Does doing poorly in a course hurt my chances of getting into grad school?

I am a tenured associate professor in the mathematics (note: not chemistry) at UGA and did graduate admissions for several years there.

I am a little surprised that the two answers so far have avoided the obvious: getting a C- grade in two required courses in your major certainly has a negative effect on your chances of getting into graduate school.  The only question is how much.  I don't want to speculate on this because you deserve answers from my opposite number in a chemistry department, and I hope you'll get one.  I'll just say: if we "transposed" this question into mathematics, getting C- grades in two core courses that are well known to be difficult enough to knock some students out of the major (say, real analysis): that would indeed be a serious flaw.  We can admit students who got good grades in all the key courses, and we usually do.

However, I don't think you have asked exactly the right question.  The issue is not whether you should abandon your graduate school plans based upon your performance in one (or two) courses.  You shouldn't.  But trying to precisely quantify the damage is our job, not yours.  Your job is to avoid if possible, and if not possible remedy, the problem.

For a very serious student (students who want to go to grad school should count as "very serious"!), getting a C- in a course and then moving on to take the continuation course with the expectation of more of the same is a tactical error.  You say you plan to retake the courses anyway.  Then why are you even taking the second course now?!?  You need to plan more precisely for your own success.  I would look into withdrawing from the second semester course if it's at all possible.

You also mention health problems.  They can certainly affect your academic and professional performance, and this can happen in an uneven way.  It is quite plausible that you're doing as well in the other courses that you have more talent / experience with / predilection for as you would have done if you were healthy and doing much worse in the course that needs more of your time and energy.  Really consider taking time off, or adding a semester or a year, or doing whatever you can to lighten your load and give yourself the chance to do well.  It is much easier to get official accommodations for serious problems while they're occurring than to try to explain two years later the dip in your transcript.

In general I think you could get better advice on which courses to take when and how to succeed in your major.  A lot of the most successful students are successful not because of superior talent but because they've been properly mentored or set up for success by others, or because they instinctively know much better than others how to set themselves up for success (which, contrary to what I said above, is certainly a talent).

Good luck.


Create contact for future postdoc without disappointing PhD supervisor

If your advisor doesn't think it is a good idea then you should trust him (this is part of his job, to advise you, after all).

You're just starting out so get your own projects going before trying to connect with another group. In a year or so if you're still interested you could bring this up to your advisor again. You could always attempt to meet people from the other group casually at a conference or something.

Short answer: Listen to your advisor, especially so early in your career.


Are MOOCs a good way to show grad schools that I've gained proficiency in a field which is not my major?

There are several issues with MOOCs, all of which make them a poor substitute for actual classes for admissions.

Poor penetration. There is more widespread knowledge of them than a couple years ago, but they are still fairly unknown. Chances are high at at least someone reading your application won't know about or understand them.
No grades. Few MOOCs offer anything more than a certificate of completion, and many don't even offer that. Even if they offered grades, verification of identity is a problem.
Wildly varying quality. College classes are generally of a certain quality/difficulty, and knowledge of the quality/difficulty levels for certain field-specific classes across schools is something that application committees will use to judge candidates against each other. MOOCs are much more of an unknown.


If I interview a professor, should I pay him or her?

Unless you're giving a veeeery long speech or speaking about something highly technical to a group of experts in the field, there is no need to interview a professor. What you're most likely trying to do is give a layman's introduction to a fairly broad field. By contrast, researchers are highly specialised in very narrow fields. A short speech is unlikely to get to any details that you need to speak to an expert to learn about.

You mention that you're supposed to speak about a topic you're not familiar with. That means you don't have the background knowledge about the field that makes speaking to an expert useful. You would most likely get more useful information from Wikipedia, blogs (possibly by professors) or finding an introductory textbook in the library. Asking a professor to give you an introduction to an area you're unfamiliar with (outside their teaching duties) is kind of a waste of time for them. If you want to waste their time, then you should certainly offer to pay them, or at least offer to take them out to a lunch you pay for while they talk to you.

Like @cag51 metioned in the comments, you'll probably have more luck with a grad student. We're still new enough to the whole "expert" thing to be flattered that you would ask, tend to have a bit more time than professors, and never say no to free food.


My main confusion was not realizing that The Open Archives Initiative Protocol for Metadata Harvesting is a separate protocol, not a subset of arXiv API.

In this case, the relevant queries are ListIdentifiers (10k items per query) and ListRecords (1k items per query). To get just identifiers we need to write:

http://export.arxiv.org/oai2?verb=ListIdentifiers&set=math&metadataPrefix=oai_dc

It results in 10k identifiers in the following form:

<OAI-PMH xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd">
  <responseDate>2015-02-16T19:28:22Z</responseDate>
  <request verb="ListIdentifiers" metadataPrefix="oai_dc" set="math">http://export.arxiv.org/oai2</request>
  <ListIdentifiers>
    <header>
      <identifier>oai:arXiv.org:0704.0002</identifier>
      <datestamp>2008-12-13</datestamp>
      <setSpec>math</setSpec>
    </header>
    ...
    <header>
      <identifier>oai:arXiv.org:0712.1769</identifier>
      <datestamp>2011-06-23</datestamp>
      <setSpec>math</setSpec>
    </header>
    <resumptionToken cursor="0" completeListSize="249546">760571|10001</resumptionToken>
  </ListIdentifiers>
</OAI-PMH>

As there are more results, to get next batch we need to specify resumptionToken, in this case:

http://export.arxiv.org/oai2?
   verb=ListIdentifiers&resumptionToken=760571|10001

and so on.

Other useful parameters are from and until, e.g. as in

http://export.arxiv.org/oai2?verb=ListIdentifiers&set=math&metadataPrefix=oai_dc&from=2015-01-14&until=2015-01-14

To directly get categories (bear in mind that set=math specifies mathematics, but there are no smaller subsets), one can write:

http://export.arxiv.org/oai2?verb=ListRecords&set=math&from=2015-01-01&until=2015-01-31&metadataPrefix=arXiv

It's important to set metadataPrefix=arXiv, so that subdisciplines will be listed:

<categories>
  math-ph cond-mat.other math.MP nlin.CD physics.class-ph
</categories>

EDIT:

I used delay as Nate Eldredge suggested, in my case - 25s. Yet, while trying to get all math (250k items so in 250 queries) it gave error at 70. I did continue it (with even higher delay) but sometime around 110 the query was not longer available.

So, the way to go is in getting smaller chunks - e.g. by month (or for mathematics - at most by year).


As for a EU-wide database of research funding opportunities, see EURAXESS:

Go to EURAXESS Funding Search.
Select your RESEARCH FIELD (probably "Formal Sciences").
Select your FUNDING TYPE ("Funding"? "Mobility Incoming/Outgoing"? "Travel Grants"?).
Select your CAREER STAGE (probably "First Stage Researcher" up to the point of PhD).
Click on Search and browse through the results!

Other than that, there are also national databases. If you tell us the country of your affiliation, perhaps we could link to it. (E.g. https://grants.at/ for Austria.)


Do semester, weekly, and daily planners work for undergrad or grad students?

Planners are good for certain things, but they aren't going to solve your problem.
Fundamentally, they are good for recording future obligations, such as project due dates, exam dates, doctor's appointments, and the like. But they won't give you better study habits.
Let me suggest two things that might help to get you on a better "schedule".
First, do an inventory of what it is that you are actually doing and compare it to what you think you should be doing to be more effective. All nighters and cramming for exams are an exceedingly poor way to succeed. The worst exam I ever wrote was actually an open book (timed) exam, for which I'd stayed up all night preparing. I couldn't actually think when it became important to do so. But, figure out whether you are wasting time, even time spent studying ineffectively by pushing too hard without breaks. Your brain needs occasional breaks. Aerobic exercise is a really good way to take a break.
Second, make a habit of carrying a pen and a few index cards with you wherever you go. Some of those cards are blank and available for recording notes, but others are summaries of recent lectures (perhaps), and one of them has a list of things to accomplish for the day. You can add time requirements as needed. You can check them off. I suggest actual index cards and not an electronic equivalent, since cards can be easily updated at any time and take up little room in your pocket.
You can read about the Hipster PDA at an answer I gave at CSEducators for more on effective use of index cards. Use that as your "planner".

More than half a century ago, when I was an undergraduate, the top student in my graduating class (valedictorian) carried a hipster pda at all times. I later used one to help manage my teaching.


Which authors should be listed in a conference presentation?

The practice that I have typically seen is to list all authors, but highlight/bold/underline the name of the speaker.  That way, credit is given both for speaking and for production of the material being spoken about.


Should I include my latest job on my CV?

Yes, you ought to include it. In committee we don't like to see gaps in a CV, it suggests that the person might be unemployable. Whereas there is nothing wrong with spending a year in the wrong job. If it comes up during an interview, you can turn it to your advantage: it was by working at that job that you understood that you were really meant for graduate work.


Do manuscripts sent for submission in Word format need to be already in two column or a specific font?

The review formatting and the final, camera-ready formatting are often quite different. You will probably get a chance to reformat it for publication after it is reviewed. If you have any doubt about that, you should contact the editor.


Publishing similar/same paper twice? (regarding Economics Letters journal)

Taken from the comments as per request

This is fairly common. For example, in CS, one might publish preliminary work at a conference, and then flesh it out for a journal (there's a "30% new material" rule in many journals to cover this situation). But to answer your question, doing this doesn't boost publication count except for very dumb ways of evaluating a publication list. Most people (except university bureaucrats) will list the conference and journal paper as one entity.

Note that it is upto the journal editors of the second venue to decide whether the paper is sufficiently different from the first one. They are free to reject it even if you think the latter paper is a nontrivially expanded version of the first one.


Fighting for academic fairness: My authorship is unaffected but my PhD advisor pushed up authorship of a co-author at the expense of other co-authors

Let it go. Maybe decide to not publish with this PI in the future. But this particular hill is not important enough for you to die on.


is there apprentice training in master of engineering?

There really aren't "apprenticeships" associated with most traditional college degree programs. On the other hand, many engineering programs, including electrical engineering, do have what are usually known as internship or co-op (short for "cooperative learning") programs available. These programs are inherently designed to allow students to work in engineering-related companies during their degree program. The conditions that apply to each program are school-specific and even department-specific, so be sure to check with the individual departments you're interested in.


Student essay feedback for a large class

Here are some options/ideas to consider:

Giving just a grade and asking to come to office hours is certainly defensible. I've read that most students don't read extensive feedback.
Commit to giving a grade and very short feedback.
Create a written rubric with check-off categories for various scoring criteria. Require students to staple this as a cover sheet on their submissions. Grade by checking appropriate boxes.
If you have an online learning management system, it may support rubric grading as above, so you can do the check-off grading without additional paper. (e.g., I do this on Blackboard for computer programming assignments).
Set a budget as far as time you can legitimately devote to this task. Keep written records (e.g., spreadsheet) of how much actual time is spent on this overall task. Have the TA track time as well. If time spent is over budget, iterate and cut/modify/streamline something.


Is it possible to get a bachelor's degree just by having more than the required credit hours?

Generally speaking, no, a degree requires more than just a certain number of credits. There are usually specific requirements for certain courses, and more requirements for credits and courses within a "major". A minimum GPA is a requirement and there may be a separate GPA-in-major requirement.
But, you may have actually accumulated all of the requirements for a degree in some field if you don't care what it is. There is also some shortest path to graduation for you in any case. Someone like the university's "registrar" knows all of these things and can give you advice. But your advisor should be able to help, or even a secretary in one of the departments in which you have a lot of courses.
So, yes, you may need to change your plans, but you need specific advice from the institution offering the degree.


Where to correct an inefficiency of algorithm in a published paper?

The change only appears trivial to you now that you know about it.

Moreover, while the change may be simple, the validation of that change is not: I'm sure there's lots of experiments to run to verify your statement, and maybe some new analyses to be performed as well.

To me, this sounds like a fine opportunity for a followup.  If your paper was published in a conference, then the improved version can go into the "extended version" journal paper.  If your paper was already published in a journal, this is a good time to follow up with a short conference paper.  If you're in a field that doesn't like conferences, there will probably be journals that take "short papers" or "application notes" or some similar.

Bottom line: one way or another, there should be a good place to put this not-as-trivial-as-you-think piece of work.


Even if the PhD research does not go as planned, I would strongly suggest you to get some teaching experience for a number of reasons:

"One learns best when one teaches" as a translation of the German "Am besten lernt man, wenn man lehrt". Teaching gives you a deeper understanding of many topics, it helped me a lot.
Character building: you as a person will benefit as well from teaching. Speaking publicly is not an issue for me since I taught during my PhD studies, this had a really positive effect on my work outside academia as well.


How should I disclose a data extraction error when submitting a revision?

It is probably better to point it out. A note to the editors/reviewers is fine. You and everyone want the best science to be published. Full disclosure is best.
I doubt that this would lessen the chance of acceptance, but it might draw a bit more scrutiny overall. But that is a good thing in general.
This is similar to pointing out other changes in the paper, those that were called for and those that you think are relevant to improving the paper.


How long between the acceptance and proof correction of Elsevier?

You can answer this question is to look at the date stamps sequences on some of the existing papers.  Many journals (including the one you have asked about), include all of the major dates in the publication process, e.g., "Received Date1, Accepted Date2, Available Online Date3," as well as the final date of publication.

Note that the "Available Online" and final date of publication may often be very different, but except in rare cases it is "Available Online" that you should care about because that is when people begin to be able to get your paper.  However, some journals do not do all of the final proof correction until closer to the date of publication, but essentially just have your preprint up online for quite some time!

Applying this analysis to this particular journal, one can find the following:

Acceptance to available online looks like 1-3 weeks
Final publication happens ~6 months later

So you will probably get contacted about the proof very quickly (if they follow the normal method of proofing before online availability), or not for several months (if they do late-binding proofing).


If I rederived a result (oblivious that it already existed), should I cite the original paper?

Citation has multiple purposes, as described by several answers on this site (e.g. 1, 2). Broadly speaking, those purposes mostly fall into three classes: giving a trustworthy source, giving credit, or suggesting further reading. Any individual citation might serve several of these purposes, or only one of them. So when you cite a paper, that doesn't necessarily make it seem like you took the result from there; you might simply be giving credit to the first person(s) to publish the result, or referencing an external source to back up what you're saying.

What this means for your case is that you should definitely cite the other paper. The exact wording you use to do so depends on several factors, including whether you think an explicit statement of the result, and/or your derivation of it, are still worth including in your paper - for example, if you think your derivation is more clear, or relaxes some assumptions of the original, or so on. Here are some possibilities along the lines of what I've used or read:

"This result was originally derived in reference [1]." (possibly in a footnote)
"For a more detailed derivation, see reference [1]."
"Here I present an alternate derivation of the result in reference [1]."
"(statement of result) [1]. In brief, this can be derived as follows: ..."
"This uses the result that (brief statement of result) [1]." (probably in a footnote)

and so on. Or you can just cite it without comment, and unless the conventions of your field are otherwise, people won't necessarily assume that you took the result from the other paper. (Nor will they even care, in most cases.)


Is it normal to feel a bit unmotivated at the start of PhD programme for not getting the exact topic of interest for my PhD?

As far as I am concerned, I don't know personally someone who is or was in the same situation as you. However, being 4 years in in my own Ph. D. and knowing a lot of people who are doing one or finished one, I can maybe bring some perspective to your situation.

Among people I know and including myself, I've seen two typical situations upon starting a Ph. D.:

either the student doesn't know exactly the topic (s)he will work on and only got a broad field to investigate,
either the student is actually deepening a topic (s)he worked on during a master thesis (this is my case).

The first situation seems fairly common in my experience and is arguably worse than yours. Not knowing what you will be working on for the 4-5 next years is probably more disheartening than having a topic that is close to your interest but not exactly matching what you had in mind at first. Sometimes, people change of topic every 6 months (because they didn't find anything with the previous topic they were working on) in the beginning and don't seem much more advanced 2 years after starting to work on their Ph. D. thesis. In fact, most people I know who stopped their Ph. D. started off like this (note that this isn't a rule of thumb; I've seen people in the same situation finishing their Ph. D. as well).

The second situation sounds, of course, ideal. You start your Ph. D. already knowing what to do; sometimes you even get to publish what you worked on during your master thesis right from the start or by slightly re-working it/expanding it (depending on how your master thesis was received). However, this doesn't necessarily shield you from other issues you can encounter while doing a Ph. D., such as:

having trouble to explain to friends and family what the heck is your thesis about (don't underestimate this problem, and if possible, train yourself to explain your topic in the simplest way),
getting sometimes the feeling that your research doesn't really interest people in your own field (because people keep asking you during conferences what's the endgoal of it, because your paper submissions get rejected because reviewers have trouble understanding what you're doing, etc.),
doubting about whether you should finish or quit your Ph. D. when you're halfway through it, even if you managed to publish some papers (a phenomenon which has been dubbed as "the Valley of Shit"),
having irregular schedules (except if your university enforce them), sometimes working all the time (even the week-end) for some weeks and sometimes not working much because you're unsure about what you will do next (or because you want to slow down a bit), which can also be a problem on the social side,
etc.

What I'm trying to say with my points above is that doing a Ph. D. is a difficult task anyway, even if you manage to get the best possible topic, and it's perfectly normal to feel unmotivated at some point. Doing a Ph. D. isn't just an intellectual challenge.

Also, be aware that the way you progress in your research can lead to developments you wouldn't have expected at first. In my case, for academic reasons, I had to write a kind of big planning for the first years at the start of my Ph. D., but I can guarantee you it looks nothing like what I actually did up to now. I don't know much about your research topic, but you can already keep in mind that you might not always work exactly on what you expected to, and you might even reconnect with the topic you first had in mind or go into completely different directions. I hope this helps.


Is it wise to select a PhD topic before choosing an advisor?

In brief: no, in mathematics in the U.S., you do not "have to choose" a research topic prior to beginning your PhD. At the same time it is _of_course_ good to have something to be enthusiastic about, curious about, fixated upon. But that can change, and probably should change as you learn more. It is apparently the case that in the U.S., and to some degree elsewhere, in mathematics, undergrads and even M.S. students really don't get enough background to understand contemporary mathematics at all, except very superficially. Fine, that's not a moral failing... maybe just evidence that there's a lot happening in mathematics... (!?!) But, then, in that light, the enthusiasms that novices have are necessarily (by-far-typically) ill-informed... and will change if/when they learn more.

This is not to say that one should not have an opinion, or should not admit interest in things because one knows one's interest will change... but only that one should anticipate that change, rather than believe that one "has arrived" at age 22 or so, and there's nothing left to learn, and now it's just "trying to solve problems/do research". I understand the appeal of that, but, if we think about it, it's better in the long run if mathematics is not that shallow or superficial.

More specifically, spectral graph theory is a quite viable research area. "Expander graphs" are popular and google-able. Lots of people work on this, both from the "spectral side", and from the "graph theory" side.

And, perhaps counter-intuitively, the possible fact that there are not so many "books" treating a topic can in fact be a very positive sign... it's unclear. That is, if there are zillions of books on something, then chances are good that it's an older topic and has been worked over pretty hard... leaving less room for beginners to contribute.

So, sure, it's entirely reasonable to have specific and fine-grained interest... as opposed to "general" interest. Like having a specific lunch rather than a lunch-in-general. :) But be utterly open to changes in your viewpoint... as you learn more, which will be for many years. :)


How can I protect my loose leaf textbooks?

You could take the book to a copy shop, and have it binded properly (e.g., hot glue, hardback, etc.). Here in the Netherlands, that costs about 3 euros for a simple but effective glued back.


My department is not concerned with publishing, is this a valid reason to move to a different one?

I did start working there 2 months ago.

and

  It will not be easy to do that and I will have wasted a lot of time by the time I move out

don't fit well together. If you're worried about the 2 months you've spent, I'd say that's insignificant. If you're worried that it might take (with application processing etc) upto a year, I'd say the same thing. Think of a 30-40 year long research career. A year (or 2 months) is not a long time.

It sounds like you've done your homework and have a plan for what you want to do, and you're just worried about taking the leap. Take it ! You only get one career, and taking action to further it is always "worth the hassle".


How to transition from pure biology PhD to bioinformatics/biostatistics?

As a PhD student in Math with Computer Science background who is working in Bioinformatics exclusively: it is definitely possible for you!

In the Computational Biology Institute at The George Washington University where I work as GRA we have PhD students, Post-docs as well as Faculty from different backgrounds (including pure biology) working purely in bioinformatics area.

I do believe you don't have to switch as much, as you think. It only takes a group that is more focused on the "informatics" part more, than on biology. But still caring about Biology to change the main daily routine of yours. And your background will be needed, as bioinformatics can not exists without biological reasoning and biological guidance / insights.

If I were you, my first step would be to find what is the most "informatics" related problem close to your current research. It might be not your group, who is doing it, but still. Educate yourself a bit about such research by reading related articles. And after that it is as simple as writing a couple of emails to PIs of respective studies and telling them, that you are very interested in collaboration on their topic. This might yield a joint publication or even a post-doc position offer from respective lad.

I wouldn't count much on pure "career" in statistics, as it usually requires more math background. But biologists in bionformatics, who at least knows how to do statistics are very hard to find. So the more you know from the programming / statistics side, the better you are off go to more informatics groups.


Special status of some physicists in France

This other kind of permanent position is very specific to a few fields of science such as astronomy, geology and probably a few other ones.

While usual permanent positions (such as something-professor) imply research and teaching, these positions add a new commitment : "observation service". 1/3 of the time should be dedicated to operate big equipments (telescope for example) for gathering and analysing data that will be useful to the community. For astronomy it implies missions on telescope sites for instance.


How to get better at identifying research gaps?

Finding good research "gaps" is indeed a challenging and important task. It has different components that all require slightly different skills.

Above all, a useful research gap is interesting, feasible, and unexplored:

interesting: I think this part goes without saying. But how do you determine 'interestingness' ? This is a complex mix of structural aspects of the field and community opinions, so it varies a lot from area to area. But probably the best way to understand what's interesting is by talking to people, asking them what they think is interesting, and why, and also understanding how even the basic questions in your field came to be deemed interesting (an advisor/senior researcher can often help with the latter).
feasible: It's not hard to list the "top 10 open questions" in your field. And for some researchers, that constitutes their entire research program. But that's not realistic for most people, and especially for students. Feasibility is about determining whether the tools exist to even make a dent on the problem. This requires a lot of experience in using different methods and understanding what they can and cannot do for you. It also involves thinking somewhat "sideways" about tools and problems, because it's likely that the obvious approach to an interesting problem has been tried. You will have to read papers very closely to find little gaps, or missing reasoning steps, that might suggest that a technique could get used. And you have to learn how to "fail quickly" when trying a new idea.
unexplored: While it might be educational to work on a new direction that has been explored before, you don't want that to be the fate of all your research explorations ! Here again, being plugged into your community and understanding what people have tried (or not) is also helpful. There are often "folklore" statements of the form "Oh this doesn't work because...". Sometimes it's true. and sometimes it's not. But it's best to understand what people have seen and what they're trying. Related to this is the idea of knowing your strengths: you'll accumulate a set of tools over time that you're an expert at. Make sure that you can use them: that gives you a competitive advantage.

We get a lot of questions here about whether anyone can do research (even if they're not in a formal academic environment). The answer of course is yes. But where amateurs (in the sense of people not being paid to do research) can often slip up is in identifying gaps that are feasible and unexplored (finding interesting gaps is usually not that difficult to do on your own) because they're not plugged into a larger commmunity.

Update: In response to the edit, here's an interview with John Baez that directly addresses the first point (of all the good problems being taken). John Baez's other suggestions are very good as well, and form a nice 'counter' to the Hamming article linked above.


Can I get a tenure track Applied Math assistant professor position in a top US college if my PhD was in a similar ranked private U.S. college?

If you want to get your "teaching career" going, I wouldn't worry a lot about the ranking of the school. Teaching focused positions are going to look at your teaching experience, if you don't have a lot of this then you may need to take a visiting position to get some experience.

A school ranked lower than the one where you got your PhD might view the name of your school as something they want associated with your department. Or they may assume you are more interested in research and not with teaching. These positions can still be incredibly competitive, but if you have the right background you may have a chance to be hired right out of your PhD.

If the school you attended was highly ranked, then schools ranked the same or higher are going to want most of their tenure track faculty to be focused on research, or at least to have a good research program to get undergraduates involved in. If you don't have a stellar publication record, you will absolutely need a postdoc. Even then, you will need a good postdoc with good research results. Even then, it will be very competitive.


After the passing of my supervisor, the department forces me to start again from zero. How to respond?

Maybe someone else in the department can supervise your work and maybe they can't--the fact is that they won't, and that's what you have to work with. My (pessimistic) gut feeling is that the department head has essentially written you off as collateral damage. He's willing to push you through for a completion because that's good for the department, but he doesn't care that you want an academic career.

On the off chance that this isn't the case, you might try approaching the possible available supervisors and get a clear timeline from them about how you can finish with work that can launch an academic career. If they tell you it will take longer than the one year that the department head seems willing to allow, you can try going over his head to pressure him to agree to your new supervisor's timeline. But this is a rather delicate situation and you are probably better off shopping your work around at another school and explaining that you lost two supervisors through no fault of your own.


Will the admission committee try to get in touch with the referees who wrote the recommendation letters? [Graduate admission]

I have written many letters of reference.
I have also been contacted, over the phone, by HR or admissions who wish to discuss the candidates, just to expand on experience or whatever.
So, if they wish to contact the people who you put as referees, then they will do so.


Increase chance of reply when e-mailing an eminent researcher?

Your chances of a reply will correlate quite strongly with two factors:

How interesting your problem is.
How long it will take the professor to respond.

Thus, you should:

Make everything as brief as possible, yet still include all necessary information.
Ask yes, no, or short-answer questions that the professor will know off the top of his/her head. Ask for references to a paper, or for whole pieces of code: not the embedded details.
Briefly mention that you're a PhD student at Fake University, supervised by Professor Jones (if the prof you're contacting likes your supervisor's work, that's a good start).


Should I hold the same writing standards for international students as I do for domestic students?

There are two different types of value judgement that you are discussing here---communication goals and grading---and I think it's important to carefully separate them.

Communication Goals: I think that it is unfair to a person who isn't a native English speaker to not expect them to aim for the same goals of clear and lucid communication.  When giving feedback, don't brush over the language and grammar errors just because a person is not a native speaker.  They should have the same chance to learn and improve as anyone else.
Grading: Unless the class is about English grammar, making English quality a significant part of the grade is generally a bad way to evaluate a person's work.  If the language is bad enough that it interferes with your ability to understand the class-relevant content, then yes, that's a problem and should receive proportional demerits.  If the class-relevant content is clear, however, it's questionable to me whether any points should be taken off at all.

In short: grade very generously on language issues, but point out the mistakes so the student can continue to learn and improve.


Is it ok to ask my professor about a project for a second time?

First and foremost if you have the option to visit their office, I would highly recommend doing so before sending the second email. Because I have had professor that have lost my email in the dozens or hundreds that they receive daily, and a simple office visit was sufficient enough to clear it up


Is it a wise decision to email graduate professors my provisional certificate of bachelor's degree?

I wouldn't include it in the initial email. The initial email should just be a few sentences where you show that you know what kind of work they do, and try to convince them that you have something interesting to add to the group. I would attach a short CV with your predicted graduation date, but not the provisional certificate.


What to do if one of my recommenders has commited a plagiarism violation that has been publicized online?

I assume that because you write "for PhD" that you are currently an undergraduate applying for graduate school.

In that case, I think there is relatively little guilt by association. Some people reading the recommender's letter might discount it because the person is discredited, but I don't think anyone will blame you in particular because we assume undergraduates don't often have a choice of which lab they work in, or any knowledge of the shenanigans their advisors might be engaging in.

Her letter might not be as strong as if she didn't have this cloud hanging over her, but I assume that in it she spoke to the quality and diligence of your work and your suitability for graduate studies.

Things might be different if you were a doctoral student in the lab and applying for postdocs or jobs. In that case, there might be stronger guilt by association, especially if you had authored papers together. But you're just an undergraduate so I wouldn't be worried.

Anecdote: As an undergraduate psych major at a R1, I worked in the lab of a psychologist who worked on ESP - that's extra-sensory perception. He only hired undergraduates because he knew of the taint that would be associated with this work for grad students. I was quite happy with the money, it was fun work coding people's free-associations due to supposed psionic powers, and it didn't hurt my graduate career in any way.


Can student be the corresponding author?

There's no problem at all with a student being the principal author (in the sense of “being in charge of the writing”) of an academic paper. In fact, I think it's very good that you consider doing so. Here are, however, some thoughts on the matter:

Discuss this with your advisor before writing anything. Once both of you have established that there is sufficient matter for publication, and that you want to publish it, you should make plans for doing so. It includes determining (right now!) the authors list, the order of authors on the list, and plan who will do what.
The corresponding author (or corresponding authors), often indicated by an asterisk in the authors list and their contact details in a footnote, do not necessarily need to be the person(s) who actually did most of the writing. The contact author is the one who is the most central to the project, and who will be able to deal with correspondence about it in the near and not-so-near future. For that reason, some groups (including mine) do not consider students a good choice for corresponding author: in two years, they may be gone to a new job and not interested any more with the paper's research.

A few more comments for first time authors:

If you've never written a paper before, don't underestimate the task. Writing a paper from A to Z is a complex project, even for experienced authors. It requires using many different skills, and is truly an exercise in both scientific reasoning and communication, with very specific constraints (style, formatting, length limits, …). Assign a lot of time to writing, and don't hesitate to get help if you're stuck!
If in doubt while writing, put yourself in the reader's shoes. And specifically, a non-specialist reader's shoes. That should be the guiding principle.


Do universities mind study delay when reviewing your application?

Admissions committees care primarily about your grades and only to a very small degree do they care about how long it takes you to graduate. People have all sorts of reasons to not graduate in the fastest possible time -- most importantly having financial needs many students need to satisfy by working while being a student.

So no, there is really no need to worry about a semester more or less. Worry about your grades :-)


Can I trust web of science citation reports?

Web of Science citations are based on a smaller pool of documents.  For one, their collection includes mostly peer-reviewed journal stuff, to the exclusion of theses, preprints and other non-journal sources which can be included by Google.
Because it relies on final journal versions, WoS also excludes citations in intermediate versions that may have been published on arXiv or elsewhere but are removed in the final manuscript.  WoS citation counts can also lag actual counts by several weeks, if not months.
On balance, WoS citation counts are subject to less fluctuations than Google’s.  I prefer Google because of the breadth of the search, but I would not compare WoS and Google numbers.


how to congratulate for professors's grant achievements?

If you feel like congratulating your professor, go ahead and do it. He might appreciate it, or in the worst case he will ignore because he has too many emails in his inbox. But I cannot imagine a scenario where the professor would take such a congratulation email negatively.

As with most emails to busy people: keep the email short and to the point. Just one sentence like the one you wrote, though maybe using a more specific term than "your recent achievements":

  Congratulations on receiving Grant X[!]

where the use of the exclamation mark [!] depends on where you are and what you have seen your colleagues do in emails (and also on whether you want to use it of course).


Which country or countries inspired the post-communism Polish higher education system?

The higher-education system is inspired by Humboldt's model and  guided by standards for higher-education defined by the Bologna process, which was "signed by education ministers from 29 European countries in 1999" and has since been adopted by 48 countries.


Averaging exam scores with very different means/distributions

Follow what you defined previously. The 'average policy' needs to be done beforehand, so nobody can argue that you defined/changed it to specifically screw/help someone. If you didn't define it previously, the safer route is the arithmetic average, which is kinda standard (or something equivalent for your institution, if different).

More than that, IMHO, you are overthinking. Grades aren't a reward that you give, they are a measure of how much the student learnt the content. A professor of mine says that he doesn't give grades, the students earn it. If they performed badly, they performed badly. You have a duty to fail under performing students.


During review, I found a superior solution. What now?

I didn't get a clear impression of your opinion of the authors' work.  "Solving an important problem" ought to make for an excellent paper, but the rest of your description seems to partially negate that.  (In particular, I don't quite know what a "nonstandard input parameter" is, but it sounds a bit like they are cheating or that the legitimacy of their solution could be a matter of debate.)

Either way, it seems to follow from what you say that you feel that you have solved an important problem, indeed in a better way than the authors.  Unless you are such a known superstar in your field that this is a commonplace occurrence for you, I would think that you deserve to get more out of this than an anonymous thanks.  To me the options seem to be:

1) If the authors' paper is strong enough to be published, say so.  You should not hide your opinions about their shortcomings, but you don't have to include your new ideas in your referee report.  Then:

1a) If just by responding to your criticism (if they care to) the authors replicate your better solution, then it seems that you did not add critical value, and I would just recommend accepting their modified version and letting the matter end there.

But

1b) If your conscientious refereeing produces a version that is worth publishing but does not replicate your superior solution, then you should prepare your solution for publication.  The timing of this is something that you should ask for other opinions about.  It would be ideal if the authors had circulated their results in preprint form.  If not, you may need to delay submission until their paper actually appears.

2) If you think the paper is not publishable in its current form in the journal to which it was submitted but that it inspired you to solve the problem in a better way, this may be a case for you to ask permission to contact the authors and add your work to theirs.

3) If the work is really not valuable and your solution has little or nothing to do with theirs, then you could just recommend the paper for rejection and then submit your own solution elsewhere.  Examine your conscience carefully before doing this though: imagine that the authors found out exactly what you did.  Would they see it your way?


Are there particular areas of mathematical research that attract universities to consider someone over another?

There is some effect, certainly, but it is probably a poor strategy to depend too much on it. If you look at what the American Mathematical Society, for example, has published in the past three or so years you will get a sense of where the current action is. It won't include my old specialty, hard classical analysis, as the number of open problems there as decreased relative to those available in newer fields.
However, a given university will usually have a specific need when they put out an announcement. It might be a hot area or maybe not, since there is value in having a broad range of specialties on a faculty if it is possible. So, if I were 35 years younger, I might have a few openings available.
But there are two negatives that I can think of. First, things change. You are unlikely to be a serious contender for a faculty position for more than five years (I'm assuming you are asking about the US, actually). A lot can happen in a field in that time if those "essential to answer" questions actually get answered. The currently hot field may cool appreciably, to be replaced by the next big thing.
The other, and this is even more serious. It is hard to say where your mathematical insights will come. Mathematical insight is specific to a field (or even a small subfield), not general. You can have (as I did) tremendous insight into real analysis and almost none in abstract algebra (especially Ring Theory). I could solve the necessary problems in a course, but lacked the insight to push against the frontiers in algebra. You can seek insight and it may come, but it is an elusive thing. So, if you pick a hot field, a priori, just because it is flaming at the moment you may find the necessary insight impossible to attain while that area cools.
Rather, I suggest at your current level of development, that you seek a broad understanding of many mathematical areas and choose later, based on your insights and the then current evidence about the academic market, what you want to do. And the market is now very tight.
Finally, there is an old saying: You don't choose mathematics. Mathematics Chooses you.
But, I think the same can be said, almost as validly, for the various subfields within mathematics. I was "chosen" by classical real analysis.


Google scholar citation problem with arxiv

So apparently you have to wait. There is a delay between your arXiv submission and detection of its citations by Google scholar. But it will eventually happen.


What could be the negative factors in getting a PhD position in theoretical computer science?

I have been in your situation, my first instinct tells me that you need to look into some developing jobs that pays and are challenging. So here are my couple of points:

How Well Is Your Personal Life?: I did obtained PhD in Computer Science and worked both as a lecturer and developer; and let me tell you that the "soul sucking" thing, needs to be deal with as a personal life solution and not professional. I did seen both academics and developers to be out of touch in personal wellness, and lived a very dark and sad life; that is nothing to do with what they are doing professionally.

Age/Industry Isn't the Issue: While I was doing my PhD, a friend of mine who was 70 years old, built 2 software companies and sold them all, retired; and start doing PhD because feels like it. So, neither age or industry isn't a problem.

What sort of developer? Ok, this might look funny but actually it is important to know what sort of software developer job you are doing? Were you dealing with old legacy software that you needed to maintained so it made you frustrated; or you were doing Web front-end stuff, which is a combination of taste and coding and not too much "science". If you are into logic related stuff, have you ever tried back-end development jobs? This is something you need to think about.

Challenges As a Developer: You mentioned the developing jobs is not challenging. I was shocked! There are so many challenges today in industry, that people are trying to figure out. Look into cluster/distributed computing, containers, operating systems, wearable technologies and all their overall networking paradigms, and so on. You can also try to get some jobs which are challenging; so you could feel to void you are feeling, instead of spending the next year betting on being a lecturer. This brings me to the next point.

Lectureships: You might think, well I study couple of years as a PhD student and then Boom! I'm a lecturer in Germany or Europe. This is not true. Right now the trend in Europe is close to madness, to become a lecturer you should do some serious research, or coming from a huge research-based company (e.g., Google, etc.). Moreover, compare to industry, the payment is not very well; and the hours you have to put up with students, meetings, etc. are too much.


What are the health impacts of standing / sitting while lecturing?

The health impacts of standing while doing a job are known to be strongly positive, compared to sitting while performing a similar function. For the seminal paper on this, see Morris et al., 1953 in the Lancet (http://www.sciencedirect.com/science/article/pii/S0140673653914950). Morris examined the incidence of heart disease in bus drivers vs. bus conductors. The former spend the day sat at the wheel while the latter spend the day walking around the bus collecting fares and enforcing the rules. This occupation was chosen because drivers and conductors come from the same socio-economic conditions and were expected to be fairly similar in every respect except for their working activity. Naturally the incidence was sharply reduced in the conductors. A casual Google Scholar search will pick up more recent references, and the health benefits of standing vs. sitting are widespread.

One can imagine that standing for very long periods of time repeatedly might cause problems, particularly on the feet or ankles, but seven hours a day a few times a week is not really anything to be excited about. Many people work in bars or restaurants, on building sites, in hospitals and so on doing much more labour intensive work with shift lengths exceeding twelve hours, six days a week.

All I would say is ensure you wear comfortable shoes!


What is "call for nomination" for senior positions in university?

The potential candidates for this kind of high-level positions typically are people that already have a very busy job, and they do not actively search for jobs. It may be that the hiring process is more of the head hunting type rather than the advertisers passively waiting to get many applications and then filtering them. Of course, direct applications are allowed for the sake of openness and for not limiting unnecessarily the pool of candidates, but it may be the case that the ideal candidates would not apply uninvited. The search committee may not be aware of all the qualified people that might be interested of or suitable for the advertised position, so nominations are useful for them in order to bring new potential candidates to their attention. Once they spot a candidate, they may make them an attractive offer that is customized to the candidate. In the case that the nominator knows nominee from a distance, a direct hint by the nominator may not even attract the interest of the nominee to apply, while if the search committee finds the nominee interesting they may actively try to convince the nominee to apply through more elaborate methods than, e.g., a simple email that may not attract the attention of a very busy person.


Interview for postdoc position via Skype

There are no defined "rules" for what a Skype interview will look like. However, to give you some pointers:

  How long will it be?

You should ask the interviewer. I have had Skype interviews between 15 minutes and a little over one hour. If the interview would go significantly longer than that, I would assume you would have been told.

  Will it be a Q&A session? In that case, what type of questions are usually asked?

Presumably there would be Q&A, yes. Questions could be any kind of typical interview questions, i.e., they could relate to your research, your teaching, how you advise students, what grants you are interested in applying for, or anything else really.

  How to react if the position is offered directly and the applicant wants some more time to decide?

"I am very happy about that. However, I will need to get back to you within [X timeframe] as I need to discuss this decision first with my wife."

(no, no reasonable PI should expect an answer from you right now; even though they may indeed offer you the position immediately, you are under no pressure to accept immediately)


Difference between Thesis and Research paper?

An undergraduate thesis (or dissertation) is: a document submitted in support of candidature for an academic degree, which presents the author's findings.

By comparison, a research paper (when differentiated from undergraduate life) is: an academic work containing original research results or a review of existing results, which are typically published after a peer-review process successfully checks suitability.

For an undergraduate, I suspect an undergraduate thesis is easier, since I believe the bar for acceptance is generally lower than the bar for acceptance of peer-review.


Paid twice by university for "same" research: how to proceed?

If the university decides one of the payments was made in error, they will almost certainly demand it back, and if you don't repay it promptly, they'll likely take steps that you won't enjoy (e.g. withholding from your paycheck, suing you, firing you, etc; specifics will depend on their policies and local law).  So don't spend the extra money until the situation is clarified.  Keep it in your bank account.  If they're paper checks, don't cash or deposit them.

Contact your advisors in both departments and explain the situation.  If somehow you're entitled to both payments, you'll get explicit confirmation and then you'll know you can keep all the money.  If not, they can negotiate between themselves as to where the money should go, and they'll tell you how much to repay, to whom, and how.


How to correctly reference a supervisor who in the meantime got a doctorate

FYI: I did not reference the name of my supervisor advisor at all in my industry-targeting resume.  I do realize this may be different in CV-land.
I personally wouldn't use any honorifics in the CV.  (Next you'll be asking about assistant versus full professor!)  Just convey the information, the name.  I would opt for FI, LN.  I.e. Advisor: D. Linger.  Keep it tight, man.


What is the benefit of review a scientific paper as a referee?

As mentioned in the other answer, reviewing is an important service to the community.
However, you will also profit yourself from reviewing: You will learn about a new topic. You will learn about how a review process works. You get to see the other side, which will most likely helpful for your own future paper writing: Since you know how reviewing a paper feels from the perspective of the reviewer, you can better understand how to make a paper accessible to reviewers and readers, and how to best respond to reviewer comments.
And, in addition to these benefits, you can indeed list in your CV that you review for journal X, Y, and Z - this does not only show that you are willing to help the community (which will recflect positively on an application), but it also shows that the editors of the journal consider you competent to review their papers.


Formulating research interests — context/motivation or not?

Don't even use bullets; just provide a list of keywords/phrases identifying your subfield.  At least in the US, departments ask for a separate research statement in addition to your CV.  That's the place to explain your research interests in detail and give them context; there's no need to do that in your CV, too.

For example, when I applied for faculty positions, my CV included the following lines between my contact information and my education history.

  Research Interests

  Algorithms, data structures, and lower bounds; computational and discrete geometry; computer graphics

I've served on the faculty recruiting committee in my (top-10 US computer science) department for several years; this approach seems both standard and effective.  Personally, when I read a CV, I only spend a second or two on the self-declared research interests and jump straight to the publication list.

(Posdef's answer suggests giving more context in your cover letter, but I think this is pointless.  I don't know anyone who has ever read a cover letter.)


Would taking up an associate's degree after finishing your bachelor's harm your resume?

Having multiple degrees would by no means harm your resume. Listing a degree that has absolutely no relation to the job you are applying for may. The answer to this question depends on what you are trying to accomplish, whether it be to have another line item on your resume or to actually obtain a degree related to the field in which you entering. It never hurts to learn more. The only thing you may lose

http://careersteering.com/executiveresume/education-on-resume/
http://www.genpink.com/10-things-to-quit-putting-on-your-resume/


How should a thesis be structured in this situation?

Ok I did this before. This is actually quite simple and straightforward, so without sugar coating it, you should have three main parts:

Introduction and Conclusion: The reader should be able to go only through your introduction and conclusion chapters, and see what is going on. I'm hoping you know what chapter numbers they are by now!
Background and Related Work: After introduction you should have a solid background and related work chapter(s). Don't introduce something that you don't use and don't hide some background read here.

Ok ok, the last two parts you didn't ask for but I wrote it to be a complete reference for others. Ok now to your questions:

'I'm a qualified PhD' chapters!: Now two to four chapters should be explicitly cover your own work. So:

3.1 Separate theory from practice: I don't want to see some theory stuff and then suddenly a pipeline to a compiler. It has many advantages in terms of defending it and then correcting it later on if necessary. Also the examiners will see that you are well rounded computer scientist; therefore you know your practice as well as theory and vice versa. So basically, you don't want to have an impression on examiners that you just injected theory/practice because you are weak in practice/theory.

3.2 Unify Your approaches: Can you find a common ground between all the techniques you used? For example, you could have a chapter on code generation techniques, and then group all your work into one chapter. The pitfall here is to repeat the same approach over and over for different models.

3.3 Solid Evaluation: You need a solid evaluation, now that you used different techniques try to honestly evaluate them. Also, more importantly try to write a comparison between all of the techniques used and highlight each individual positive and/or negative outcomes.

3.4 Appendices: Moreover don't just drop boilerplate code in your own chapters, try to use number of appendix for different parts of your code.


Grad school - Is transferring to another school for a Master's program (Computer Science) a good option?

I think you should stay where you are. My thoughts below.

Research. At the beginning, the classes seem hugely important and there is a lot of angst about whether you are at the "right" grad school. By the end, the only thing that matters is your research.

You write:

  Fortunately, I am working with one of the best profs the university has to offer on a very impactful project and the research is going great. But that's the only plus point I see from sticking around.

This may be the "only plus point", but it's the crucial one. If you're doing good research, learning something, and publishing good papers in good journals, then your PhD is going very well.

Rankings.
I think you would have a legitimate concern if you were at a predatory grad school that no one had ever heard of. But you say your school is ranked ~50, so presumably it's a "real" school that people have heard of. Going to a "slightly" better school will make ~no difference to a hiring committee. Going to a famous, top-10 school might make a difference, but even that is maybe less than you imagine.

Other students. I would point out that it's not necessarily that the other students are dumb; it's that they haven't covered this material before. But even if they are dumb, that just makes it easier for you to get the resources you need. One of the best talks I ever attended was from Karen Kelsky, who made the point that hire-able grad students are able to "pass" as a professor -- in the way they dress, the way they interact with colleagues, and the work they do -- so the other students are really irrelevant here, your "colleagues" are the faculty.

Time. I would also consider that transferring schools is a lot of work and, if you start from scratch, it will mean wasting a year of your life while you repeat "year-1" of grad school. Grad school is worth taking your time and doing well, but I would also seriously hesitate to lose an entire year -- you only get so many years in the workforce, so an extra year in grad school means one fewer year in the meaningful, interesting job you'll eventually find.

That said, I admit that getting a degree from MIT or Harvard would be exciting. If there's a way to apply to such schools without burning bridges, it might be worth sending in an application "on a lark". If you get in and have an advisor lined up, then I might even consider switching. But I would remain fully committed to your program until then -- it seems like things are going fine, and there are definite downsides to transferring even to a top school. Good luck!


Publisher has changed many terms in section/subsection titles to acronyms

You should not assume that all changes introduced by the typesetters are the result of enforcing some house style. You should also not assume that these people are particularly competent. If they modify your text in some nonsensical way, you have two choices:

Page 7, line 15: Replace "Estimating the CPTs of a BN" by "Estimating the Conditional Probability Tables of a Bayesian Network".

Page 7, line 15: Please replace "Estimating the CPTs of a BN" by "Estimating the Conditional Probability Tables of a Bayesian Network".

Personally, I'd choose the first variant. This is not a request, this is an order. If they don't comply, escalate to their supervisor.


Technical editor changed author order of the paper

Is this a field where author order is assumed to matter (e.g., applied CS)? If yes, this is completely unacceptable. If no, it is still very strange, but maybe not a big deal in the end. I can only imagine that your paper was handled by a very inexperienced technical editor who is simply not aware that the order of authors is not just a stylistic question, but actually has CV implications (in some cases, at least).

One way or another, you should get in touch with the organizers of the conference (e.g., the publication chair if they have one, the general chair if not) and let them know. Maybe it is still possible to fix this, but at least the responsible people should be aware of this issue.


Letters of Recommendation for economics grad school for non-economics majors?

Most committees are happy to see letters from mathematicians, although they might like at least one from an economist (and you probably should have at least one upper division course in economics if possible).

Just be careful. One eminent mathematician once wrote "X is not smart enough to be a mathematician, so I suggested he study economics." I don't think we admitted him.


How to go about obtaining large amounts of obscure data?

I do not think that there is a general strategy to obtain obscure data other than:

Think about who might have such data (legally and ethically).
See whether they provide this data for free.
Ask them.

You may have luck in crowdsourcing steps 1 and 2 of this process on Open Data Stackexchange, half of whose questions are data requests. However, given the nature of your specific enquiry, I doubt that you will be successful there, as such data is very unlikely to be open.


The aim of the document is to have a verifiable version of your citation count, which is commonly used for filtering out some applicants in an application process. It should provide a list of your papers together with their citation counts, and it needs to back this up by data (such that it is verifiable). This means listing for each of your papers which other paper cites it.

There seems to be only one reasonable way to structure such a document, to  first list all of your papers with the citation counts, and to then use seperate sections for each of your papers with the biliography entries for the papers citing your paper. In this way, you give the information that is mainly useful for verifying your citation count later in the document, while giving the important information first.

I doubt that there is any "official" information on how to format such a document. After all, scientists know that citation counts are a bad way to evaluate a researcher's output. So there is no urge to stress the importance of these documents by providing additional formatting requirements.


I submitted the correct personal statement to the correct schools, but I realized I left highlights in my submission what should I do?

what should I do?

No action is necessary.


Proper way of referencing ranges of chapters

According to Wiktionary and a number of other sites, "chs." seems to be the appropriate pluralization of the "ch." abbreviation for chapters.  Note, however, that either is likely to be quite intelligible to a reader, and if the typesetters disagree with your choice, they'll surely fix it to their preferred style.  In short: just use "chs." and don't worry about it.


What is the exact meaning of a "Prof. Dr. med. Dr. med. dent. Dr. med. habil."?

The usual doctoral degrees in medicine and dentistry in the U.S. are not Ph.D.'s but M.D. and D.D.S. (for "medical doctor" and "doctor of dental surgery" or some Latin variant of those). So I'd use those to translate Dr. med. Dr. med. dent.

As for habilitation, I don't know exactly what it involves in medicine, but in mathematics it indicates research accomplishment after the doctoral degree. In many cases, it involves a second thesis ("Habilitationsschrift" in German), but it can also be just a collection of published papers.  I imagine medicine is similar, but I have no real knowledge of that.


Are gap semesters frowned upon in graduate school applications? Should I explain mental health situation that led to the gap?

I'm going to give a slightly different advice from the previous answers.  I don't want to counsel dishonesty here, but I think it would be very unwise to write anything in your personal statement that suggests any mental health problems, especially if the only thing that needs explaining is taking a semester off.

I want to emphasize that I think the stigma around mental health problems is very unfair and based on ignorance.  However, the people reading these applications will have probably internalized it to some degree: if you, for example, mention attempting to commit suicide, that will be the most vivid and memorable thing from your application, whereas your master's degree ending a semester early will be barely noticeable.  I think you will probably be fine not mentioning it at all, but if you do, I would just say it is for health reasons, or to prepare for moving to another country (which are, of course, true).  One of the primary things an admissions committee will have in mind is whether a student is capable of finishing the program, while not creating a lot of trouble for people in the department. They have had pain-in-the-butt students before, and would really prefer to avoid having any more.  Mentioning "personal and social challenges" or "excruciating circumstances" (which, incidentally, sounds very strange in English; it's hard to imagine what you really mean by it) is not going to give them confidence that you won't make a lot of trouble for them.


How do I refuse to work on military-focused contracts?

This answer is for the US, based on my experience with US admissions.

I would say that this is generally not an applications/admissions question, only because it's unlikely to be meaningful to admissions committees. Many graduate departments in computer science work on a cohort-admissions model, where a group of students are admitted each year and then are expected to find a faculty adviser once accepted. In this model it is up to you to find a research program that personally motivates you and then to persuade an adviser to take you on. It is at this stage that you would (and should) make it clear to a potential adviser that you're not willing to work on defense related projects. However, at this point it's probably moot because you're going to be talking to potential advisers based on your perceived compatibility.

What might be a better thing to do during the application process is to ask whether a candidate department conducts any defense related research. Then you can just not apply to defense-related organizations rather than make it a point of contention with programs that you're interested in. Additionally, most CS research is not defense related, and most all broad-based research departments will have plenty of research opportunities that are not defense projects. Consider that about 60% of US PhD students in Computer Science are foreign nationals and ineligible for this kind of work anyway. You will have no problem finding non-military projects to work on.

Some places are well-known as defense-related institutions- for example the MIT Lincoln Laboratory, the Naval Research Laboratory, or the Johns Hopkins Applied Physics Laboratory. It is usually obvious from these organization's websites that this is a focus of theirs, and you can just avoid them. However, if you wanted to apply to a place such as this I would definitely discuss your personal ethics eariler rather than later, and your ethics definitely don't disqualify you. These labs do a lot of research that is "defense-related" in the sense that it provides for the common defense of the country, not because it's a military project. They work on everything from actual weapons systems to civil defense projects like weather satellites, making the energy grid more robust, and information security.


Should I use what the professor says to me in the email as a material to write in the SOP?

Yes, you should delete that. It doesn't add value. You should mention that you were accepted and what you plan to do, but there is no need to include the following smalltalk. Getting the Prof to say "You would be a terrific addition to our group!" is politeness not an achievement in itself. An achievement would be if he said that after you worked there for a month.

Also, I don't think that is the only thing that makes you stand out. The Prof surely has reasons why he accepted you, he doesn't accept at random. Maybe you could ask him what led to that decision.

How is the following:

Professor X wholeheartedly accepted me to work on the relation between
A and B, which will help to formulate C theory. I very much look forward
to work on this topic because ...


How to conduct an effective regular group meeting?

You have a lot of questions interspersed within your question, but it sounds like the main issue is

  the research area of the group is very diverse, every time I just listen on something I cannot understand and have totally no interest on it, and I believe other members think the same way as I do when I am presenting.

I have had the same problem in the past.  I'm a professor who works in a variety of related subfields, some very theoretical and some fairly applied.  Most of my students and postdocs have been focused exclusively on either something theoretical or something applied, and their backgrounds range from computer science to mathematics to electrical engineering, so there is often a disconnect when they try to communicate what they are doing.  Here is my advice.

For students:

Try to broaden your focus and interests.  It is natural that you have a very narrow research focus as a grad student, but if you want to get and keep a job afterward you'll almost certainly need to broaden your focus.  I find that in general the best researchers almost always have broad interests (though they are able to focus their energy narrowly when needed).  Group meetings are an opportunity to become acquainted with topics that are on the horizon of your current knowledge.
Use group meetings as an opportunity to improve your communication skills.  Teaching non-experts about your work is a critical skill in any research career.  Other students in the group do not know nearly as much as you about your research topic, but that doesn't mean that you cannot make it interesting and accessible to them.  Often this means leaving out the "details" and explaining just the essence of a problem.  Trust me, some day soon you will need to make your work interesting and intelligible to people who are much further removed from your specialty.

For advisors:

Help students to present their work in a way that the others can understand.  Often this means prompting the student, especially at the beginning of a presentation, to add important assumptions, motivation, or background.  The student has started to take these things for granted, but without them any non-expert is quickly lost.
Don't let the conversation drift too far into a very specialized discussion.  If you and the student are the only ones who have any idea of what is being discussed, it's probably time to say "let's discuss this further after the meeting".
Use meetings for skills development.  This was already mentioned in this related answer.  Instead of focusing exclusively on research, group meetings can also include discussions of things like:

How to write papers
How to read papers
How to search the literature
How to manage a bibliography
How to give good presentations
How to write a proposal
How to keep a lab notebook
How to keep up with newly published research
How to stay organized and be productive
How to referee a paper
Software tools for all of the above, and for research

These topics are useful and interesting to anyone involved in research.

Answers to other parts of the question

I hold group meetings once a week, and they last 1-2 hours
Students are strongly encouraged to question and comment on each other's work
We meet at lunch time, and there is food.  That doesn't sound important, but I think it is.
I try to save very detailed comments for my one-on-one meetings with students.  Otherwise, the group meeting can devolve into a conversation between the advisor and just one student.


Strong is subjective and likely to mean one of two things, either thought provoking or emotionally moving (and possibly both). In general a closing paragraph should not only summarize what has been said before, but synthesize a new statement (or direction of inquiry) from the supporting statements. In academic papers, one leans more towards logic and less towards emotion, however in a proposal like this, you want to get your reader excited about your idea.

You want to stand out for the work you plan to do. Use language that is not 'soft', be confident and point towards facts. Show how your ideas will lead to increased knowledge or productivity and do not make it about you.

Use your conclusion to state how your idea builds on what you have done, what others of done and what positive advances it might lead to if the work is done. Then you might state how this has inspired you to pursue this field.


At which point in your PhD should you feel like you're in the edge of human knowledge/ know exactly what is your contribution?

You may never "feel" it. But you might be there. You might "feel" it always, but not be even close. Results will tell you that you were there. Especially if others (reviewers) find your results and methods to be "interesting".

Human knowledge is sometimes viewed as a vast sphere with researchers chipping away at the "edge of the known" to make advances and push out the boundaries. That is probably more or less accurate. But imagine, instead, that human knowledge is fractal instead. With the boundary everywhere about us. The edge isn't smooth. You can be at the edge no matter where you are.

But you have to be able to look beyond the edge, into the unknown. You have to be able to formulate questions about the unknown for which you don't have the answer. In some fields (math, physics) there may not even be an answer to some questions. But to be "at the edge" you need to also have ideas about how to go about answering those questions or showing that the answers are impossible.

Note, for example, that few would question whether Einstein was at the edge. But note also that he was very tentative about some things. And he backtracked a few times. He posed big questions, interesting questions. He sought ways to answer them. He proposed ways to answer them that were beyond the state of knowledge and technology at the time.

But if you want to get a good sense of whether you are there or not get feedback on your ideas. Two good ways are to submit papers and get reviewer feedback and to form a circle of collaborators with whom you can propose questions and evaluate them. In most fields, unless they are very new, it isn't possible to know everything about the field. In mathematics that was last possible about a hundred years ago. But a collaborative group will have a better overall grasp of what is known and what is not and what is an "interesting" direction in which to push.

But the unknown is unknown. At least until you make part of it known.

Personal note: I guess I learned I was there in about the fifth year of a graduate program. But only in a couple of very narrow (fractal, again) areas.


Why "ETH" in degrees awarded by ETH Zurich?

This seems to be historical. ETH is a university. Switzerland also has institutes formerly called Höhere Technische Lehranstalten (HTL), which are now called Fachhochschule.

The preconditions to enter the ETH and a Fachhochschule differ significantly. Finishing a degree at ETH used to take significantly longer, and the curriculum at ETH involved far more advanced mathematics.

Formerly the titles attained at a Fachhochschule was Dipl. Ing., Dipl. Ing HTL or Dipl. Ing. FH and the title you got at ETH was Dipl. Ing. ETH. As you guessed correctly, Dipl. Ing. ETH was a clearly superior different and more extensive education. The title from a Fachhochschule was roughly equivalent with a BSc while the title from ETH was comparable to a MSc from a competitive international university. This changed only recently, with the introduction of Bachelor and Master degrees in Switzerland a few years after the year 2000.

Nowadays graduates of a Fachhochschule usually get the title BSc, and graduates of ETH usually get MSc degrees, and have the option to cut their studies short and end them with a BSc degree, although last I heard it was still very unusual to do so.


Is it advisable to talk about "learning things I don't know in the field" as one of the plans for future in statement of intent?

Although I don't want to say what you should or should not write, this is my suggestion.

There is a difference between a Masters by Coursework and Masters by Research, as in the latter you most likely will be asked to provide a new contribution to science, while for the former you will most likely 'simply' extend your knowledge through subjects.

Knowing it's an application for Masters by Research, I suggest reading up on the research you're interested in, mention why you're interested in it and how you can contribute to that field. I think the reviewers are more interested in your enthusiasm and how you can contribute.

Mentioning that you're willing to take credits is a sign that you're afraid of not knowing enough, and could be a sign for reviewers that you're not confident. On the other hand, it does show that you know your limitations - but when you decide to mention it, don't make it the main item of your letter.

In the research field however the learning does not always happen through subjects, it most often occurs through literature review. Although subjects are very beneficial if exactly in the area of research, I think that it's sufficient to demonstrate that you are capable of working in the field of study.


Do researchers from some universities not attend top CS conferences anymore because of conflicting open access requirements?

No. The conferences acquiesce to the university policy.

The way it works is that, when the publication agreement is signed, an open access addendum is attached and next to their signature the author writes “my agreement is subject to the attached addendum”. At least that was my experience when coauthoring with Harvard faculty.


What to do when manuscript is in latex but journal requires submission in MS Word

I've used pandoc for this problem previously and it worked pretty well. Problems I have encountered are;

Multi-line equations (e.g. align or matrix environments) are not converted correctly to word. (I don't think there is an equivalent of align in word).
Converted all citations to the ones within parentheses (much more minor a fix).

Last publication I did this because I got so frustrated with the journal (it would accept and compile my Latex file, but gave no instructions about what packages I could use nor any instructions on how to get the bibliography to compile - and emailing for three weeks with the staff did not help). But it only took me a few hours to convert the paper (that publication had minimal math though).


Software for extracting data from a graph without having to click on every single point?

Here is a very good online tool: http://arohatgi.info/WebPlotDigitizer/app/


Career advice: Post-doc away from my primary interest, or not

The most important thing is to evaluate if you will be able to keep a steady output of papers during this post-doc, if you can't hit the ground running than you will lose time to get comfortable with new material, two years go by very quickly. Also you should consider if in your country a post-doc in a different place is valuable experience to get tenure. You are the only one that can decide.


I'm admitted to a PhD program in mathematics, but only achieved a pass (no distinction) in masters. Will this affect my reputation in the PhD program?

I am a former 'pass' Part III student. I am going to be blunt here, as I feel emotionally attached to your case and I know why you may feel frustrated (it may be due to the typical atmosphere that part III students are supplied). Part III is just a course that people want to show-off in their CVs (only one final exam at the end of the year, busy professors, for no particular reason unhealthily competitive students). Nobody has ever asked me what my grades were in Part III. Never. I am a Ph.D., did postdocs and am finalizing a good academic job.

All that matters is your hard work in your research. Forget about the scores in Part III. If research is what you want to do in the coming years, just do it without thinking about part III results. You may end up proving that the Part III degree doesn't make any difference in anyone's life for better or worse!


How to format a citation in the abstract

I was not able to find any mention of references in the abstracts in APA, MLA, Chicago, ASA (both statistics and sociology). There is no indication of if they are allowed and if so, if new formatting is required. I have found a few style guides that do describe references in the abstract.

APS style says:

  References cited in the abstract must also be found in the Reference List, where the complete information for the reference is provided. However, in the abstract, these references are not cited by their reference number alone. Instead, the following form of citation is used: the entire author list with initials (in roman); the journal name (in italics); and the volume, page numbers, and year (in roman). The article title is omitted for the sake of brevity.

which is pretty thin in regards to a citation style

IEEE style says:

  Numbered reference citations are not allowed.

which might imply full text citations are allowed like APS, but it goes on to say

  The abstract must be self-contained, without abbreviations, footnotes, or references. It should be a microcosm of the full article.

AMS style seems to be the most complete:

  The abstract needs to be edited to
  remove
  or
  rewrite
  reference citations.
  Rewrite reference citations by placing the following information within
  brackets at the callout point. For journal article references, insert (in
  all lightface roman text) the journal abbreviation, volume, year, and
  page numbers, but not the article title. For book references, insert the
  title, publisher, location of publisher, and year. Only
  book titles
  appear
  in italics

it then gives three examples (article, book, and what looks like a book chapter).


Yes you can leverage.  At my university, these people work in the EECS department.  You could just apply to be a graduate student.
Study vector calculus and linear algebra.
Not really.  However, "big data" is quite popular in astro/astrophysics currently, so maybe you could get hired as a programmer.


What stops an assistant/associate professor with a strong publication record from being promoted?

Remember, a promotion/tenure review package is just that: a package. While you are correct that a record of strong publications is the driving factor, there are still a number of items in the package that could lead to a tenure/promotion denial:

Weak letters of recommendation. You need to get your name out in more ways than just cranking out a lot of papers. This includes presenting talks at other institutions, sitting on program committees, and making sure that prominent people outside your institution write you good letters for your package.
Lots of publications ≠ good publications. You need to be published in reputable, peer-reviewed publications. Some of those professors may list a ton of publications that aren't particularly notable.
Poor record of graduate student supervision. A professor who never has any students, or who hasn't graduated a student in years isn't going to be competitive for promotion.
Poor fundraising. If you're not applying for and getting grants (in many fields), you aren't going to be able to sustain a good research lab. It's tough to keep publishing relevant work without money coming in, although over time you can still build up a fair number of publications (many of which may be mediocre).
Poor teaching record. At some institutions, good teaching is more than just something the admissions office declares in all of its trifolds. If you've had consistently poor teaching evaluations, or if students have complained multiple times to the Dean or department chair, this could hurt your chance at promotion.
Personality. Your department has to make a recommendation to the tenure/promotion committee, and if you're genuinely not liked around your department, they aren't likely to make that recommendation, regardless of how strong your publications are (within reason).

Bottom line: publications are a part of the larger promotion picture in academia.


In general, how in-depth do graduate schools analyze the difficulty of the classes you take?

When it comes to linear algebra, there are two basic types of course, proof-based and more cookbook, that just goes through the procedures, manipulating matrices, finding eigenvalues, and so on.  (As you described in your question.)  I can't say whether a graduate admissions committee would care which you took, because:

It depends on what field you are applying for.  For example, if you are pre-med, no one will care if you can write a proof.
It depends on the approach of the university you are applying to.

However, I can answer a similar, related question:

How do colleges and universities evaluate the two types of linear algebra classes when making transfer credit decisions?

In this case, there is a clear distinction between the two.  If you took your linear algebra at College A, the institution you are transferring into, call it College B, will look at A's course description carefully.  If the course you took at A was primarily procedural, you won't get credit for B's proof-based course.  And if they don't have a procedural version, it will just come in as an unspecified elective.

Please feel free to specify your field and a particular university you wish to apply to.  No guarantees, but that might help you get a more useful answer.

Editorial notes (feel free to ignore): if you're interested in doing research in STEM, unless the proof-based course is very badly taught, you'd get much more out of taking that one -- even if you don't end up with an A.  Proofs are like green leafy vegetables -- they're good for you!  On the other hand, there are no prizes given out for completing a Bachelor's degree in record time.  Linear algebra with proofs is an important foundational course and deserves to be savored.


Is it reasonable to mention being shortlisted for a prize in CV?

It is fine to list your presence on the shortlist, since that list was published by the awarding group. I would say otherwise if there was no clearly public record and the finalists were merely privately notified.

But the group itself has seen to honor a few candidates separately from all nominees and you can make a note of that.

Not essential, but reinforcing, is the fact that the three "finalists" are asked to present a special lecture at the conference. Congratulations.


How to greet the audience at the beginning of a PhD defense talk/presentation?

I would like to second both xLeitix and Koldito's comments and convert them into an answer:

In most cases, there is no requirement, and you can just say, "Good [morning/afternoon], my name is [name], and welcome to my thesis defense."
A very few institutions have a much more formal set of requirements.  For example, when I was an examiner for a defense at TU Delft, I had to learn a few words of Dutch in order to ask my questions with the required formality.  Also, I had to come a day early to get fitted for a special archaic form of suit. Don't worry about this, though: if this is the case for your institution, then somebody will make sure that you are instructed in what to do.