendation (all not necessarily in this order). What kind of postdoc position (endowed, grant-funded, teaching-supported) you had is not a relevant decision criterion in my experience.


In the US, Psychology is rarely considered part of the arts, and is generally called a "social science", with most degrees being offered as "bachelor's of science". Oddly, psychology is often excluded from "STEM" designations, where it is often not considered under the umbrella of either "science" or "technology". For more info on this, see the American Psychological Association's article on Psychology as a Core Science.

Regardless, at least in the US, Psychology is generally not classified as an art. It's a field in kind of a weird place, classification-wise. There often is some flexibility in degree classification here, as many Universities allow you to get a "bachelor or science" (BS) or "bachelor of arts" (BA) in nearly any field (even something like Physics or Math). The BS vs BA classification often is just a question of what other classes you take, such as in language (BA's usually require foreign languages and more classes in humanities). Just in case things aren't quite confusing enough for you.

Psychology's position as "social science" is something in-between the humanities and science-proper, with some areas clearly being heavily related to the arts (such as dance psychology), while some are actually housed within engineering schools (human factors, psychology of engineering, etc). Still other fields - or descendants - of psychology are hosted in schools of technology like computer science (human computer interaction, for instance). So the field of psychology, perhaps more than most fields, tends to defy easy classification and every institution has their own unique interpretations and departmental history.


Should those more interested in research choose a postdoc or teaching position?

If you want a research position, you should go for the postdoc: a heavy load teaching-centric position will make it hard to publish, which will make getting a research position much harder.


Decision making paradigm for career planning

Since the purpose of this question is to ask for general decision-making strategies that might apply more generally, here are some (that also impinge on this case):

Acquire information: Get as much information as you can that would affect the decision: in your case, estimates of time for the visa process, and so on.
Determine the "real" timeline for decision making: in this case, do you really have to decide in three weeks ? can it be delayed slightly ? and so on.
Determine how "permanent" the decisions are: can you negotiate a 1 year contract ? Can you defer the postdoc ?
Separate out facts that affect the decision from feelings/opinions: Is it true that "if the visa comes through I'm going without a doubt" ? If so, then everything depends on facts regarding the visa. Is it instead true that "if the visa comes through I have a preference, but I do enjoy teaching and like staying in the US" ? In that case, there's a personal preference coming into play that isn't usually resolved by "facts", and so timelines and data collection don't matter as much as (or are influenced by)  some soul searching.


Can I ask again about a postdoc position after a year has elapsed?

You can certainly ask again after a year (or less, perhaps). She may have forgotten, or may just be busy. There shouldn't be any issue with such a mail. You might also use the mail to fill her in on what you've accomplished in the interim - briefly.


Just starting in grad school, I haven't heard from my advisor in three weeks …

It is very important to have frequent communication with your advisor, even if you think you have nothing new to say. And it is NEVER too late to email her. Just tell her the truth, just like you described above. Advisors want students who are honest and can make adjustments as needed. I am well aware of how awkward it can feel to meet with your advisor when you haven't accomplished everything you think you should have or when you think you're running behind schedule, but that's what weekly meetings with advisors are especially good for - evaluating what the next steps should be and how to change things around to get things done.


Could anyone judge whether or not what I have experienced are types of abuse?

I would not call this abuse, but I would say that this professor is clearly not interested in working with you. Not answering emails, not meeting with people in a timely fashion etc. are all indicators that the professor just thinks that you're not worth their time. This may or may not be true, but that really doesn't matter - it takes two to tango in an advisor/advisee relationship, and you don't have a partner in this professor.

I don't quite know how your university works. It sounds like you were assigned to this professor semi-randomly to (I'm guessing here) start some project while you look for a permanent advisor. Whether the professor violated some of the rules of this mentorship process (say, they have to meet you a certain number of times or help you actively, however that's defined) is really not for me to judge - you should consult with your student counseling center/ombudsperson/graduate handbook about this.

Overall, my advice is to look for someone else to advise you, ASAP. This professor is not going to offer you a happy PhD experience in my opinion. If that means changing your field slightly to accommodate some other professor's interests, I would do it. If that professor is the only person in the department qualified to advise you on that field, and you are unwilling to change fields, you have a problem. No one can force a professor to advise someone (I would never want to work under someone who was forced to take me anyway, that would be hell for us both!), so you need to figure out what matters to you more - staying within that narrow field, or actually getting an advisor in that university.

Good luck!


Do I have any potential in the academic field?

since I have to study anyway, why not go for GRE+TOEFL, MS in IT or Computer Science and then a PhD degree from USA

Maybe you're aware of this, but "studying" has little to do with getting a Ph.D. It might suffice for an MS, but a good MS involves more than just "studying" as well.

In other words, if (as stated) your idea is that instead of "study" to get a promotion, you want to study to get an advanced degree, you're in for some disappointment. A graduate degree (especially a Ph.D) involves a lot more "doing" and independent creative thinking.


I drunkenly told a professor something fundamentally wrong about a friend's thesis work. Should I clarify and/or apologize?

I don't see why Germany should be any different from other places, but generally it is a good idea to apologize for stupid things said drunkenly. And since this may have a bearing on the reputation of a third party you probably have an obligation to make sure the record is correct.

Sooner is better than later in such things, so the professor doesn't spend effort on a lost cause.


Permission for changing the title of a paper

What you write seems fine. Until very late in the process, the title should, in my view, be tentative. It should best express what the paper says. Especially if recommended revisions have changed that, or your view of it, by all means change it and just let the editor know.

If you get pushback, or refusal, from an editor, you can deal with it then. But, IMO, it would be improper to refuse.


Is it OK to contact authors of the research paper requesting an implementation?

That is three questions, i.e. two more than the allowed quota for a
post :-)

Seeking more information on a topic, within legal limits, is your privilege.

It is always OK to write to an author about any aspect of his works,
as long as it remains a civilized exchange (which is sometimes not
the case). It should be preferably clear that you have a technical level that justifies taking his time. This should show in the style of your request, not by listing degrees and achievements.  Just be very simple, clear, and direct.

He may reply or not, or tell you what are the limits on what he can
tell you if some of the work is confidential.

But you should first try to see what is available on the net from him
or others who may have collaborated.  People are usually friendly, but
sometimes swamped with requests, and try to save time by preparing
answers on their web site, or the web site of their organization.

So, writing is encouraged. Asking for more papers or implementation,
or experimental results, is fine. But always try to spare the time of
the people you write to, and avoid asking idle questions or using the
exchange of mail as free tutoring.

All papers, all writings are intellectual property (IP), including this
answer to you, which I happen to put under a creatve common licence,
so that you do not even notice it is intellectual property.

An IEEE paper is also IP, usually owned mostly by IEEE, but there are
many more detais to this (search the web for "open access" and "Berlin
declaration").

But the IP concerns only the text of the papers, not the ideas you can
find in it.  So you are quite free to rewrite the content of a
scientific paper (not a novel) in your own words and distribute it ...
with due acknowledgement to the original author as the creator of the
ideas, and reference to his original paper.

IEEE may own IP rights on a paper, but that implies in no way any
right on the implementation of the ideas, on the experimental results or other preliminary work conducted to produce the paper, or on derived work,
including the notes a teacher can write for his class on the topic of
the paper.

Does this answer your questions?


What am I expected to say about teaching plans in an interview (UK)?

You can always ask if they can give you any further guidance about what they are looking for in the 'teaching' part of the presentation. I imagine this is also somewhat field-dependent: what is expected in a humanities department may be rather different from what is expected in a lab-based science area. However, generally people:

Summarise what teaching they've done in the past, highlighting anything impressive (positive student outcomes, innovative approaches to teaching...);
Identify which aspects of the department's current courses they could contribute to, and particularly any areas where the department is currently lacking expertise (tactfully!);
Perhaps sketch an idea for a new course that they'd like to put together if they got the job.

In a 15-minute talk, one slide on each of the above is probably a reasonable starting point.

In response to OP's clarification that the advertised position is specific about the module to be taught: I think the same general points apply, but you should focus a bit more specifically on that module: Why is it important? How would you approach teaching it? What makes your version of that module better than the other candidates' versions? However, I don't think it ever hurts to show versatility: don't focus on that module to the exclusion of all others.


How can a prospective PhD student assess whether a potential PhD advisor is hands-on or hands-off?

Just ask their graduate students.  There’s no reason people won’t be frank about this question, hands-off advisors don’t think being hands-off is a bad thing and vice-versa.


What are the acceptance rates at various CS masters degree programs?

I suspect that most programs do not post their acceptance rates at the master's level. That's in part because they could be subject to wild fluctuations from year to year, as the number of applications change.

In particular, one other thing to consider: most graduate programs have a target of incoming students they want to enroll. They will generally admit only as many students as they feel they need to reach the goal. If students are accepting offers at higher-than-expected rates, they may lower the admit rate in subsequent years to compensate. Similarly, if they are under their target, they may admit a larger than expected pool.

Considering top-tier schools, my suspicion (although I don't have the numerical evidence) is that they get enough qualified applications that admissions now are partly a "lottery": if you meet the qualifications of a typical student, you may or may not get in, depending on the needs of the department in that particular year. So just do your best.


Why do universities have to spend money on journals?

This is a really big question, which unfortunately has no simple answer.  Some short comments:

Universities have very little choice about subscribing to journals, as long they publish good papers, since faculty need access to those papers to do their research.  The solution has to start on the publishing side.

Collaborating to create free, open access, peer-reviewed journals is a fine idea, but either you need to convince universities to support this financially, or you need to recruit enormous numbers of dedicated volunteers.  (Whenever this topic comes up, someone is sure to point out that volunteers run some free, high-quality online journals.  Of course they do, but the question is how to recruit hundreds of times as many volunteers.)

Printing is a non-issue.  Everything is already available online, with printed copies only for those who want them.

In a mathematics context, see http://gowers.files.wordpress.com/2012/02/elsevierstatementfinal.pdf and http://arxiv.org/abs/1204.1351 for more details.


How can I find the DOI for an old mathematical paper which is not in English?

As others have said, not every (old) article has a DOI or a URL. However, in mathematics every article since 1940 has an MR number which uniquely identifies it. So go to mathscinet and look up this article. I just did, it has MR number MR0844292. The bibliographical information on mathscinet (like the transliteration of the author's name) would also be considered the "canonical information".


My answer is more to the question How future proof is the arXiv?.
How future proof is anything in this day and age?
The license itself is built on the idea that the system will continue roughly as it currently does, but substantial unforeseen changes both technological and of society (doesn't have to be a war) can easily derail it, as you have outlined in the various scenarios.
However, I don't think there is any reason to worry (your scenarios are too pessimistic), since the arXiv serves a very good purpose to all involved parties:

authors can quickly disseminate their results to all interested,
the scientific community (in fact the world community) get open access to (preprint versions) of many published articles (most in certain fields), and
the journals get a free preprint publication service which boosts their visibility and hence impact (since citations will be to the journal version, not the arXiv version - I know of no journal that disallows publication at arXiv). If a journal reverts this policy (in order to earn on copyrights), most authors of good articles will turn away from it.

Because of these points, funding at Cornell should be possible into foreseeable future.


I have the highest regard for Georgia Tech and a couple of my former students earned doctorates there. But I worry about any online program that has over 10,000 enrolled students. My worry is that, unless you are extremely well motivated and already know how to learn at a high level, you won't get the support you need. Certainly not the support that you get in a smaller face to face program.
Getting some publications out is a good idea, of course.
But, you've asked another question here about studying in US. I suggest that you apply to some universities here, covering a wide range of research universities, and see it you can get accepted. You may well not need any additional steps.
Don't just jump into a program because you've read that it is "important". In fact, others will also try to jump in, increasing the competition. Think, instead, of what you want to do as a career and take steps to achieve it.


Should I say anything having found out (accidentally) problems with my teaching?

Consider that it may not have been the quality of your teaching that was the issue.

From your description it sounds as if the course was a shambles (probably best not tell us what university this was). Asking an inexperienced teacher to create 32 hours of Masters-level lectures, from scratch, to a large-ish class, without (from your account) any significant discussion of curriculum or assessment?! And hourly paid?  There are circumstances in which each of these would be semi-reasonable, but your account paints a very disappointing picture.

It's quite possible, for example, that the ‘obvious reasons’ are that the course leader/convenor/chair discovered after the fact that you'd omitted to cover a topic that was deemed vital for that course – perhaps the curriculum is constrained by pre-existing assessment or other course dependencies – but which the course leader had never told you about.

The above is of course speculation, but it might be useful for your peace of mind if you can discover if the issue was the quality of your teaching or some other organisational issue. If you are sensitive enough to your teaching, and to its reception, to be able to detect that it improved notably between the first and second cycles, then I would guess that it was at least OK.

Bear in mind, however, that if the real problem was that the course was badly organised, and you badly briefed, then the course leader and their colleagues might be rather sensitive or defensive about it, and you might have to bear that in mind when discussing it.  Also, bear in mind the possibility that – unfortunately and very discreditably – the course administration may have dealt with the problem by blaming the conveniently temporary and now-departed teacher: ‘an inexperienced teacher...; I'm sure I told them what to cover...; anyway, they never asked me....’

If anything like that is true, then it seems unlikely to me that there'd be any longer-term comeback to you. It's even possible that they think of you as someone who was placed in an impossible position but still managed to achieve something.

If you only want to find out details, rather than complain, then an informal setting for a chat might be more informative than a multi-person meeting; and if you know any permanent staff who taught on the course, they might be more usefully indiscreet than the course leader.


What research expenses to request for early career fellowship?

The following list is very subject dependent, but some items you might want to include are:

High Performance Computing time (e.g. comp-sci, physics, maths, chemistry etc)
Lab or equipment hire costs
Research technician time (i.e someone who might help acquire data or do some other more routine tasks)
The all-encompassing "computer-consumables" (that covers quite a lot)


What to do with teachers who think their subject is "extra special" and gives students too heavy a load?

This is just what you should be expecting from your postgraduate degree. Each module is special. It should push you further than any undergraduate module would.

You are also now assumed to be a grown-up, and to learn how to manage your own workload, and to balance competing demands on your time and energy. Part of what a Masters or Doctorate course does, is to teach you research skills, and project management. These are (at least, in the courses I've been involved with), an important part of the process.

If you are having trouble balancing your workload, talk to your personal tutor, the graduate tutor or whoever else it is who's been assigned to you by the department to manage these cross-module issues.


Screwing up a single small quotation in the manner that you describe could not reasonably be considered plagiarism.

While yes, it is true that you did not correctly attribute some words, from your description is appears that the attribution is not so much missing as misplaced.  Moreover, while I cannot entirely judge without reading the actual text, it seems likely that any reasonable reader would likely be able to tell from the context that you are not attempting to claim the quoted text as your own.

It's still good practice to go back and correct, if your institution allows it, but don't worry about being accused of plagiarism over a single typo-level error.


Coping with not speaking local language, as an academic?

Learning a language is a lot of work, particularly if it is not that similar to languages you already know.  So it's not an endeavour to undertake just because you might get a job somewhere later.  You need real motivation to learn a language properly.  The main reasons I see for an academic to learn a language properly are: because you enjoy learning languages, because you plan to spend a lot of time in a place it will be useful, or because you need it for your academic work.

If you are serious, in academia there are resources that may be easily accessible to you.  The main ones are:

take/audit language classes at your university before going there
take language classes for foreigners at your destination university

Universities get a lot of foreign visitors, and depending on the university, they may have other support besides their own language classes.

I did a 1-year postdoc in Japan, and one piece of advice I got from someone who was doing a postdoc there before me was start learning Japanese as soon as possible.  So I studied Japanese for about a year beforehand both by taking university classes in the US, as well as some extra studying on my own.  I also took lessons in Japan, as well as studied on my own.  While my Japanese is still far from a native level, after a couple months in Japan, I could handle most non-technical communications on my own in Japanese.

I do want to stress this requires real effort on your part, and it's hard if you don't really enjoy it or aren't serious about it.  I met several foreigners there who just attempted to learn Japanese by osmosis and maybe some small efforts on their own, and even if they had been their many years, they couldn't have a real conversation in Japanese.


What should you ask an applicant's reference?

This may well depend on the country. In the US, being the litigious society that it is, there have been some people going after (legally and non-legally) people who give negative references. The candidate can have a stronger case if you are contacting someone they didn't approve. Now, there is freedom of speech and many, many other issues but simply put, some people in the US are scared to give candid assessments unless the assessment is positive.

So, I would tend to take the response you received as an implied negative but I would also have to keep an open mind that the referee simply did not want to answer and it might not reflect at all on the candidate.

As for the questions you ask, they seem quite standard and I don't believe anyone would be taken by surprise by them. However, they might not answer out of fear.

On a side note, when it comes to reference checking, you need to be sure you are getting are response from the proper person. Emails get hacked, fake accounts get created. I personally prefer doing my reference checking over the phone. This may also come across as a casual conversation without written evidence, making the referee more comfortable in being candid.


non-responsive academic program advisor/manager

This seems to be an administrator level problem. Escalate it through the administration as necessary. And get your advisor to argue on your behalf. It seems odd that someone would disapprove a course that the advisor approves.
But there is probably a better advocate for the visa problem. If they aren't doing their job, escalation is warranted, and perhaps necessary.


Etiquette of wearing the wrong academic robes at graduation as a lecturer in the UK

In the United States, there are typically two acceptable pieces of regalia to wear: either your university-specific regalia or a "generic Ph.D." regalia that is just simple black robes plus your doctoral hood.  It would seem rather gauche to me to wear non-Ph.D. regalia or to wear the regalia of a school that is not your alma mater, even if that is where your post is.  I don't know if "generic Ph.D." regalia is also accepted in the UK, where many universities have a much longer and more formal set of traditions than in the US, but I would recommend that you look into that as a possibility.


You won't have done your work in isolation: so you've already built up a list of references that you're working from. From this list, pull out the top ten that are most pertinent to technology foresight.  If necessary, supplement this with a quick literature search in the usual places for papers in technology foresight in other areas.

From that list of papers, take the list of authors. Now, look at the web pages for each of the authors - they'll mostly, if not all, have a page of publications. You're looking for the section on conference papers.

Make a note of the conferences that they've presented technology foresight work at. You're looking for those conferences which keep cropping up on the pages of your authors of interest.

This should build up a picture of where the key players present at.

Just be careful with "futurology" conferences - they can be a real mixed bag. Some lack rigour, don't report on the development of protocols and methods, and lack other academic qualities. And thus they will bring you no useful networking, nor constructive feedback.

You might find some of the energy-systems modelling conferences useful too, as they can have sections devoted to scenario development, which will overlap a fair bit with technology foresight - but don't invest too much effort there, because it's a bit of a stretch, unles your own work overlaps a lot with energy-systems models. FWIW, my opinion is that you shouldn't spend too much time looking at the International Energy Agency (IEA): they've been behind the curve for decades, and that's not changing yet.

The International Renewable Energy Agency (IRENA) have been looking a bit at foresight and technology transfer: they're a very young and growing organisation, so there might or might not be something useful there, but do keep an eye on them.

And the UK Energy Research Centre (UKERC) maintains a list of international energy conferences that you might find useful.

On the technology transfer aspect, I guess development conferences might be where it's at, but that's a lot further from my own area, so that's just wild speculation on my part.

Disclosure: I'm not directly affiliated with any of those organisations, but friends and colleagues are.


Writing a reviewed article in resume/ Statement of purpose

I don'n know about pure math, but I have seen faculty in science and engineering departments, having "published", "in press", "in preparation" articles in their cv. Your article is in a state further than what is understood "in preparation". Mentioning it in your statement of purpose/cv is quite OK.


Postgraduate certification/diploma in software engineering

Short term wise, the postgraduate certificate will help you to find a better job with a higher salary because the certificate shows that you have some skill printed on the certificate. However, whatever the technology you learn while getting the certificate could become obsolete in a few years.

Long term wise, the master degree proves that you know more fundamentals than just a bachelor. It may not help you that much when looking for a job with better salary. Some employers would think you don't have the skills they want immediately. However, you'll learn those needed skills faster and better because you know more fundamentals.

If you want to find a job as of now, you want to have certificates. If you want to be an excellent software engineer in the future, you should get a master degree


Applying for industry job after accepting postdoc offer

After accepting a postdoc position, it is not necessarily appropriate to keep seeking a faculty position.  This might be appropriate if the faculty position was expected to start far in the future.  The fundamental difference between a faculty position and an industry position is that industry positions are usually intended to be filled in about a month, while faculty positions are filled after somewhere between a few months and a year.  This allows the faculty position to be accepted without conflict with the postdoc position.


Does doing an undergraduate math major make an applicant for philosophy phd programs more competitive?

Recommend getting the math major if you can. (I have double bachelor's in philosophy & math myself, although my graduate school and professional work was in math.)

The undergraduate study is the best time to expand yourself into as many fields as you'd care to take. Generally, graduate school is the place that demands exclusive focus on one narrow area. So the opportunity you have now will not be available later on; and the degree will document permanently that you can achieve in any field you need to work in.

Plus, there's the possibility that later in life you may wish to adjust or switch fields. Having the math degree will allow you to immediately step into programs in any science-related area you wish.

Standing astride two separate fields like an academic Colossus gives you a perspective and options that few others can match, and now is the very best time to establish that.


My friend listed my name as a co-author on two journal papers without my permission

Your academic standing should be your primary concern, so if the quality of paper 1 is so poor contact the editor(s) and get the paper withdrawn or your name removed.

For paper 2 if it offends your beliefs such that you want to be disassociated with the paper, again contact the editor(s) and get the paper withdrawn or your name removed.

You have to decide if the issues warrant your subsequent actions, we cannot decide, but worrying about the effect on your "friend" is secondary.


Doing masters thesis in another institute

This depends strongly upon what university you're attending now, and where you want to do your research. For instance, in Germany, students are allowed to do a master's thesis anywhere in the world, but they are responsible for organizing this themselves. Other schools and departments in other countries may have more restrictive policies.

An exchange program may or may not be necessary, but this is entirely dependent on the specific policies of both the school you're attending and the school or institute you'd like to do your thesis work at. The best guidance I can give you is to first ask the graduate students' office or "graduate officer" of your current department to ask what the relevant regulations are for your home institute. Then talk to the other institute. Of course, start such a process well in advance of when you want to do the thesis work; a semester at the minimum, a year is more strongly recommended, as it may take several months to organize the required paperwork and visas (if you're planning on traveling abroad to do the thesis).


Will the research activity during my Master's program seriously impact my PhD or career path?

The further you are in your studies, the more your track record will dictate where you go. But I think that you are not at a point that experience in a related field is going to harm you. And, if you do things cleverly, you can gain very relevant experience.

For instance, you can gain experience in a relevant programming language doing bioinformatics (which is basically open to any programming language), and this technical experience will be relevant to any computational work you do. This seems like a great opportunity to gain that experience while improving your academic track record. I believe that in both these fields a PI will be most interested in someone with technical knowledge (given that a PhD in applied CS is not a course in CS), and luckily for you, this knowledge is independent of whether you are studying genes or phonemes (sorry for that terrible pun).

It's really rare in academia to be able to do exactly what you want. You'll always be carrying out research under someone else's vision, and rather than trying to find the perfect position or such, you just need to find a way to shine in that project/position/etc. As I said above, I believe that the credit and technical experience you will gain in this current position will be relevant for computational linguistics also, especially given the stage you are at. If there is a time to diversify your abilities, earlier is better. At a later stage this will have different consequences.

So I think you should take the bull by the horns and learn as much as you can. I can't imagine someone turning you down from a PhD because of being involved in a computational project simply because it doesn't perfectly overlap their field. All these computational-related fields have a huge overlap nowadays, and computational linguistics is in itself an interdisciplinary field.


Vancouver style citation and multiple sentences

I'm not certain whether or not you are technically current about the meaning of a dot after a citation in this particular style.

What I am certain about, however, is that any such convention is extremely subtle and easy for a reader to misinterpret, both because it's not standard in most styles and because a period is not particularly visually salient.  I would thus strongly suggest using other means, such as how you actually construct your prose, to signal more clearly to the reader which facts belong together as a cited bundle.


DOIs are assigned by CrossRef on behalf of members. CrossRef is an association of scholarly publishers, so the members are therefore publishers rather than authors.

DOIs were introduce because of "link-rot": citing a paper by URL and within 6 months the URL doesn't work. When a publisher joins CrossRef they make a commitment to keep the DOI link metadata updated, so the DOI always points to the paper if, for example, the publisher is bought out and all the URLs change. This agreement is an important part of the DOI system and explains why publishers are members rather than authors.

Assigning a DOI is normally done during the process of publication, and will normally be done automatically. That's not to say that DOIs can't be assigned after publication: DOI 10.1098/rstl.1672.0051 is for a paper published in 1672. Publishers generally assign DOIs to new content but not to back files because new content is more likely to be cited.

It's not free to register a DOI, off the top of my head, around a dollar per DOI. It's normal (and cheaper) for publishers to deposit back-files, i.e. for publications older than 2 years (again, off the top of my head).

So, if you want to get a DOI assigned you can go to the publisher and request that they register a CrossRef DOI.

STM (Science Technology and Medicine) is a very fast-moving field with lots of papers published and cited. Humanities publishing tends to move at a different pace and tends to have different priorities. Therefore you may find STM publishers more likely to assign (and to need to assign) DOIs than in other fields.

The alternative is that you get a DOI from another organisation, for example FigShare. There are examples of people registering FigShare DOIs for their publications.

CrossRef was created to solve the problems of assigning persistent identifiers (DOIs) and linking between papers (one DOI cites another DOI). CrossRef also has lots of other infrastructure, such as bibliographic metadata, FundRef, CrossMark, metadata API etc so it's the best place to register scholarly publications.

Disclaimer: I work for CrossRef


How to select a dissertation committee member wisely?

First, ask your adviser.  He/she likely knows more about most of your department faculty than you do.  You don't have to do exactly as you're told.  But if you don't, this should be an intentional choice on your part, and you should have a good reason for that choice.  Beyond that, I see at least 3 broad areas to consider.  You want committee members who will

strengthen your professional network: introduce you to potential collaborators, and possibly help with your search for a postdoc or tenure track position; and/or write a letter of recommendation for you
give valuable feedback on your work: you think they'll actually read your thesis (you might be surprised how uncommon this is), and might have something constructive to say
be easy to work with in the defense process: likely to be flexible on the date of your defense, and likely to sign off on your dissertation without demanding lots of changes (fitting into 4 schedules besides your own can be a nightmare; it's nice to have a few committee members who are easy to work with on this)

Which of these contributions you value most will depend on what you're hoping to do after your PhD.  If you're looking to move into industry, many of your professors' contacts may be less valuable to you than if you hope to stay in academia.  Do you plan to stay research active? In the field of your dissertation?  Practically, you may have limited options.  At the very least, you should weigh 1, 2, and 3, and estimate how you think each candidate will contribute in each area.


What is the threshold for a software paper to be publishable?

There is no bright line threshold for such things and the answer should be the same as for any scientific paper, hinging on questions of novelty and extension of knowledge. If it doesn't have that, then it probably isn't a good candidate, though the standards of different journals vary widely.

But you seem to describe a small-if-any advance with little novelty and you also seem to have made up your mind. We can't help you with the judgement and you just need to take a risk and call it. Others may disagree with you, but that is always the case in reviewing.

I don't really understand your point 5 and might disagree with your emphasis on it. Why is work done within a group less valuable that work that crosses institutional lines? Lots of papers are done by one or a few people within a research group. However, I might agree more if you mean all of their cited papers come from those same people. That isn't necessarily a red flag, but might be.


Consider technical staff jobs at a national lab.

That being said, the post-docs in my groups have had to learn that the technologists should be doing much of the hands-on work. That is what they are there for, that is what they are good at. The techs may need hands-on help for really new stuff, but they should do the vast majority of day-to-day stuff in the lab.

You, the PhD staff member, are not paid to optimize beam, or machine and build something. You are paid to think up new research topics, get funding for those, and oversee the project to successful completion (whether or not that includes publications). Yes, you get to think deep thoughts and analyze the data generated by the techs. Even then, the very best techs will do most of the data analysis for you. If somebody else can do it, let them - you should be doing the things nobody else can do.


Unless UK universities differ significantly between each other, your supervisor will not have any role in assessing your final thesis - this will be done by the internal and external examiner.

Your supervisor will normally propose these based on personal experience - and I suspect in most cases the university will go along with those suggestions (at least that was my experience).
So a malicious supervisor can give you an examiner who will give you a hard time - while a friendly supervisor will suggest a friendly examiner.

So where am I going:
If the relationship with your supervisor has deteriorated to the level where you feel you would just quit - but are nevertheless motivated to complete your work, it would be highly advisable to seek some advice within the university (and possibly also if you aren't motivated to make sure you don't make a mistake). There should be a person responsible for dealing with such situations - I forgot what they are called...
Ideally, you could be given an administrative supervisor and submit the thesis under their "guidance" - they won't need to be an expert in the field, but should understand your work.

The key question in this case is whether the work is sufficient to be considered for a PhD, but only you or your supervisor (be it old or new) can determine that.

A side note on funding:
The university as an institution is unlikely to continue your funding, unless you are employed doing some work, say on a part time basis to carry on with your work. Where people are paid beyond the standard grant duration, this is done by the department - potentially the sponsor if there is an industry sponsor. I believe it is up to the department ow they organise this - i.e. whether they pay you to write up or whether they pay you to continue/complete your work before/after writing up but before defending the thesis.


How often do graduate students help connect professors with each other?

It happens, but rarely through co-advising.  In my experience, co-advisors usually know each other before the student enters the picture, and the student has little effect on how much the faculty collaborate.

More often, students create new connections by becoming active independent researchers and working with a diverse set of collaborators.  The various actors' roles as "student" and "professor" are simply irrelevant.

(I'm speaking for theoretical computer science, where PhD students are expected to become full-fledged independent researchers before they graduate.  Your mileage may vary.)


Very short phd interview presentation in just 2 slides

They want you to be very specific and very quick, that's fine. That's good.

Slide 1: Who are you? Your academic past, or some other relevant information (e.g. industry experience, if relevant to your future research). That should take about 1 minute.

Slide 2: What are your research interests? Did you do a masters, and if so what is it about, what was the main result? Other things that you'd be interested in doing during your years as a student. Here it's important not to veer too far off course. Especially if you're joining a "pre-defined" program, but showing additional interests is a good thing.

Both of these slides can be set up as bullet points that cover the main sentence from each point, with or without "reveals", up to your preference. And practice with a friend, and with yourself (record and time yourself).

Good luck!


How to advise a student looking for an under-grad thesis topic?

An undergrad thesis is not expected to be mind-blowing or even necessarily that original (see @Cape Code's response about Lit Reviews, often a great option). Look to make some incremental improvements on a paper you've read that really interests you. Maybe you did a project for a class that you did very well on and would like to explore a bit more deeply. Starting from scratch is quite daunting for an undergrad (even a grad student or professor).

The least successful undergrad theses are often the ones that tried to be too groundbreaking and in the end the author had nothing because they couldn't make significant progress. Most theses are good enough to be accepted, if you get the work done. They do not have to be publishable. You usually only have about 1 year to finish an undergrad thesis, while completing a full load of courses. This is way different from a PhD or even a masters thesis where usually more time can be devoted. This is your first time at research, so have fun with it and don't worry too much about the consequences.

Often an advisor might hand you a project to work on, but you should come to him/her with general interests and having already read some of their papers and personal website.


My Supervisors are not helping in writing recommendations letters

I don't know how many letters you're asking people to write for you. However, when there is a separate form that needs to be filled out for each letter, that is asking for a considerable expenditure of time for your advisors. You need to be aware of this, and plan accordingly. You can't ask people to fill out fifty forms for you at once, and then complain when they can't get it done!

So it's not really about applying to "as many PhD programs as possible." Your advisors should be working with you to select the schools and programs you are going to apply to, and you should be working with them to ensure that you are not placing too large a burden on them. This includes giving them a list that clearly states all the schools and programs to which you are applying, as well as the deadlines, as early as possible, so that they have time to plan accordingly. Then, if there's no response a few days beforehand, you need to send a polite email.

But to keep sending out request after request for more letters in a season is a good way to annoy your letter writers. Organize and plan in advance.


Is having recommendation letter writers from the searching institution valuable?

1- The seminal point in the effectiveness of a letter of recommendation is neither the affiliation of the recommender nor his relation to the university, in which you are keen on applying...

The best letters of recommendation have always been composed by fellows, who know the applicant, deservedly, to count his/her personal and scientific characteristics and to pinpoint the unique factors, could which be effective to distinguish the target applicant among the others. Now, if you take a letter of recommendation from someone attending in the target department, where he/she could not reasonably convince the reader upon his knowledge about you, the weight of the letter would not be high. Instead, your contentment to give a letter from one of your resident professors might be more influencing, as they would assess you, in a better fashion.

2- Explicit distinction of an applicant's case would be more assuring, because that "faculty discussion" maybe will not happen on the right time to be fruitful for you. Therefore, you better to stick to the more reliable choice, i.e. explicit letter of recommendation.


You have assumed that students' performance follows a normal distribution, with a grade of C in the middle of that bell curve and very few grades of A or F at the tails.  My own experience, and that of my peers, is that a typical college class has a cohort of good students who will mainly earn grades of A or B, some number of poor students who will earn unsatisfactory grades, and a few "in the middle" students.  That gives a bimodal distribution, with the valley just about where the peak is in that bell curve.

I urge you to look at past classes and check the grade distributions when you have used absolute grading.  If you don't already have something very like a normal distribution, forcing one will distort the assessment results badly.

Your question says your goal is to help students, and the problem is that assessments may be too difficult or the course didn't go as planned.

I'd like to suggest a different approach that's a little more work than artificially distorting the grade distribution, but is much easier to explain to students.  (Um, and to department chairs, if it comes to that.)  You haven't mentioned your field, nor whether your students are undergraduates, but if your examinations can have a reasonable number of questions, measure the performance on every question and then exclude from the computed grade any where performance of the class as a whole is below some cutoff you establish heuristically.  Almost everyone's grade will go up, and you can easily explain that you excluded those questions or problems that were "too hard."  (In the rare case where a student gets only the "hard" problems right, you can make an independent adjustment; that never happened to me.)  I do this with a spreadsheet that has student names in the left column, then one column for each question.

Once you've evaluated an assessment, you must look at the questions you excluded as "too hard" and If the difficulty was with the question, fix it.  If you believe the question is reasonable, then you need to review the material with the class again.  When that happened to me, I'd warn the students that they would see that question or problem again, and so they should prepare for it.

If you do this for every assessment, you will find that your exam questions and your coverage of the material converge, and after a very few semesters, you will no longer have questions that are "too hard" and you'll be comfortable with absolute grading.


For H2020 submissions in Europe, there are many companies specialized in improving a grant proposal, and managing administratively the project if it gets funded. Such projects have to have several partners (both academic and from industry) from several European countries in their consortium.

In particular, because H2020 requires (see this template) a chapter like Impact (on the European economy or society) on which academics are probably not the best to write about. Sometimes that chapter is written by industrial partners of the H2020 consortium.


What is the term for intended consequences of an activity other than intended learning outcomes?

Presumably the distinction is between those intended outcomes that can be measured in some reasonable way at or soon after the end of the course and other intended consequences that can't be measured effectively. Any distinction will probably do the job, even "Other intended outcomes" or "Unmeasured intended/potential outcomes" or "Hoped-for behavioral changes".

Just make the distinction clear both in how you intend to both have students arrive at the outcomes (perhaps not the same for the two categories) and how you distinguish between the categories.


This is a tricky one. It probably sounds like academic plagiarism, but your licensing concerns are probably not going to resolve the problem at the core of this. There's two sides to this, the academic (plagiarism) side and the commercial (licensing) side. They're almost entirely separate, so I'm going to break them up.

Academic/Plagiarism Claim

  The code in the repo is over 97% direct copy of code that I had produced while working in my previous employment...

Without attribution, this is plagiarism, and may be grounds to have the PhD rescinded, but this would be a serious procedure as it's likely to have life-altering affects on the PhD student in question. You'd need to be 100% sure of what you're doing and the validity of your claims going into this. Even if the case was black and white (which I don't think this one necessarily is), the student's University isn't going to take rescinding a PhD lightly as it reflects badly on them.

Additionally, it sounds like there is a some attribution within the work:

  The indirect mention of my name is as a maintainer not the sole developer

...which might well be sufficient for the University to write this off as a referencing error, maybe requiring the student to make a small addendum to their thesis.

  The code is just part of the story, since the person also claimed that in addition to writing the code they used the code to produce the results in that chapter. They didn't - since I know that I ran the batches in question (this was around 2 years of work).

If you can prove it, the experiments that they claim to have run, that you performed while under the employ of their department are probably your strongest leg to stand on here. But you'd have to have good evidence, and be able to show they haven't run the experiments themselves. If yours were not published previously, and they've generated the data themselves using your code, this may well be null and void.

Commercial/Licensing Claim

The licensing perspective of this is completely separate to the plagiarism side - if the work was published as GPL, they can basically do what they like with it, without attribution, provided that any code based upon it remains GPL. This bit is important, as it's probably where you have a leg to stand on, based on this comment:

  although the person has also removed the GPL from the repo, which I thought was against the license terms

That is absolutely in breach of the terms, which is why most industrial entities won't touch GPL code with a bargepole (due to what's commonly called "license bleed").

Based on this, you might have a valid claim to get their repo pulled, but that's not going to solve your actual problem.

Again, from the comments:

  ...I feel that the supervisor (who used to be my boss)...

I understand this to mean that the PhD student in question is supervised by your old boss, which means you had a contract with their institution. Depending on the contract you had with them, they could therefore own all the rights to it regardless, making your initial GPL license in breach of your contract with them without prior stated agreement. This wouldn't affect the legitimacy of your plagiarism complaint, as that's a genuine academic concern, but might affect how the department deals with your request.


What are the tradeoffs involved in taking a postdoc at a top university versus an assistant professorship at a non-top university?

Getting experience at a top university is good for your CV and for you as a researcher.
Getting more research experience under your belt can increase your chance of getting a job in the future, but there are no guarantees.
A post-doc will give you a chance to write more papers and to find out what topic you really want to do your research on.
Taking the assistant professorship now would get you immediately on the track to full professor, which may be delayed if you spend years doing a post doc.
Working at a non-top university might mean that the students you have access to, for example, as RAs or PhD students, to develop your research vision, will not be as good as at the top university. That said, as a post-doc, you will generally not have access to such students anyway, except perhaps as part of a collaboration.
The pressure to succeed at a top university is much greater than at a non-top university.


My student told me his mother has cancer, what do I do?

As an instructor, the best you can do is to offer your condolences and tell him to just ask you if he needs anything. For example, you could offer an extension on assignments. If he needs some time off from lectures, maybe a classmate who takes good lecture notes will agree to make a photocopy, or you could get the lectures to be recorded for him.

Your university might also have a policy that allows students to withdraw from the course and receive a refund of fees without penalty to grades: it would be worth finding this out and advising your student if this is possible. Depending on the severity of the illness and how much it is affecting your student, he might wish to take fewer (or zero) courses for a while.

If the course is nearly finished, perhaps an aegrotat (compassionate consideration) will be applicable to the final exam. But neither an illness in the family, nor a bereavement or any personal physical or mental health issue can excuse a student from having to learn the material and complete assessments in order to pass a course. He will still have to demonstrate mastery of most of the material.

Just be compassionate, and as flexible as you feasibly can. Nobody could ask for more.


What is the most important aspects of Ph.D. application other than previous university and GPA?

Acceptance into a doctoral program isn't a matter of accounting and counting chits. Someone, or a group, needs to make the assessment that you are highly likely to be successful. To that end your GPA is relevant, but so is everything you write or say as part of the process. If you are considered to be a serious candidate with a fairly easily predictable good future, you will be considered.

After that, it can be a matter of competition. There will be a lot of other candidates that have excellent records and they are also being "weighed".

But certainly, anything that shows past success in the kinds of things that doctoral students actually do (pubs, research) is a big plus. But don't neglect your SOP, where you talk about your envisioned future.


How should I structure exams when individual problems could use up the entire class time?

The most time-consuming and least information-bearing step (at least for the purpose of evaluating understanding of the material) is 4. In this situation I've often just given questions asking the students to do 1-3 and explicitly told them to not go through the calculation. It's better if you prep them for this by giving such a question on a quiz first since many students tend to go on autopilot after a couple of decades of being trained to come up with an answer.


Should I remind someone of a previous invitation to give a talk?

It's certainly reasonable to send another email just saying that you would really like to visit, and that you would like to take up the old invitation. By far the most likely thing is that the professor in question just forgot, and will appreciate being reminded.


Do graduate schools check the disciplinary record of PhD applicants?

Generally speaking, in the US, you can depend to some extent on a "right to privacy" that would make such an inquiry improper and replying to it also improper. But it isn't necessarily assured.
The US Constitution is silent on a right to privacy, but many Supreme Court decisions have expanded that right, though not to the extent of the EU's Right to be Forgotten. Also, many US states will have privacy protections in place that make the communication of certain kinds of information improper without the consent of the person involved.
However, if some transgression of a student is also law-breaking, then the rules may change and the information may be part of the public record in that case.
In addition, most (I think) US colleges and universities would treat disciplinary action against a student as a private matter and some might purge the record upon graduation (or after some time period). Part of the philosophy is that if we are to punish a student for some act then that should be the end of it, though the record might be retained until graduation to guard against recurrences.
Overall, I doubt that, given the more or less general, if informal, sense that privacy is a right, that any graduate school would ask and that the likelihood of getting an answer would be very small.
Part of the reasoning here is that the grad school would have no particular reason to ask, having no evidence of any wrongdoing on the part of an applicant.
Of course, it is not outside the realm of possibility that the candidate would be asked directly about certain kinds of misbehavior, and if asked it would be a potential problem if a candidate were to lie (as noted by Anonymous Physicist).


Is it possible a post-doc position for a specialist in medicine without PhD?

The organization to ask is the organization that wants to employ you. The name postdoc suggest that a postdoc starts after you became a doctor, but there is often some leeway in interpreting those rules. However, how much leeway depends a lot on the specific country and institution. Even within institutions departments can differ quite a lot in the extend to which they are willing to make use of the leeway offered by the rules set at the higher levels. So the only advise we can give you is to talk to HR department of the university that wants to hire you.