How to pursue graduate admissions in mathematics seven years after a humanities undergrad degree?

To get admitted to a graduate program in math, although work experience may suggest greater maturity, etc., the issues will be letters of recommendation and documentable standard-material background (whether in conventional courses or somehow-verifiable self-study...), and possibly a GRE subject test score if only to show that one is aware that the thing exists and is widely believed to be relevant (even while many, including myself, do not consider it a good predictor of anything much beyond multiple-choice-test-taking abilities).

Unless you've self-studied into a quite unusual state of expertise, you'll most likely not have much success in getting an idea of what contemporary research in mathematics is about, and it might be awkward to attempt a conversation with faculty about their current work. Perhaps such a thing would be feasible in other fields (I have no idea...) it is not typical in mathematics. That is, people going to grad school usually have only a general idea of the direction of their interests, even with a solid coursework background. In particular, funding for graduate work is rarely dependent upon connecting with any particular faculty more than tentatively. (Again, this is evidently unlike other fields.)

Helpful letters of recommendations would be from professional mathematicians actively involved in research, acquainted with graduate programs in mathematics, who can speak from direct personal experience both about what such programs will demand of you, and about your qualifications to meet those challenges in terms of prior preparation and in terms of interest.

Probably the way to put yourself in a position to have such letter writers is to take upper-division or beginning-graduate courses at a solid university, as a "non-degree student", do well, and thereby be able to ask the instructor for such letters. It's not the credits themselves, but the information and the certification by faculty (beyond "getting a good grade"). That is, you'll want people to attest to your future potential, beyond accomplishments to date, in the sense that (hopefully) "you've only just begun", rather than having peaked-out.

If you are an outstanding multiple-choice test-taker, getting a stellar score on the math subject test GRE will catch the eye of many! :)

Other routes for certifying that your self-study has made progress are difficult. E.g., certificates from on-line courses are not worth much, and, most often, those courses are too elementary to be relevant to graduate study in mathematics.

If you are not geographically flexible, going to the nearby universities mathematics departments and asking "what it would take" for admission, _with_funding_ (don't go without funding), and try to do it. The whole process might take long enough that it'd be wise to keep the job you have, even if you don't like it, to support yourself (and others?) through the preliminary stages of gaining entry into a graduate mathematics program.


You go to their website, find a job posting, and apply. Example of a PhD Research Fellowship at the University of Oslo.

Not all positions are free, and not every PhD student is paid. You'll have to look.


Is the Cambridge Certificate of English accepted in US?

You should read the minimum requirements of the program at the university to which you are applying. Some universities only accept TOEFL, some other only accept IELTS, some universities accept both of these, and some universities accept those certificates like FCE, CAE or CPE as well as TOEFL or IELTS. (Some other universities also accept the English tests which are designed by themselves.)

I have seen some tables in which the minimum scores of each test is mentioned. For instance a university may accept a 7.0 of IELTS, 100 iBT (internet based TOEFL) and an A of FCE.

So the only advice I can give you is to check the minimum English language requirements of the university and the program you are applying.


What is the scope of an unregistered IRB?

Do I even need IRB approval for my research?

Quite probably, but if you are exempt you must get the exemption from an IRB.

What do you recommend for my situation?

You are trying to use a community college to solve a problem (research and product development) that community colleges are not intended to solve.  Don't do that.  If you want to learn to do research, get a PhD at a research university.  If you want to make a product, go get a job at a company that makes products.


Can an author decline to be on a biorxiv paper?

In common with other publishing platforms, bioRxiv requires the submitting author to confirm that all authors have agreed.

  An article may be deposited in bioRxiv in draft or final form, provided that it concerns a relevant scientific field, the content is unpublished at the time of submission, and all its authors have consented to its deposition.

Your friend should contact bioRxiv to explain the situation. The contact email listed on the FAQ page is:

  biorxiv.feedback [at] cshl.edu

Submitting a manuscript for publication without the consent of all of its authors is serious misconduct. Depending on the specifics of the situation, your friend should complain about this to administration at the relevant institutions.


How do I make submitting letters of recommendation to multiple institutions easier for my supervisors?

If I apply to 5 different grad programs, will my supervisors have to
  email the same letter to 5 different institutions?

Unless they write customized letters for each institution, then yes.

Or more likely, they'll have to email their letter one institution and fill out four different forms on four different web sites.  At least one of those web sites will require setting up a new account with a secure password (containing at least one upper case letter, one lower case letter, one digit, and one special character, but no spaces, hyphens, asterisks, or emoji) and two-factor authentication.  Four of the institutions will email instructions for submitting the letters to the email address you provide; one will assume that you've already given the submission instructions to each of your references.  One of the reference web sites will require a recent version of Java; another will silently fail if an ad-blocker is active.

(I'm exaggerating, but only a little.)

Some of your references may be able to delegate the submission process to someone in HR, or to a clerical assistant, but everyone needs to agree on the precise protocol well in advance, so that you can include the correct contact information in your applications.  As Buffy suggests, be sure that the actual letters are written by people who know you personally, who have the technical expertise to judge your suitability for graduate study, not by a random person in HR or by a clerical assistant.

I also agree with Buffy that letters that are customized to each institution are stronger, provided the customization is truly substantive.  If there are clear significant differences in emphasis at different institutions—for example, one department that focuses on biology, versus another that focuses on manufacturing—then you should communicate those differences to your letter-writers.  (That said, the vast majority of recommendation letters I read for successful graduate school and faculty applications are not customized, so customization may not be necessary.)

Finally, do not, under any circumstances, write the letter yourself.  You do not know how to write a strong recommendation letter.  You certainly do not know how to write strong recommendation letters in three different voices, all different from your own, which are consistent with previous letters "written" in those voices.  I think even drafting the letter yourself is dangerous.  If one of your references needs more information about your background (that isn't already adequately described in your statement of purpose and your CV, which of course you've already shared with them) to write a strong letter, talk to them face to face.


Why older papers are more difficult to read than the new ones?

I cannot comment on those specific fields, but I had a similar experience with reading old papers in my fields as well with old textbooks on undergraduate mathematics (in particular linear algebra).

The main reason I made out for this is: Didactics marches on:

It usually takes decades for a field to establish a useful notation and terminology. And during that time, new insights may shed new light on what once was considered a reasonable convention – and thus the process repeats. And that’s not even taking into account people sticking persistently to some notation or terminology that everybody else abandoned.

The new terminology and notation usually prevailed for a reason, usually that it makes it more easy to communicate about your field. Also, even if you may be generally familiar with old terminology and notation, you are not as used to reading it, which slows things down.
Similar to the above, scientists have learnt how to write about their fields problems over the decades, allowing them to write more concisely.
Helpful abstractions and generalisations as well as mathematical background are often only discovered after a field has made some progress.
The target readership changed, knowing more about certain aspects of the required background and less about others. For example, many early works on quantum mechanics did not make use of abstract linear algebra as the audience could not be expected to be familiar with it. Nowadays, physicists are taught linear algebra in a more abstract way (due to its importance for quantum mechanics), however, they may not be so familiar with solutions of spherical partial differential equations.


Can I study textbooks with exclusive rights and teach in India?

I can't speak to what would be allowed or not in India, but consider this: is it good for the students if the textbook is really expensive?

Are the students supposed to read the textbook themselves? If it's really expensive then you can get the following problems:

They don't use the book because they can't afford it.
They use a pirated version of the book.
They spend a lot of money on a book and get into financial difficulty.
Only rich students can take your class.
They complain about the lecturer who insists on using an expensive textbook.
They use a different textbook that they can afford, and you have to deal with the differences that will surely arise.


I’ve reviewed for several journals that asked us to pick our overall recommendation from a four-item list:

Accept, with minor revisions
Accept, with major revisions
Revise and resubmit
Reject

So “Revise and resubmit” is (in very crude terms) ranked between “Accept, major revisions” and “Reject” on a scale of favourability.  The editor is not rejecting your paper, but they are not committing to accepting it yet either — they want to re-review the revised version, before making a final decision.  At least in my field, I would typically expect that the referees for the revised version will be the same as the original referees, looking to see if their original concerns have been satisfactorily addressed.

This generally means that the revisions they want are more on the “major” side — not necessarily in their extent, but in their importance to the paper, in the reviewers’ opinion.  A example in my field (pure maths) might be: you have a theorem where the referee cannot follow your proof, and is concerned the theorem may be wrong.  The referee then asks you to give the proof in more detail, but wants to re-review the new version to ensure they are now convinced it is correct.


Should I agree to teach a class for my supervisor even though I don't get any acknowledgement for it?

This already has too many answers, but I can't help myself: academia entirely runs on people doing stuff they are not contractually obligated to do.  This generates a lot of problems along the way, but that is how things stand.  "It's not a formal requirement that I do this" is not likely to be a satisfying answer for your supervisor.  If the amount of lecturing is not a huge burden, and you feel like it will not make a huge dent in your productivity, then it is probably a worthwhile thing to do (if only as a favor to your supervisor); if you feel like the amount asked is a large burden, see if you can negotiate to reduce it.  I also agree that you want to get something in writing.  I would phrase it as "I want to be sure I understand what needs to be done for the class.  If it's writing, it's less likely I'll forget or misunderstand," rather than making it seem like you are suspicious.


How normal is it to have published as an undergraduate?

Throughout every country and every field that I am familiar with, it is fairly unusual to be part of a publication as an undergraduate.

It is also the case, however, that those who did publish are more likely to go on to graduate school, and that it would be unusual to have a class of any significant size with nobody who had published in it.  I don't know the actual statistics, but let's assume only 1 in 10 undergraduates who go on to grad school have published something as an undergraduate, in which case in a class of 20 students, there is a ~88% chance that at least one person would have published.

Thus, it might well be surprising to the lecturer that nobody had published, even though publishing as an undergraduate is fairly rare.

Note: the numbers that I gave were notional, just in order to illustrate the way likelihood is non-intuitive for a whole class.  As a point of reference on the high extreme, however, consider that 85% of MIT undergraduates participate in on-campus research programs.  A lecturer coming from a high-density research environment like that may well have biased expectations about research frequency.


What kinds of reference letters sound best to letter readers?

For the targets you mention, the perception of the letter is highly biased by prior familiarity with the letter writer. It's very common to say things like "Well Prof. X doesn't like anyone, so if they call this person 'decent' they must be pretty awesome", or "Prof. Y loves everyone, so this letter is more useful for what it doesn't say than what it does", and so on.

Having said that, some of the things that help me when I read a letter (for postdocs or faculty hiring)

(Caveat: I'm at a US university and am most experienced in reading letters from US-based researchers, so cultural differences are important)

Who writes the letter
the nature of involvement they have with the applicant: "was a student in my class" is barely adequate, "was my summer intern" is not terrible, "worked with as a colleague" is excellent, "was my Ph.D student" is important, but can also get downweighted.
The level of specificity in the letter: "We worked on problem X and Applicant came up with the key idea and did all the work" is good. "We were stumped on problem Y for ages and Applicant made the breakthrough" is even better. "We all worked on this problem and Applicant contributed ideas to it" is lukewarm.
Points of reference: "You've probably heard of Prof. Awesome who works in this area, and Applicant is awesome-er", or "there are 5 people on the market this year in this area, and Applicant is at least 2nd best".
Things not said, or said in code: "Applicant prefers to work alone" could sometimes mean "Applicant is an obnoxious lout" or "Applicant has no social skills", depending on the context. "Applicant works hard at their presentation skills" could mean "they give lousy talks". And so on. Here again, some prior familiarity with the letter writer helps.


I think you just lay out the facts as you see them, pointing to supporting evidence as necessary. If the editor can't be convinced then how you say things isn't going to matter much. Let the facts speak for themselves. Point up the flaws in X as applied to your work. And if you need to reference textbooks, do so, even citing page numbers.

You may lose the battle, but it may not be winnable at this journal. If the reviewer is wrong, but is someone trusted by the editor you have a losing situation. If you sense that then withdraw politely and go to another journal.


Pedagogical reasons for closed-book exams in graduate-level courses?

It depends on what you're trying to teach, and what you're trying to assess.

If your goal is to convey concepts, or to teach the things that everyone needs to be able to do without consulting references in order to be productive, closed book may be entirely appropriate.

If your goal is to test their ability to combine and apply the concepts, open book may be more appropriate.

(And yes, I too remember tests with "official" cheat sheets as a balance between these. Then again, I also remember one test whose official cheat sheet was essentially a set of mathematical jokes, because the test itself didn't require any of the rote-memorization material. Then again again, I also remember closed book tests where one of the tools I used was a set of mnemonics that would let me quickly scribble out my own cheat sheet for the formulas/simplifications I most needed -- I can still recite "quasineutrality, uniformity, equilibrium, low-level injection, steady state" but I'd have to hit the books to again remember how those assumptions were used.)


Can we add a finding to a paper which is known by other communities but not ours?

Taking an approach to one problem and translating it to another problem is a valid scientific contribution and can be a considerable creative achievement.
I know a handful of important papers that essentially do this.
If you actually achieved an improvement and it was a very obvious thing to do, why didn’t people do it before?

As you have already noted, the crucial point is how you sell your insight.
The first step is to identify the level on which you actually solved an unsolved problem (in a broad sense that captures performance boosts).
For example, you may not have developed a new method to track the movement of fast-moving objects, but you have found a new approach to study the movement of arrows by translating established techniques for studying the movement of sparrows.
This should be the leitmotif of your paper (or the respective part thereof).
Also, do not forget to cite previous studies which could have been improved by your insight.

The only thing that probably nobody cares about is your reverse engineering (unless you developed some new reverse-engineering methodologies or similar).
But as a scientist you are in company when spending a considerable amount of time on something that you could have achieved easier.
Science always looks simpler when it’s finished and nicely wrapped.


Choosing between a masters at a top tier university, and a PhD at a lower tier university

On balance, I'd say go to Cambridge. If you do good research and write a high quality MPhil thesis, it is very unlikely that you will not get an opportunity to stay on for a PhD.


I am a secondary school student and I think I have proven an open result, how do I get it out?

Well, as I always say, the academia is a circle with its own established convention to follow. In terms of paper publication, you have to learn how to describe things using the terminology and way of expression accepted by the academia. Normally you need several years of regular university education to master these.

But in your particular case, I think it would be easier if you could find a mentor in the university (e.g. a professor or a research) who really understands and recognize your research result and has your trust. He could teach you what is a logic and sound research and how to speak in the language used in the academic community.

Another solution is just publish your result on your personal blog (I mean a well-known blog system like google+ or wordpress, so that the timestamp of your post will tell the world you're the original holder of the idea) and try to make your result get noticed by the academic people.

If you really want to challenge people's stereotype about academic paper author, you could also try to publish paper yourself. But it is definitely extremely hard.


How to respond to a comment when two reviewers ask the same or similar question?

This is very common and there's no need to overthink it.  Answer the question for Reviewer 1, and then when listing and answering Reviewer 2 questions, write out the question and answer "This is the same point as question 3 from Reviewer 1, and is addressed in my response there."

You should be very sure you've addressed the question clearly and thoroughly, because if multiple reviewers flag it then there's some problem you need to sort out.


No GRE offered in my country and I cannot really afford traveling elsewhere

First, not all universities require the GRE for graduate admissions, but you will need to explore that yourself. Second, under the conditions you cite, you can ask for an exception and it is possible, but not guaranteed, that it will be granted.

The GRE is only one measure of likely success. Its only real advantage is that it is standardized. Any university wants assurance that admitted students are likely to succeed, hence they ask for such standard things. But, it is possible, in some places anyway, to provide that assurance through other means, such as an exceptional record or exceptional letters of recommendation. A prior research record can also help in some fields.


Is Google Docs an appropriate tool to write a PhD thesis?

My prefered tool would be markdown / latex, but my primary supervisor really does not like it, to the point that collaboration with this involves printing the document, hand writing notes on it and me transcribing these notes to the original.

This is an excellent way to collaborate!

  We are currently preparing a paper on the initial work of my PhD, and this is being done successfully through google docs. Would this be an appropriate tool to use for my whole thesis?

Google Docs is as good as Microsoft Word, LibreOffice, etc. Personally I think they are all awful for academic writing.

Perhaps your supervisor can use Overleaf? You can then use LaTeX/git in the usual way.


Can participation in online academic competitions destroy patent rights?

It very well could. Talk to a patent attorney. If you can get the contest runner to sign a non-disclosure agreement, then you might be able to protect your patent rights.

That being said, algorithms are not patentable in most jurisdictions, and software is quickly losing its patentability in the US.


How to deal with the postdoc offer without a contract

A top-three institution will certainly have experience with hiring international postdocs, and it is likely they have a standard process for doing so. In my opinion, you can ask your PI to advance the process without worrying about sounding skeptical. You might simply sound excited or eager instead. How about an email like:

Dear PI,

Thank you for your kind offer. I am excited for the opportunity to work together.

If you have the time to send me an official offer letter or similar document, I can apply for the appropriate work permits immediately to prevent any delay in the start date. Is there any additional information I can provide that might be helpful?

Best,

MAPK


What is the best way to explain the change of my research interest in my Statement of Purpose for a PhD application?

How about explaining just along the same lines within your statement of purpose, as you do in your question, in a more developed way?

If you have a strong line of argument to underpin your change of research interests, and you can demonstrate you are committed to go further with this line of enquiry, and how your previous research can help with what is to come, and/or demonstrate how the knowledge and skills you've acquired and developed so far will support your future research efforts, that would be a good way to address this change in your application.


MLA: Do I have to cite the editors of a book for a research paper?

For all works in a research paper you should give credit to authors (unless the requested format of citations does not include the author heading).

On the source your provided, there are many examples where they included the author, or the author "company". If there are so many authors that they would take up ample space in the resources/citation section of the research paper, you can write the first author along with "et al" after to designate there are more authors (again, this is dependent on the citation style).

MLA in particular requests:
Last Name, First Name. Title of Book. Publisher, Publication Date.


Handling editor sent me a review invitation

Yes, it's a sign that they don't think you're a complete crank. That may not sound like progress, but it is a good thing nevertheless. It doesn't mean anything else about the handling of your own paper.

And remember, part of the art of getting published is keeping on the good side of editors.


Giving up before even starting: life without a PhD

It's quite likely you'll be able to get a job in industry with a mediocre Masters.

Think about it this way: there's a sizable population that never finish their Bachelor's degree. Among those that did complete their Bachelor's, a sizable fraction never do a Masters. In other words, you are already quite rare. So you'll probably be able to get a job in industry, if only because you don't have many competitors. Another way to think about it is, given that you're doing Masters, I'll guess that you did quite well during your Bachelor's. Odds are you know people who did worse than you (i.e. had "mediocre grades"). Did they manage to get a job? You can check, although I predict the answer is "yes". They might not have gotten their dream job or one that pays as much as they want, but they got something.

It sounds like you are asking this question because you're unfamiliar with the job market. Therefore I suggest searching for jobs in your vicinity that require a Masters degree in whatever field you're studying. It's imperative to know, because then you'll have some idea of what you're going to be working as after you graduate. If you find there're lots of vacancies, your chances of getting a job goes up.

One more thing: don't view not getting a PhD as "giving up". I know quite a few PhD holders who, in retrospect, think they should not have gotten a PhD.

  What's the point of producing mediocre (research) results?

I don't know, do you? If you don't know either, why are you even considering it? You're in charge of your own happiness; you have to alter your own fate.


Can being a reviewer for a top journal improve my chances in PhD admissions?

Yes, this helps.

Regarding the CV, I've seen frequently that people include sections like "Other scientific activity" or "Community service" where there is subsection like "Referee for:" followed by a list of journals (sometimes even with numbers indicating how many reviews have been done). So you can make this service visible in your CV.

There is another way in which reviewing may help your career: If you write a sensible review for a relevant paper it will be read by at least one editor of the journal and it's safe to assume that this editor is a respected and reputable member of the community. In this way, writing good reviews helps to build your reputation (albeit slowly as not many people see your reviews with your name attached, but at least these are the "right" people).


What happens if I forget to add taxonomy topics when I submit my paper?

If this is an issue, it will most likely be flagged by the production staff when the paper is returned from review. But it typically takes a few days to get sorted through the editorial system, so it shouldn't be the lack of taxonomy holding it up.


Does Trump's federal hiring freeze affect academic jobs in any way?

It's complicated.

In the United States the interplay between federal employment and academic positions isn't very clear-cut. This has resulted in unusual situations where members of the same department may be employees of a number of different entities and may be either federal employees, university employees, or organization employees (ex. Harvard-Smithsonian Center for Astrophysics (CaF)).

The text of the memorandum includes the following:

  As part of this freeze, no vacant positions existing at noon on
  January 22, 2017, may be filled and no new positions may be created,
  except in limited circumstances.

and

  Moreover, it does not limit the hiring of personnel where such a limit
  would conflict with applicable law.

The "except in limited circumstances" is the relevant bit because it means it means that open (or opening) positions may still be filled. From a pragmatical standpoint, it means that if a job positing went up after January 22, 2017, odds are someone can be hired into it.

Another line that is relevant is the following:

  Contracting outside the Government to circumvent the intent of this
  memorandum shall not be permitted.

This means that organizations that hire contractors are likely to put new contract roles on hold unless the position is vital to national defense. This may impact national labs, but is heavily dependent upon what the line of funding for the contract is. Be sure to ask about this if you are interviewing for a role.

Since this memorandum does not impact grant funding, academic and research positions that are paid through an existing line of funding are exempt.

In terms of actually conducting a job search. If you are on USAJOBS you should pay close attention to the details of the posting since some since some organizations like the CaF advertise for non-federal employees on there. These jobs would not be impacted by a federal hiring freeze. Likewise, positions that are in exempt from hiring freezes due to legislation (ex. medical professionals) are also not impacted. Positions at state and private universities would also not be impacted, and would unlikely to be advertised on USAJOBS.

Generally the most basic rule of thumb is that if you are applying for a job that is listed under the General Schedule there is a high likelihood that the hiring freeze applies.


Asking a PhD interviewer about preparation

Firstly, I want to point out that my opinions are based on my own experiences. Having said that a few years ago I interviewed with professors form several "top" ranked computer science, information science and business programs for potential doctoral admissions. Second, I have an admissions season's worth of experience from the "other" side where I have interviewed potential PhD applicants as well.

You do not need a research proposal. In fact, treat this "interview" as a conversation between an academic and a potential future colleague. There is nothing to "prepare" per se. Basically, what's going to happen is that the professor is going to ask you about your research interests and experiences in greater detail than what can be evidenced from your CV or publications. You will have the chance to tell him all about yourself. Do not mis-represent yourself or veer off paths you have not trodden before. What's also going to happen is that this professor will tell you about his project or his lab if he a potential adviser or person whom you want to work with during your PhD.

tl;dr

There is nothing ask him about preparation. Just be ready to discuss your own works and have some questions ready to ask him. Just treat it as a discussion between two professionals and you will be fine.


Fixing insignificant errors of an article after publication, only in the preprint version

There is nothing wrong with updating a paper on the arxiv after it has been accepted or published, from a legal point of view. The paper on the arxiv is not necessarily identical to the published one. (In fact, it is rather the opposite: Changes introduced during the copyediting process are usually something which you are not supposed to include in the journal version.)
Whether this is a smart thing is a different question. As has been pointed out, people might get confused if the published version and the arxiv version differ, especially if they differ in terms of content: If someone cites the arxiv version, it might be that the same result is not contained in the published version, yet the reference might be at some point changed to the published paper. However, this is something which can (at least partly) be remedied by putting a suitable comment on the arxiv.
(Note that there are plenty of papers where the arxiv version differs from the published version, mostly because the authors did not bother updating it. Not that this is recommended, but it is common, so people often are aware that those versions differ.)


How common is it to get an academic position in a different country after getting a PhD in the US?

I wouldn't think there would be discrimination either in favor of or against a PhD from any particular place. That isn't how people make decisions about who to hire. Instead, they will look at what you have done and whether they find it "interesting" and "deep". You can produce such work anywhere and it will be valued everywhere.

In any application, whether for a degree or for employment (a) there will likely be a lot of competition and (b) you need to make your case. These things aren't decided by plugging things into spreadsheets, but by  people looking at your output and your perceived potential to contribute.

That said, you may need to make sure that you speak the local language and are comfortable in the local culture. If a job involves teaching, for example, not speaking the lingo may be disqualifying - at least in some minds. But even in a non-teaching position, you will be expected to interact with others in the institution. Don't take a math postdoc in, say, Italy just because you want to begin to learn Italian.

I recognize that I answered a slightly different question: How difficult is it... I hope that serves your needs.


Grant fraud, should I bust my PhD advisor?

TLDR: You need a lawyer.

I think, ethically, speaking out is the right thing. Falsifying grants is despicable and has a very negative impact on science in general. It has happened to me multiple times that when I say in a pub that I am in science and that I got a grant people say things like "All those grants are just frauds to get money from the government/EU". I don't think I need to explain why this kind of perception hurts on both personal and systemic level.

Regarding your own well being, things are much more difficult. The fact is that you have willingly participated in a non-trivial fraud for a prolonged period of time. Speaking out will not erase this neither ethically nor legally.

You need to consult a lawyer (not an Internet law advice, a real lawyer). As pointed out in the comments - you may easily be considered a part of the fraud. You may want to check your country's whistleblower/cooperating defendant protection laws, but those (if existent) usually do not provide any strict protection - court will have to decide whether you will face charges. OTOH, if the scheme is revealed later without your involvement, you will be in much worse situation than if you had spoken.
You may also claim to have acted in good faith or under serious threat (losing employment). Once again, a lawyer should be able to tell you to what extent this may protect you under the relevant jurisdiction, given the specific circumstances (there is no simple general rule).

Be aware, that you are in trouble. I don't think there are so many grants of this kind and much fewer of them are being cheated like the one you speak about. There is a non-negligible chance that someone overseeing the project reads this post and may consider checking whether this isn't "his" project. Some other participant of the grant may read this as well and consider speaking out himself to get into a better situation. And as this sounds like a big and ongoing fraud, it may easily burst on its own - once people get too much used to bending rules they usually do not know when to stop.

This is not a "we used a questionable accounting trick to be able to buy a new device we really needed for research" kind of problem, there is no good intent, neither was the money used in the spirit of the grant.

EDIT: One more bad scenario in response to some of the comments. Let's suppose the fraud is exposed. Even if the funding agency does not initiate a criminal investigation and even if they cannot directly claim money from you (as your contract is probably with the uni) you still have trouble. Since the uni will likely have to return a large sum of money, they can file civil suit against the people involved in the fraud seeking financial compensation for the loss. As you have made false statements about accommodation and other stuff, this can easily include you.

EDIT 2: I would like to highlight a good point made in AndrejaKo's answer: If the corruption is sufficiently deep in the system, it might not be actually possible to bust your advisor (read the answer for detailed reasoning).


Correct latex format for standard IEEE Computer Society Press proceedings style guide

You should use \documentclass[conference,compsoc]{IEEEtran} as stated in the How To (here). You may find it helpful to follow the bare_
conf_compsoc.tex that is inside the zip file with the templates (here).

Extra information

Take special attention if you should send it in draft mode or not. And also if it should be blind.
Once accepted you have to include the DOI and copyright information.
You will also have to submit the final PDF to a signing website (instructions will be sent)
Finally, the submission process will provide a pre IEEExplore publication copy of your text you MUST download it because this is the version that you are authorized to publish on your own website or ResearchGate.


First step
When I'm not sure about citation format, I usually use Google Scholar to create it for me.

BibTeX code will look similar to this:
@misc{abbreviation,
   author = {Name Surname},
   title = {Title},
   institution = {University},
   url = {URL}
}

If your style does not have the 'url' parameter, then 'note' is usually used for this purpose.
  note = "[Online; accessed 19-July-2008]"

And as Aleksandr Blekh pointed out, it's good to look in the list of possible BibTeX entries and choose the right format (phdthesis, article, book etc.).

Editors
Otherwise, for creating and editing larger citation "databases" I use JabRef. And lately I've found a simple online program for creating BibTeX citations too.


My PhD advisor writes funding proposals based on my ideas without involving me

Maybe your advisor is up to something... but I wonder if it's just poor communication between the two of you. Let me explain how my advisors and I work, and it might give you a different perspective on the situation. Or at least a starting point for talking to your advisor.

I have more ideas than I could personally work on, and some of those ideas led to funding for MSc students to build upon my research. That's great for me, because it means more citations of my papers, possible co-authorship on their papers, and the satisfaction of seeing my research go in multiple directions. Perhaps your advisor is thinking along those lines, but hasn't communicated that to you or asked what you want.

My advisors typically write the proposals without me, apart from asking me a technical question now and then, or asking me to review the proposal. I'm glad, because I'm trying to finish up my PhD and don't need any extra work right now. But if I did want to be more involved in the proposal writing, I know that all I would need to do is ask.

My advisors do keep me informed of all the proposals they are writing or even thinking of writing based on my ideas. If one of the ideas was important to me and I wanted to work on it personally after my PhD, I have no doubt that they would respect that. Either they'd drop the idea, or they might suggest that an MsC student work on one aspect of the problem, while I focussed on the main idea. We'd talk about it, and work out the best solution for all concerned.

If you have shared an idea with your advisor, but haven't told him that you want to work on it yourself, maybe he doesn't realise it. So maybe all you need is to have a good talk.


Can I publicly mention my paper once it is accepted?

In general, this may depend on cultural expectations in your research community and the legal requirements imposed by the publisher.  But for computer science conference papers published by ACM: As soon as your paper is accepted, you an add it to your list of publications, and you can post a copy of the paper online.

Once a paper is accepted, its acceptance is a fact that you can include in your CV and/or your online list of publications.  I have never heard of a computer science conference or journal publisher imposing a press embargo on the existence of a future publication.

ACM's copyright policy explicitly acknowledge authors' rights to post their papers online, even before the paper is accepted, including the following:

  Post the Accepted Version of the Work on (1) the Author's home page, (2) the Owner's institutional repository, (3) any repository legally mandated by an agency funding the research on which the Work is based, and (4) any non-commercial repository or aggregation that does not duplicate ACM tables of contents, i.e., whose patterns of links do not substantially duplicate an ACM-copyrighted volume or issue. Non-commercial repositories are here understood as repositories owned by non-profit organizations that do not charge a fee for accessing deposited articles and that do not sell advertising or otherwise profit from serving articles.
  Prior to commencement of the ACM peer review process, post the version of the Work as submitted to ACM ("Submitted Version") to non-peer reviewed servers;

In particular, non-commercial repositories in point (4) include arXiv.  (ACM asks for copyright transfer only after papers are accepted, so I'm not convinced that the second bullet is anything other than an acknowledgement that ACM can't control what they don't own.)  However, note that the Accepted Version is different from the Version of Record, or as human beings call it, the camera-ready version—the one that ACM actually publishes.

From a practical standpoint, however, very few computer scientists actually care what ACM or any other publisher thinks.  A significant majority of computer science research papers are available online, either on the author's web page, in some institutional repository, or on arXiv.  You are not only legally allowed to post your work, you are culturally expected to do so.  Although ACM and other CS publishers claim the legal right to go after authors for posting camera-ready papers without permission, they have shown no interest in actually doing so, and there would be a huge community backlash if they did.


What might be some reasons to ask to stop reviewing an article by the editor?

There are many possible reasons. Perhaps the author(s) withdrew it. Perhaps the editor made a decision somehow, though given the time, probably a reject.
Of course, you can ask the editor, and you may or may not get a real reason.


Should I oppose reviewers whose results I show to be wrong?

If possible, it is good form to contact these people a few days before you submit so they can "check" your counterexample.  Phrase your counterexample in a constructive manner v.g. avoid saying it is false but rather suggest their proof is incomplete.

If these people are reasonable, they will double check, confirm that the counterexample is valid, thank you for it, and maybe cite your own work.  If they are not reasonable you have still been gracious.

People don't like to be criticized in public - nobody likes it.  Avoid "springing a trap" that will get these people in a bad mood if they learn of your counterexample in a journal or as referee of the paper.


Costs for colored figures in Chemistry - A European Journal

The author guidelines report:

  The publication of graphical material in color is expensive, and we
  request that part of the additional costs be carried by the author. As
  a result of the production process, the online and print versions of
  the manuscript must be identical. If color is deemed essential for the
  scientific understanding and the author does not have access to funds
  for publication costs, the journal may consider covering the
  additional costs.

It seems that unlike many other journals, for what concerns colour figures, this one publishes a printed version which equals the online one. Note, however, the bold part.

An alternative possibility, which is less expensive, would be that of producing the manuscript with all black and white pictures and then delivering the coloured ones as online supplementary material. In fact, from the author guidelines,

  Color and animated multimedia applications are welcome and published
  online at no cost to the author or reader. Please refer to such
  applications in the article itself where appropriate (see the
  Supporting Information).

They might accept pictures too.

In any case, before making any decision, I'd suggest to contact the editor or the journal publishing services.


Identifying assumptions in a research article

There is no clear way to distinguish hidden assumptions, but let's discuss your example (I'm unfamiliar with the field):

  open source operating systems are more secure than propriety operating systems

Some possibilities:

The author makes an assumption here. It can be, e.g., based on their personal experience, or justified by some common sense.
The community makes an assumption. This may be a generally accepted assumption, but nobody has actually done research on it.
This is a generalization / rule of thumb which usually holds true.
This is a well known fact, so old or trivial that nobody bothers to cite it anymore.

I usually consider all nontrivial statements as assumptions/hypotheses/conjectures unless I find evidence to the contrary.


Should I include the proposed method name in manuscript Keywords section?

If the method is important to your work (e.g. if the method has a "blind spot" so the results might have a loophole) then yes, include it as a keyword.

As for whether to use the full name or the acronym, either is fine. When the template says "3-6 keywords", chances are very good that each group of words is one keyword. For example, "United States" would be one keyword, even though it's two English words.


Is "flowery language" frowned upon in engineering and STEM related research?

There's nothing wrong with long words. The real issue with your writing is that it is redundant.

"these related works are germane to our present discussion."

In this sentence, "germane" just stands for "related", so you're effectively saying "these related works are related". Here you are using the English cliche of pairing a common word with a rare synonym, which we also see in phrases like "trials and tribulations" or "vim and vigor". As in these examples, you include the common word because without it, people won't always know what the rare word means. But the very act of doing that makes the rare word completely useless. Redundancy in this form should basically always be removed.

"...therefore, the scenario considered in [reference] is situated diametrically opposite to ours."

This is another example of the cliche above. The word "diametrically" isn't doing any work the word "opposite" isn't already doing. It's only there for the purpose of being a long word.

"The experiments in [references] corroborates with our results".

This is not correct usage: the word "with" shouldn't be there. Incorrect usage of a long word is very bad: people who don't know it will be annoyed with you, and people who do will judge you.


Is it okay to open up the thesis file during the defense?

While I agree that it would be OK to open a pdf of the thesis to show a specific part as an answer to a question I would like to add:

Opening up the thesis and show something in addition to the slides in the middle of the talk would show that the talk was not well prepared. So don't do that and prepare your talk such that this will not be necessary.
Having answers and arguments to questions ready without going to the thesis would appear better. Of course, nobody expects you to know every word from your thesis but it is expected that you know all results of your thesis and also all your arguments.
Opening the thesis when a question like "on page X in Theorem Y you state that…" comes is totally OK. Especially, since this gives the rest of the audience the chance to follow the discussion.

But finally: It's a thesis defense. It usually not an event where anybody fails terribly. If you know what you have written about and know what you are talking about nothing bad will happen.


Two ideas:

Ask around for a student assistant job that can yield a first glimpse inside the world of research.
Write your thesis about one of the topics that you alluded to in your question. This can be a first step towards a paper and it is an opportunity to discuss your topic with a professor.


Should I tell a PhD student's supervisor about a lack of understanding and somewhat ethically dubious conduct?

You wrote:

  The statement claimed he had a leading role in the project (he didn't) and claimed that he contributed significantly to the manuscript (this is somewhat arguable, but he certainly wrote some of it). I signed the document because I assumed that this was just some formality that he needed to graduate, and I wasn't prepared to cause a fuss over the wording in a document that I didn't view as important.[...]However, now it turns out that he needed this agreement because he wants to write a chapter about my work in his thesis."

In order to include joint work in your thesis, many graduate programs require a statement to the effect that you are "a first author" on the paper.  So, in fact, that is just what that kind of document is going to be used for.  It's entirely reasonable that the purpose of the document was not clear to you (a master's student).  Maybe your collaborator should have been more explicit about what it was being used for.  Maybe you could have asked.

However, since he is a coauthor on the work, it is also his work, and he is perfectly entitled to represent it in that way.  The fact that he needs to be a first author in order to include in his thesis sounds like "a formality that he needed to graduate" to me.  Your signing this document does not undermine your first authorship on the paper (I assume you are; you don't quite say so) in any way known to me.

One could put a positive spin on the fact that you, a master's student, have done work that has formed a part of someone else's PhD thesis.  That is just about the strongest possible certification that you are doing PhD level work.  Maybe think about how to capitalize on that, e.g. in recommendation letters.  In summary, so far -- no problem.

  Furthermore, he is asking me questions about the paper that are extremely basic. I don't want to come across like I am exaggerating, but the questions he is asking me are the sort of questions that are covered in first-year undergraduate chemistry courses - not the sort of thing that should be being asked by a PhD student about to graduate.

Well, that sounds bad rather than good, but without further context it's hard to evaluate.  Presumably this is just a part of his thesis work (you said "a chapter"), so maybe his real expertise is elsewhere?  Maybe his background in his field is really spotty or worse, and somehow he managed to do enough work to get a PhD anyway.  Maybe he's not so bad but you're really great and thereby have higher standards for what a PhD student should know than others.

Yes, it is also possible that he is some kind of fraud or charlatan.  I kind of wonder that you wrote a paper with him and didn't notice until now, but maybe indeed his role on the paper was minimal.  My feeling is that while you can respond to this however you like, you have no "whistle-blowing" responsibility here: you are not one of the several qualified, professional academics who are charged with evaluating the student and his work before he gets his PhD.  It's on them, not you.

My recommendation: stop answering his questions, and instead say "I think you should ask your advisor about this."  He can't lean on you if you don't let him, and you don't need to let him -- as you say, he is about to get his PhD.  If his supervisor is also your supervisor, and you have a good relationship with him, then you might want to bring up the fact that the student has been asking you a lot of basic questions.  If the supervisor doesn't have an issue with that, that's their problem and not yours.  (Even if the PhD student didn't know what an atom was, you still can't do anything directly to stop him from getting his PhD.  The advisor can.)  If you don't have a pre-existing relationship with his supervisor -- I recommend letting it go.


Should I encourage foreign students to adopt local handwriting customs?

In ordinary text, this might help a little but probably doesn't matter much, since there's plenty of redundancy to aid in understanding.  However, it can make a big difference for equations.

If the students are in a math-intensive field, I would definitely point this out, but in a broader context.  When I teach beginning American undergraduates in mathematics, I offer them handwriting advice for equations: make sure t doesn't look like +, z doesn't look like 2, the letter l doesn't look like the number 1, etc.  Furthermore, mathematics students have to learn how to write all sorts of potentially unfamiliar symbols as they progress in their studies (aleph, Weierstrass P, fraktur letters for Lie theory, etc.).  If you are working on a calculation on a whiteboard with someone, it's a real issue if they can't easily and reliably parse your equations, so just about every mathematician has put at least a little thought into this.

From this perspective, I wouldn't tell people "You're in America now and have to write like the Americans", but rather "Writing equations clearly is something everyone has to deal with.  Here are some issues you may need to adapt to, some of which are generic and others of which are specific to your background."


Work flow for publishing figures under Common Creative license (in order to ease re-use in journal publications)

The software used to create a work does not change anything with respect to the its copyright status.  I can create a work in Photoshop and distribute it (the work) under CC-0 if I want.  The fact that someone needs to have a non-free software to open it isn't important. Where things could get tricky for something like a PS file is if each layer has elements that could be considered fair use within the overall final image may be being distributed in full and hence no longer subject to fair use exceptions.  That won't be concern for most LᴬTEX / TikZ stuff

You seem to be talking only about the final version of figures, so CC-BY should be fine.  If you want to release the LᴬTEX / TikZ code, it seems that Creative Commons is indeed the preferred license type in the community (see TeXample.net which requires user to submit their TikZ stuff as CC-licensed works).  If the code is GPLv2, though, the visual result isn't covered by GPLv2.

The correct attribution will depend on your style guide.  I don't think you would go wrong to follow whatever standard it uses for works of art unless there is a more specific format in your style guide.

I'm not aware of any workflows to do this, but they shouldn't be too hard to write if you're using that many figures that it's worth your time.


Why do we call a research paper, a "paper"?

Although I agree with Cape Code that this is not a question related to academia and should be closed, I know this one of the top of my head so i'll save you some Google-ing.

The reason is because the first mass production of "paper"s of a standard size where printed for distributing the news. The word "news" is a very funny English word, for all sorts of reasons. It ends in an "s" but is not plural, eg "what are the scores?" is correct, but "what are the news?" is not. Furthermore, it is uncountable, so although it can be followed by a singular verb, you cannot count it like "Do you have a news for me?". People instinctively know "Do you have news for me?" sounds unusual, and so they often pop in an "any" into the middle to make it sound more grammatically compliant.

For this reason, early usage of "news paper" referred to a collection of 1 or more printed news. "news papers" referred to several of these collections. This eventually became 1 word, newspaper, which as a single noun now plays by the rules a bit better, masking the weirdness of "news". However, the concept of a "paper" being one or more sheets of printed information stuck, and is still used in academia and elsewhere where some form of news is being printed, but not as a newspaper.

For the record, I know all this because I got into an argument with a colleague about it, and I insisted it must be because of paper (the material) is what people are referring to. "I brought the paper!", since the common person would have only seen paper in relation to multiple sheets of it. I was wrong.


Applying for postdoc positions without first author papers?

I doubt that very many employers treat hiring post-docs as an accounting problem, counting up the chits. Instead, I would ask, how do your skills meet our needs? Some places with great reputations and heavy competition for positions want a way to encourage only the top candidates to apply, but even there, they have needs for skills that you may have, or not.

As in any application, stress your positives, your skills, and interests. If you get rejected then keep looking. The competition may be at a high level, but the evaluation is much more varied than just counting publications.


What unusual/innovative methods are there to deal with late submissions of assessment?

In an effort to avoid whining and prolong the lives of grandmothers, I experimented with giving students a bank of "late days" which they could use to defer submission of homework.  In an effort to teach some time management, I made the students responsible for telling me that they intended to use late days before the due date of the assignment.
That did not work.  "I'm sorry my assignment was late, but...." turned into "I'm sorry I didn't tell you I was going to use late days, but..."


It's to make the application form easier to review. That way, all the fields on the application form can be printed in one handy package, which could then be sent to a program chair for easy review.

No one in the admissions office wants to have to gather and collate transcripts, GRE reports, and other application information into one printout (or file) just to be able to send the package somewhere for review. Moreover, when reviewing, no one wants to shuffle through a bunch of papers just to find the information they are looking for. This way, GRE scores are always right there on the left-hand side, in Box 10.

In a word, it's for the sake of convenience. It's much easier on everyone at the university if you simply type your GRE scores into an application form where you are already typing so much other pertinent information.

As for why you have to submit the official results, too, that's simply to verify the scores you self-reported.


What should I do if I have just observed minor mathematical typos in my accepted paper?

As you wrote yourself:

  The editor has told me that the paper has been sent already for printing, and nothing can be done anymore.

Given that the editor decides how a publication runs, there is nothing you can do. "Normal" journals usually publish errata but conference papers often do not have that possibility.

Don't worry about it too much: everybody makes mistakes/typos and it is not a big problem. The intelligent reader will spot the mistakes and not mind too much because he gets the point anyway, the other readers will not spot the mistake so they won't care either.

Just make sure you learn from this: next time double check everything and ask a meticulous, friendly colleague to do the same.


Will a mistake in my data collection for my thesis effect my whole grade?

If age is not a variable used in the later analysis, then it cannot be wrong.

If you should have included age in the later analysis, then that may cost some points - depends on what they are looking for...

Including age in the original survey is usually a good thing as it means that that data may be suitable for different variations of studies ie the data is possibly more useful.


I would like to suggest that you read the speech "You and Your Research" by Richard Hamming on how to do great research.  It's one that I revisit every once in a while when my own scientific motivations are becoming unclear and need to be refreshed.

In reading it, it's important to keep in mind that the speech is thirty years old, and it is addressing things that happened even decades before that, so there are some jarring cultural gaps both with regards to science and with regards to the rest of society.  Nevertheless, I find the central ideas to be still very relevant and valuable today.

Importantly, Hamming distinguishes between things that you need to do in order to not fail and things that you need to do in order to have a real impact.  These are very different, and it is important to distinguish between them.  Important research is not the same as any of the "productivity metrics," and the correlation is often a trailing indicator, not a leading indicator.

For example: you say you are concerned that you are publishing only one paper per year.  Step back and ask: why am I concerned about this?  You can publish lots of papers without ever doing anything really creative or important.  You can have a full, tenured, and comfortable career that way.  And honestly, that's an OK choice to make.  Some people go too far the other way, and strike out so deep into their own creative world that they can never publish their ideas, and they also fail to have an impact (indeed, the most extreme of them we label cranks).

In between is the dangerous and subversive world that Hamming describes, where you teeter back and forth on the balance between compliant conformity to metrics and egotistical creative rebellion.  It doesn't guarantee greatness, but it may be a fascinating ride, and it just might get you somewhere really worth going.


What makes a standout profile for applying to a top-ten ranked CS masters in the US?

You seem to have little time to do a huge number of things, but a few things you can do:

contribute to some open source projects there are many many and all need help of at level
show that you have played with some ideas on GitHub
show you can turn your hand to many languages again stick it up on GitHub
have a shot at project Euler, and stick it all up on Github
build an App or website that does something/anything

Publications for Undergrads are great, but not really expected.


What is the difference between dual degree, 2 Bachelors and double major?

My understanding is that:

Double Degree often means you get two full Bachelors degrees, which may be from two different universities, in two entirely unrelated subject areas. Often these programs are designed to be completed in 5--6 years total. I have also sometimes seen it used with reference to graduate programs. For example, a double degree Masters/PhD program, though this is rarer in my experience.

Double Major means you get a single degree from one university, but with a speciality in two related subject areas. For example, you could be a Physics/Chemistry double major. Typically this means you satisfy the core requirements of both programs, possibly using the electives of one to fill in the core of the other.

Two Bachelors means you get two full Bachelors degrees. Sometimes this is used as a synonym for a Double Degree, sometimes it is differentiated by requiring that both degrees be granted by the same institution.


Can a university retract a degree for actions taken after the degree is awarded?

It would depend on the jurisdiction. In the US, you have a property right to the degree that you earn and pay for (regardless of the ultimate source of funding -- the student has the responsibility to pay), and as long as you don't violate the conditions for obtaining the degree (various forms of dishonesty in admissions and satisfaction of the degree), improper actions after the fact don't license depriving a person of what they have earned. In Europe, the legal basis may be different. Whereas in much of Europe state law governs revocation, in the US revocation is governed by university rules.

In the case of Dutch psychologist Diederik Stapel, the thesis data had been destroyed so it was impossible to prove fraud in the thesis, and also impossible to disprove it (Stapel short-circuited the university's proceedings by returning his degree). It appears that there are, in The Netherlands and possibly other European nations, vows that you must take in order to receive the degree, to act honorably (defined locally). "Not committing fraud in the future" is a likely candidate for such a vow.


List of approved Competency-Based Education schools

There's a preliminary list here of experimental sites with programs participating in the DoE's Competency-Based Education experiment. (Via this page about current DoE experimental initiatives.)

The list is watermarked "Preliminary" and is dated 4/16/15, so keep this in mind in how you use it - it may not be completely reliable or up to date.


Professor wants to include a specific (maybe unnecessary) issue and focus less on other necessary ones in LoR. Please share your perspective

I think you should defer to the advisor on both counts. I don't see any negative implication in the first point. It is actually pretty high praise.
And on the second, I'll have to guess that his judgment is based on more experience than you have.
Moreover, if he doesn't feel constrained by your "instructions", then he will probably write in a more natural way and that, alone, could make a difference when the letter is read.
I think that trying to micromanage this would hurt, not help.


Should I report apparent conflict with handling editor during peer review?

You have not identified any conflict of interest in your post.  The managing editor can, and should, criticize your work.

It seems that the colleague who invited your paper mislead you by failing to clearly state they were not actually editing the special issue.

The reason you have not encountered this situation before is that most editors are not thorough enough to provide their own advice to the authors.  This is unfortunate.

Do not claim someone has a conflict of interest unless you have solid evidence.  The evidence needs to show that they have some way of directly benefiting from the rejection of your manuscript.  Unsupported claims of conflict of interest hurt your reputation.  Your negative reviewer is much more likely to be lazy, rather than a competitor.


Is it beneficial to publish papers not related to your primary research field?

I'm honestly surprised at the question.  "Primary" does not mean "only"!

If it's a good paper, then of course you should publish it.  Aside from the obvious personal benefits of making you look more diverse, increasing your visibility in another field, and possibly creating opportunities for future collaboration, you're doing what research is for: expanding human knowledge.  And if it's not a good paper, then of course you shouldn't publish it, even if it is in your primary field.

But to echo shan23's comment: Don't use grants in area X to fund research in area Y.


How will the success of my previous projects affect future funding?

While a common practice, that would be fraud.
Less fraudulent would be to bill everything that 'counts for both' to the stronger project, to conserve money to get the weaker projects done. (Equipment, staff meetings, etc).

For you, depends on how your department weights grants brought in vs. papers published. If they value grant money more, that you've damaged your chances of getting more is not something your should reveal, while papers are something you can play up.


How to know when you should change what is taught during a lab classes

The interesting question is, does the project feel stale for you or for the students? The students are, after all, only doing the project once, so there is in principle no harm in using the same project year after year.

Of course, there is the possibility that the project that was cutting-edge when you defined it is now an old relic, using methods and technologies that nobody actually cares about anymore. In this case, you should of course move on, but if this is not the case, I see no inherent value in changing the project (especially since any change also means that the first iteration of the new project will be a bit rough around the edges).


Optimizing a thesis writing workflow for Bachelor and Master theses

It is a very good set of advice. There are two very practical areas that seem unaddressed and that are, in my experience, somewhat… problematic with some students:

Proof-reading. Find someone, other than yourself, who will do a final proofreading of the thesis for language and clarity. Not necessarily someone from your field, but checking typos, missing figures, acronyms that are never defined, that sort of stuff… That person should not be you, because when you've spent so much time writing the thesis, you won't even see these details any more when you read it.
Also, check with your supervisor what are his expectations regarding proofreading/corrections. It depends on your university and the supervisor himself, but in many cases they will want to read it themselves, and possibly offer some remarks and corrections.

Scheduling. You are aware of the submission deadline, but mind that the final stuff takes time. In particular, if your supervisor has to read it, make sure to give him enough time to do so. So, start with a clear set of intermediate deadlines, and if you start to miss them, take action! Nothing's as bad as procrastinating ’til the last day thinking “I can still write that in 24 hours if I get to it”.


How to start a cover letter during submission?

Don't obsess over it. Dear Editor is fine unless you have already corresponded with them. In fact, if you direct it to an individual by name it might well be handled by someone else - especially in a large organization.

Eventually you may get the name of someone who is responsible for managing your paper. Then you can be a bit more personal.


Probably the question cannot really be about plagiarism, literally, because most traditional senses of "plagiarism" refer to specific choices of language, rather than "ideas".

In the first three cases, Bob's behavior would be completely within the range of standard operating procedure. Public information is public. Yet, also, at the same time, many people would consider such behavior rude and mercenary. That's not the same as illegal or unethical, whether or not it is immoral.

(The fourth case is harder for me to simulate in my head, and I have no comment on it.)

Yes, one could imagine that mentioning a problem or idea publicly gives one some sort of right to it. However, in practice, this cannot possibly work, because it is extremely difficult to gauge what more is required to make an idea into something substantial. The only viable default is to imagine that whatever one says publicly is then truly available for all. One cannot control it, or guarantee "getting credit". Yes, the most virtuous people will give credit to the origins of their ideas, etc. ("Duh!")

If the real question is how to stake a claim on ideas in a fashion that prohibits others from doing anything with them ... as opposed to taking the idea, doing something, and giving credit for origins... I have no suggestion except keeping secrets.

EDIT: and, no, merely expressing an idea does not create "possession"... Not at all. But, among decent people, credit would be given. Can't rely on this, etc.


As far as I know, there is no data available of rejection rates enriched with information about the paper type. Therefore, you can't tell objectively.


Change of interest right before qualifying exam

Given that you're in the US, my advice to you is slow down.  You don't need to pass your oral exams in your first year, and studying for and passing an exam in a subject that you intend to drop completely is not a good use of your (or anyone's) time.  Moreover, you can stop working with (or not start working with) your advisor without jeopardizing your future in the program, so there is absolutely no reason not to be forthcoming about your concerns.

I suggest talking to your current faculty advisor and devising a program of study which allows you to explore ML while not quitting symplectic topology "cold turkey".  As a first year student you can afford to spend at least a year taking courses trying to figure out what you want to study and building up background in that area.  In fact, it is very unusual for a first year US math PhD student to know exactly what they want to study in the future: that kind of decision usually lies at least a year away.

It sounds like you thought you did and that you have some pride in your own advanced standing.  That's understandable, but the thought of going ahead with an examination in a subject that you plan to drop soon thereafter and with an advisor that you plan to drop immediately thereafter is really not a rational, wise or kind way to proceed.  I think you need to take some time to gain a better perspective.  Sharing your proclivities and your plans with your peers and mentors is a good way to do so, but again: take it slow.


What limits the number of PhD students in universities with and without PhD tution fee?

What limits the number of PhD students in universities without PhD tution fee?

I'm not sure countries exist without a PhD tuition fee. Rather there is a scholarship system in place to cover the cost of tuition. The limiting factor here is the number of scholarships allocated by the government. So the answer is the government.

  And when there is normal tution fee, isn't there any limitation for the number of PhD students as long as there are good candidates?

This would be dependant upon the institution. There may be a hard limit imposed by the faculty. Otherwise there is a soft limit in the number of students one professor can reasonably manage.


Value of unpublished (i.e. submitted) papers?

The rule of thumb with writing a CV is to keep things relevant. If what you are writing is relevant for the purpose you are writing your CV (you should really have a template CV, and customize it for each application), then yes add them.

So a couple of ways how I could see that being relevant for you, specifically:

you mention applying to a PhD program, so it might be relevant to show whoever is taking the decision that you have worked on something similar before
in a similar way, it could be meaningful to show that you have some research experience, as opposed to other graduates that have 0 research experience.
if your manuscript in review has been uploaded to a preprint server (like arXiv or BioRxiv) then you might even be able to showcase the work you have done.


How do you include a poster in an academic resume?

In academia, one lists things related to accomplishments and dissemination of research in the CV.  This typically includes things like papers or preprints, software, as well as presentations one gives.  In particular, your list of presentations gives one piece of information into how active you are in your research community.  So yes, assuming your poster presentations are academic/research related, it's appropriate to put them in your CV, though in-class presentations are typically not included.

General comments:  a CV is different than a resume so there's a lot of flexibility in what you include and how you format it.  Still, there are some dos and don'ts.  You can find loads of example CVs online, but it might be most helpful for you to look at sample CVs of young researchers (students, postdocs) in your field for some models.

Specific comments: there are different ways you can organize your presentations, but my suggestion is make a section titled presentations, and within that two subsections, one for oral presentations or "talks" and one for poster presentations.  Then for each presentation, list the title, venue including conference name and date.  E.g.

From Cervantes to Swift, 33rd AEIOU Conference, University of Lillipilut, Mildendo, Lilliput, April 1, 1726.


How many people are generally shortlisted for a postdoc interview?

I cannot tell for this particular case, nor for that matter for a typical German Physics Department. But in my experience (also in Physics), it is a few, i.e. 4 ± 2, for a single position (depends also on the number of good applications, could be as few as 0 but unlikely more than 8).


Will the prestige of my masters program affect my phd application choices?

I would recommend that you apply directly to doctoral programs and use this offer as a backup if nothing materializes. In mathematics and some other fields acceptance into doctoral programs with only a BS or BA is more or less the norm. Your vita looks pretty good and I think that many doctoral programs would be happy to have you.

Most likely you would also be offered some sort of funding, though it would be as a TA or similar, though funded research isn't impossible. Places with doctoral programs in math in the US need a lot of TAs.

Apply first and then consider your options. You might even be able to get some indication about the likelihood of your acceptance from a faculty member at a proposed university.

Also, in many doctoral programs in the US, you will have the chance to get a Master's along the way. Sometimes just by filling out a request after a certain amount of coursework. In my case a small thesis was also needed.


Is it bad if I am not a teaching assistant during my PhD?

Outside of academia, the lack of teaching experience will have little or no negative effect on your employment prospects.

If you are going into academic positions, the significance of not having been a TA will depend greatly on your field and the type of institution you will be working at. For instance, if you are at a research-intensive university, teaching experience isn't as essential as at a small liberal-arts college. In a similar vein, an engineering graduate is less likely to be expected to have teaching experience than a PhD recipient in, say, mathematics or the humanities.


To what degree does earning a pure math PhD in dynamical systems limit my career options outside of academia

A lot of PhDs in theoretical mathematics end up "in industry" of one part or another.  Many times this is not by choice, which is sad, but it also means the learning curve is not too steep.  There is a reputation, reasonably well-deserved, that a PhD in mathematics teaches you how to think and solve problems in a rather fundamental and robust way, and that all other skills can be overlaid on top of that.  Certainly I've seen PhDs in "purely theoretical" mathematics with no programming skills, actuarial or statistical knowledge, etc. be hired by industry.  In fact many of these people get on-the-job training in the first year of their job...while they are getting well paid.

Well, but the job market is pretty tight all around these days, as perhaps you've heard.  If being totally clueless outside of theoretical mathematics can land you an industrial job, being less than totally clueless will be even better. I advise PhD students that as soon as they have real thought of a non-academic post-PhD career they should explore this in a positive way, including mentioning it to their advisor so that aspects of their program of study can be adjusted. For instance, in my PhD program you need to take two exams in foreign languages, but one of these can be replaced by a computer project.  Although I think the computer requirement would serve many would-be academics better as well, if you think you may go into industry, then reading in a third language is obviously not going to be as marketable as computer skills.

While you're in a PhD program in mathematics, talk to the students and faculty who have connections and experience in industry.  (Realize that your thesis advisor may not be such a person.  For instance I have zero industrial experience. I do not pretend to give advice in this area -- well, not specific advice, anyway! -- but I try to find other people who can.)  Don't be shy or embarrassed about this.  It's your life and you get to do what you want to do.

My feeling is that solidifying basic industrially applicable skills -- e.g. programming and even lower-level tech-savviness like spreadsheets, learning how to share and transfer files, etc. -- and supplementing with coursework and other training (e.g. taking actuarial exams; taking one solid course in statistics or financial mathematics) is a better bet and easier to do in your spare time than trying to change your thesis topic to something more applied.  As above, my feeling is that most industrial jobs don't care what you did your thesis on, and having done it on something rarefied and inapplicable is actually fine with them as long as you have, or can make them confident that you can learn, the skills you will need on the job.  But again, talk to people other than the academic lifers like me!


Should major awards be included in an NSF postdoc application? If so where?

I think that you should follow the NSF's application instructions to the letter and not include any information that has not been asked for. In particular you should not add any sections to the Biographical Sketch beyond what appears in the NSF Proposal & Award Policies & Procedures Guide. This guide explicitly states, by the way, that "Inclusion of additional information beyond that specified below may result in the proposal being returned without review."

As you state, you need to convince the NSF that the work you are proposing is interesting and that you can actually complete it. For the former, this is what your Project Summary and Project Description are for. As for the latter, your best argument will be to rely on your previous work. You'll be able to list some of your publications in the Biographical Sketch, and can mention your previous work more explicitly in your Project Description.

Finally, if you really think that it will help to point out departmental awards, invited lectures and whatnot (and it is far from clear to me that this will help you all that much), you can always ask your letter writers to include this information in their letters.


Accepted into university for MS in CS but rejected by professor for research

If you can get a TA or otherwise afford to go, you might still consider it. You are likely to take around six classes your first year. You might meet several professors that you want to work with and who want to work with you. Plenty of students come to grad school without an advisor lined up and manage to find one during their first year.

It's unlikely but not impossible that you will work by yourself to complete a publishable paper in CS. Even if your work is purely theoretical, you are likely to need guidance at the very least and other resources in general.


Accepted letter for Ph.D. in February, but now they say they don't have funding! Is that possible?

If they did not say they had funding at the time of the offer, then it is quite likely they do not have funding now. This is especially true in the humanities. Cases where the offer include a statement about funding generally mean the department has funding, but it is not unheard of for things to happen. Generally statements about funding include lots of conditional clauses protecting the department in case things fall through. In the humanities funding for a PhD is much harder to get. It is worth asking about the possibility of teaching.


Is experience teaching college statistics sufficient to apply for a non-research stats professor jobs?

As long as you are still at the assistant professor level, I think your application should be competitive at many schools, provided you have evidence of good teaching.  Many mathematicians have gone over to statistics, and at a school that is primarily teaching oriented, what they typically look for is someone who teach well, provide good service and be a good colleague.  They probably won't care much about your actual area of research, just that you can cover well the courses they have in mind for that position.  If you've taught several similar courses, and have good letters about them, then this is sufficient evidence of teaching capability to me.

In fact, your position would be viewed as advantageous by many, as you should have more experience in both teaching---in fact, possibly more experience teaching statistics---and service than a fresh statistics PhD.  Also, presumably you've shown that you can sustain your research on your own.


Unexpected long delay with paper review and no answer from editors

First thing first, I would suggest planning to never submit to this journal again.  Some journals take a very long time to review, and in some fields more than a year of reviewing is not uncommon.  Editors, however, should be reasonably responsive to email and months without reply is not reasonable.

Although, there is one case where it might be reasonable: it might be that all of your email has been going into their spam filter.  You don't say where you are from, but there can be problems of this type: I recently had an experience where some international colleagues had their entire domain blacklisted by anti-spam systems and it made every interaction very painful and difficult.

Either way, at this point, you've basically got two options for escalation in attempting to find out the status of your paper:

Make contact via another medium than email, preferably by phone so you can get a human on the line.
If that fails, get in touch with the publisher and let them know what's going on with their journal.

You also need to be more persistent in your attempts to contact: emailing once every two months and just taking no response as your answer is really letting things slide.

If all of this fails, then you're stuck with an unpalatable choice: leave the paper in limbo or withdraw.  Neither is a particularly good option, but neither is the end of the world, either.


Can I work as a software engineer and be a PhD student?

I did combine PhD and work for 4 years, so, theoretically - yes, it's possible. But I didn't like the process because I wasn't fully invested in either activity. It also significantly delayed my defense. It depends on how productive you are. At times you will be facing certain deadlines and will be feeling torn between two major activities.

I think you should go ahead with PhD if you are serious about it. It will take some 3-6 years of your time, so why to postpone it? I think it's totally possible to get internships at summer time and you may have to develop software as a part of your research, so you'll be practicing your skills.

You can also consider free-lance work so that you have more control over your time.


Proper pronoun in a response letter for a single author manuscript

You're really overthinking this. Response to reviewers are relatively informal, and frequently quite terse1; you can certainly use "I" and no one will raise an eyebrow.

1For example, if I've made a change suggested by a reviewer, I simply reply: "Done".


How to follow up with a professor on graduate school admissions decision

A follow up email is fine. Be polite and to the point.


What is the reason of the disparity between single article price and yearly subscription in scientific journals?

On the principle a subscription is always better than individual sales from the journal's point of view because it's a fixed income on which they can count. It's also well known to increase sales that explain why you always get a discount when you subscribe to a service.

As for the seemingly large difference you mention, my guess is that individual subscriptions for scientific articles are rare, and thus not very interesting financially. People needing frequent access to the content of these journals typically access them via institutional subscriptions.


How to react to your work being cited incorrectly or in a misleading way?

It is no different from finding any other mistake in a paper that you read --- just write e-mails to the authors politely explaining the errors. It is in their interest to fix them.


Difference between a Virtual issue and a special issue?

Virtual issues, which are also referred to as "collections" or by other names, are a set of papers that were already published in various issues of a journal and are centered around a single topic. This is usually done to highlight a certain topic or simply to help readers find papers on a topic. This is done on the editorial/website level and that is why it is "virtual" - usually no special content is created for this.

Special issues are issues in which the journal decides in advance about a certain topic, and invites submissions of papers on this topic. Often there is also an invited guest editor for the issue, who is an expert in the field. The final result could actually look similar to a virtual issue (a collection of papers on a single topic), but in a special issue these would be new papers submitted specifically for this issue. Sometimes there will also be some overview piece written by the editor.

Special issues might indeed affect the impact factor of the journal. For example, the journal Bioinformatics sometimes has a special issue in which the papers published are papers that were accepted to ISMB, a major bioinformatics conference. These papers probably get cited on average more than other papers in the journal, so it would increase the impact factor.


Progress to Ph.D. delayed due to COVID-19: How to convince advisor to let me finish degree without taking an extra year?

Very sorry to hear about your situation. I know of others, like yourself, who've had their research stalled as a result of the COVID-19 situation. I must say, I was taken aback shocked to hear about such inflexibility on part of your supervisor:

I asked about proposing a partially online experiment so I could gather data this summer, but she refuses to let me do any online data collection for my dissertation.

If you haven't yet already, then you should really have a heart to heart with your supervisor and explain to them how you're feeling. Try and see if it is, in fact, the case that they are fixed on this issue. Should collecting data online be a feasible means for you to collect data for dissertation and defend by the fall, it would be very unreasonable on your supervisor's part to not allow you to do this. So if your supervisor is firm on this position, I'd recommend consulting with your department's ombudsman or even head. It is definitely not fair that you should be held back if that is not a necessary outcome, and merely reflects your supervisor's research motivations.


You can of course omit the recipients postal address, but you need to properly identify him (incl. his institute, faculty, university). Otherwise a number of people will simply discard your letter.

Definitely put your own full postal address. Email addresses, even if signed and certified etc., do not feel very trustworthy.


Statistics PhD - Sending the math GRE score

It really depends. Obviously if the score is required you need to send it. If you are applying to top programs, a 68% at anything is not going to help your case so I would not send it if it wasn't required. At lower ranked schools, a 68% might be okay, but again it is probably not going to impress anyone. I would probably draw the line at the 90th percentile for providing something that is not required.


In a job talk for a postdoc position, should I refocus my talk to be closer to the research at this research center?

No. Having given these talks (and attended a great many of them) in the past, I can say from experience that most likely the research center wants to know how you present work in general, and if you can speak to a wide audience.

If you want to tailor the your talk at all, make sure it is providing sufficient background and give a "big-picture" version of your work. It is fine to include details (indeed that is expected), but don't get your self hung up on minuscule details related to your methods (unless asked).

Best of luck.


When listing refereed papers in a CV, should I highlight my name in authors lists?

I do not generally see people highlighting their name in a CV in this way, and I do not think that it is necessary (though perhaps the culture in experimental physics is different).  In a CV, you are by definition an author of every listed paper, and papers where you are first author leap out pretty easily to the eye already---unless you've got lots of papers, in which case, why worry about it?  If you highlight your name, on the other hand, I think that it could come across as insecure, since it is not normally done.


Should I put the raw data in the appendix of an investigation if it is available in the GitHub repository?

There is no need to put the data into the paper itself if it is accessible and you point to its location. For a printed paper it is mostly useless, of course, and if it is online, then it is only a click or two away. No one is likely to complain about the minimal added effort.
But, like any other web resources, your reference to it should include a date (last referenced). Then if it is later changed for any reason, the reader will have a better sense of what is going on.


Is this a correct way of using a literature review in a thesis?

Shouldn't I rather look at the reviews and then go directly to the
  sources[A] and derive valuable information in the way I interpret it?

Yes. You need to read anything that you cite, and you should read the original articles.

But if the review articles were helpful to you, you should cite them too. For example, the review article [B] might compare techniques used in two of the original [A] papers. You might want to cite that comparison in [B].

  I have listed more than 30 mechanisms. If I were not to use these [B]
  articles I'd have to go trough 30+ [A] papers and basically recreate
  [B] papers and recreate a redundant literature review of said
  mechanisms that already exist in earlier papers.

Do use the review articles; they can help you and save you a lot of time. Without the review article, it would probably taken you a lot of time to figure out which [A] articles are relevant to your research, and to see how they relate to each other. Also, the people who write review articles tend to be experts in their field, so you're getting an expert opinion on what the state of the art is on a particular topic at the time the review was written.

You do still have to read the original articles, summarise them, and draw your own conclusions. And you should check for any important developments in the field that were published after the review article. But it's not nearly as much work as doing a literature review from scratch.


What are the pros and cons of writing papers alone?

The advantage of writing with someone else, someone more experienced in particular, is that you may end up publishing quicker since you're not doing all of the work. It can also allow you to write papers that you may not be able to write on your own assuming the co-author(s) bring(s) something to the table that you can't offer. For graduate students, it is a good idea to write their first paper with someone more seasoned so that they also get advice on the logistics of publishing a paper (how to pick the right venue, how to write the cover letter when you submit, how to respond to reviewers - some of these an advisor can help with regardless of co-authorship, but a co-author will be more invested). In some fields, it may be frowned upon that you have no co-authored papers as it may signal a bad relationship with an advisor or that you are generally hard to work with. This part is completely field-dependent. The downside of having too many co-authored papers is that people may wonder whether you can work independently.


Locating the journal in which a paper was published

You can certainly write to the authors to ask for the code even if the paper is not yet formally published. While the chance of them sharing it might be more if it is formally published, I don't think it is rude to ask. You could perhaps include some context on why you are interested, if you do so.

Nevertheless, to find out where a paper has been published (if any), you could try the following:

Search Google / Google Scholar.
Check the "Comments" metadata in the arXiv submission. The final publication venue is often mentioned there.
Check the websites, Google Scholar profiles, DBLP profiles, etc. of the authors.
Check with your university library.

You could check the databases of individual conferences, journals, or societies as well, but these would almost certainly also show up on a Google search.

For your broader goal of finding the code, a few suggestions, before contacting the authors:

Check the paper thoroughly, look for any links in the text, particularly in the introduction or experimental sections, and in the footnotes.
Search Google, GitHub, and similar resources. Sometimes there are third-party implementations available, in case that is helpful to you. If the authors have given a name to their technique / tool, searching by this name, in addition to the paper title, can help.
In certain fields, there may be specific resources available. For example, in machine learning, paperswithcode.com maintains a database of papers along with code by authors and third-party implementations. For several popular tasks, it also maintains leaderboards of methods and their associated paper and code.
Check the authors' web pages and their labs' web pages. A link to the code might be available in the publication list.
Check for implementations in future papers that cite this paper (unless the paper you are looking at is very new). Others may have compared their methods with that of the paper, and may have an implementation included in their own code. Survey papers are also a good place to look.