Which one is more beneficial, working independently or collaborating with other researchers?

I'm trying to coin a phrase: interior point maximum.  Well, the phrase already exists: it means that the function you are trying to maximize which is defined on some closed, bounded interval [a,b] does not have its maximum value at either a or b but rather at some point c somewhere strictly in between.

Most functions one studies in calculus have interior point maxima, though there are obvious exceptions: especially if the function is increasing its maximum is at b, and if it is decreasing its maximum is at a.  Perhaps this is because the methods of calculus only speak to interior point maxima: the basic observation is that if the function is differentiable, an interior maximum must occur at a stationary point, i.e., for which the instantaneous rate of change is zero.  (Famously, the converse is not true.)

What's the point of this math lesson?  It's this: when we step outside of math class we tend to completely forget about this phenomenon and try to stare off into space and figure out which of the two extreme points, a and b, is better.  But in many real-world situations it is actually pretty obvious that the maximum must be at an interior point.

To me at least, the current question is a case of this.

If you never collaborate, then you never benefit from anyone else's expertise.  In research we almost never do exactly what we want: rather we collect various pieces of what we want to do, and then have to make hard choices about how and when to combine those pieces into published work.  If you can find someone else whose pieces are complementary to your pieces, then you both benefit tremendously form collaboration, because academia (justly) rates complete solutions more than twice as highly as half solutions.  This is, to me, the best argument for collaboration, and it already shows that "no collaboration" is not going to be your optimal choice.

Another argument for collaboration, not nearly as good, is that it allows you to increase your multiplicity: in a given year, maybe you can write one paper all by yourself, or maybe you can write one fourth of four papers and put your name on all of them.  In some academic cultures, depending upon how you play it, you will get more credit with the second option.  However, there is no inherent advantage to this -- in other words, there is no added value to those outside your circle of collaborators -- so this is really rather specious.  (But it works, to a certain extent...unfortunately.)

Another legitimate benefit of collaboration is that your collaborators get to know you and know your skills.  I have several collaborators that don't write as many papers as I do and are perhaps not as high-profile in the community as I am.  I wouldn't have thought they were anything special if I hadn't worked with them -- worked with them because they brought to the table key pieces that I could use to advance my work.  Whenever anyone asks me about these people, I say how great they are.

If you always collaborate, then people begin to wonder whether you can in fact write a paper / complete an experiment / do one unit of substantial academic work by yourself.  If you always collaborate with the same people, and especially if they are more senior than you and/or have other papers without you, then a lot of hard-nosed academics [including me] are going to suspect that you are not the brains of the operation and eventually wonder whether you may not have been gifted coauthorship.  The details of this must be entirely field dependent, but I am in a field in which senior people usually don't get added as coauthors unless their intellectual contribution was decisive [in many cases, this means most decisive], so if I see someone with a sequence of strong papers all of which are joint with their eminent thesis advisor and no others, then I really need to hear their thesis advisor describe specifically and cogently the value added by their student.  (In some fields collaboration is not an option, it's a reality.  But this seems to nullify the question: if a = b, you can maximize the function.)

So it seems clear that it's an interior point maximum: it will be best for your research if you collaborate x% of the time for some 0 < x < 100.  As with all interior maxima, one way to figure out x is: take a rough guess as to what you think a good value of x would be, and then explore the nearby space.  Definitely do at least one collaborative work and at least one solo work and then evaluate how they went.  At the risk of ruining my meme, I will say though that in this case the amount of collaboration is less important -- if you make it safely between 0 and 100% -- than the type of collaboration.  As above, you want to choose collaborations that qualitatively augment your work.  You do not want to "trade papers" or get involved in projects just to have your name on one more paper.  Definitely make sure that you are bringing something to the table whenever you collaborate: you really don't want people wondering whether you've added anything of value.


How to find double blind peer review journals in physics?

Why is "double blind" your principal concern?

There are many sites that will list major journals by discipline and sub-discipline.

Here is a listing of Physics journals with bibliometric data http://www.scimagojr.com/journalrank.php?area=3100

Once you've found relevant journals, just read the journal website to find out how they do peer review.

However, normally the "double-blind" aspect would be a minor consideration relative to other criteria for choosing a journal, such as impact, relevance of manuscript to journal, and quality. In other cases, you may be able to request double blind review if you are particularly concerned about that aspect.


How to find h-index in microsoft academic?

The h-index was removed from Microsoft Academic Search in January 2013, according to the features update list (which, not surprisingly, is the first Google result for “h-index Microsoft Academic Search”).


How to cite that something is *not* on Wikipedia

I don't think one needs a citation for the fact that no citation exists. If you're identifying a gap in the regular literature, you can say something like 'to the authors' knowledge, no study of this kind has been published' or words to that effect and you don't need a citation to confirm that you are identifying a gap in the literature.

I find it highly unlikely that you would be criticised for wording along the lines of 'at the time of writing (possibly give date), no article exists on this topic at Wikipedia' and then maybe give a general citation for Wikipedia as a whole. As Wikipedia time stamps every edit to every article, this is something that could very easily be verified at any time in the future. I'm not sure having a Wikipedia page or not is the best measure of obscurity, but that's a different question entirely.


The answer to this question is extremely simple and clear-cut. No, you are not being unreasonable. You don’t want to appear on YouTube, so don’t - this is not a job requirement for a professor (or for a graduate student) anywhere. You don’t owe anyone any explanations. Do not let yourself be guilt-tripped or manipulated into giving up more of your privacy than you feel comfortable doing. And do not get drawn into a debate about the nuances of precisely which careers require agreeing to be a public figure and which don’t - this just opens the door for other people to try to manipulate you with irrelevant sophistry.

Just say no.


How do professors get positions in multiple departments?

So I would love one day to be able to be a professor in say stats/CS department.

I don’t think you can really plan for this, other than by acquiring the skills and reputation that would make you an attractive hire for people in both disciplines. If the time comes and you see a position of this sort listed, go ahead and apply of course, but this is quite a rare event. Alternatively, once you secure a position in one department (already a hard enough thing to do in most people’s estimation), you can bring up the possibility of a joint appointment, either when you are offered the position or at any future time after you are hired, and see if the people involved are open to that idea. If you are very sought after and have multiple job offers on the table, that will give you useful negotiating leverage and increase your chances, but still be prepared for the answer to be “no”, or “not right now” - university politics is such that joint hires are not easy to arrange, and not always favored by all parties who need to sign off on them.

Finally, keep in mind that even if you can make it happen, it’s not necessarily the dream job you are thinking it is. As a joint member of two departments you will be paying a rather large (in my observation) “tax” of doing lots of things twice - getting to know and be on friendly terms with two large sets of colleagues; going to faculty meeting of two departments; being evaluated for promotion by two groups of people, each of which speaks a unique scientific dialect you’ll need to speak to convince them the work you are doing is good (and who will often look down on, or misunderstand, anything that you’re working on having to do with the other discipline); having two offices in two buildings that are halfway across campus from each other and needing to keep track of which one of them you left that textbook in that you really need right now; etc. - generally speaking there are a good number of inefficiencies of this sort. I’m not saying it has to be bad, and I’m sure there can be nice things about it, just be aware of these and other complications that you may not be taking into account. Good luck!


Should I take delay " a few days" as a polite decline or literal?

Of course it’s impossible to be sure, but if the professor didn’t intend to do anything about your paper, I consider it likely that he would not have answered at all or that he would have answered that he lacks time. The latter would have been the polite decline – there is nothing polite about saying that you will do something without ever intending to do it.

What is uncertain is whether and when the professor actually does as he intended. Many professors are notoriously busy and underestimating when they will find time to do something. Moreover, they may be disorganised and just forget about it. Depending on how urgent and important this paper is to you and whether you delay anything waiting on the professor’s response, I suggest to write a polite and short e-mail stating when you would need the response and that you understand if he would reply that he is not able to respond to your request up to that point.


Should I quit if I'm having problems with the Marie Curie industry partner?

I would not quit a MCS fellowship. Either you solve the problem with the industry partner, maybe by collaborating with another person or unit (if possible), or try to minimize as much as possible their importance in your project. Usually secondments are a nice addition but a MCS project should stand on its own even without the secondment.

You could also try to reach out to someone in the Horizon2020 and see if they have a person that can help with this kind of problem. In the meantime I would also gather some proofs that you can use to build your case. In the worst case you will have to justify to H2020/EU why the secondment was not useful/successful.

PS: how to improve the working relationship with industry partner seems more a question for another Stack.


Is it advisable to underline some key points in a statement of purpose?

No.  Never underline anything.  Underlining is left over from typewriters.  It instructs the typesetter to put things in italics.  Nowadays, you should put things in italics yourself.


What to do with threats of blacklisting?

You went to the administrative person. That was your error and the core issue.

Allow me to give an example from the other side in which this happened:

While I was at another institute, I was asked to take over a lab for another person. The lab hosted a guest cohort from another country so the university needed someone with content knowledge and dual language fluency on short notice. So I was asked if I could take over the lab for a week.

Suffice to say, I did not know that there were particular rules for this lab. Some were obvious (like not leaving equipment plugged in) but I was a little overwhelmed with taking over a course last minute. Further, my work is primarily computational rather than lab focused so the reflex nature of lab rules was not there for me.

After a few nights, the lab manager came in and saw the lab after I had left it. Equipment was left out and plugged in. All a very big mistake on my part. The way she responded was where things got messy.

In hindsight, a more measured response would have been talking to me or even the lab's PI to find out what was going; even going to the department head. Instead she went to the Dean. She did not know the situation with the lab and the dean didnt, but as soon as it went to the dean, the situation became "administrative". Funds were threatened and it ended with me having to write a formal apology to the department head and the lab manager with everyone CCed on the email.  Everyone was aware the situation and most parties were mainly pleased that I was willing to write the apology so the "administrative" side of the situation could go away and we could fix things in house. (I ended up just getting an assistant who was a little more lab savvy). The department head came by and gave me a sympathetic pat on the back.

Was I wrong, certainly. But it was likely an issue that could have been dealt with "in house".

So, what was the end result of going to the administration rather than keeping things in house?  At one end, awkward elevator rides when the lab manager and I crossed paths. She found out the situation, and to find out, she didnt even know I was in the lab. I heard she thought it was an undergraduate group. On the other end, it did leave some lasting trust issues and undermined what had been before a very good working relationship between two labs. But I think that things have smoothed out since that happened.

In other words, once you go to the administration, the situation becomes administrative.


How to handle lecturer who doesn't let me use my phone?

this may sound immature

And it is.

You're acting as if you have the right to do what you want.  You don't!

It's a teaching session in a building owned and run by other people and they set the rules and delegate the authority.

You have two legitimate choices (1) obey the rules and the authority or (2) leave.

If you want to protest the rule, contact your student union (a legitimate channel for complaints).  You can pass your opinion along that way.  However the decision still rests with the people in authority, and ultimately you will have to accept that fact.

Note also that the people making that decision are both experienced teachers and students themselves.  You are not.  Respect their experience.

There's one more important reason:

You are there to learn.  You should be paying attention and listening.  You may need to ask questions and you may miss something if you don't.

I watch a driving show where bad drivers are educated and it's astonishing to see how many of the bad drivers put forward all sorts of elaborate rationalizations for using a phone when driving.  People are, simply, addicted to their phones.  Learn to do without it.  If you can't sit through a lecture without your phone, it bodes ill for when you hit the real world.

Note then if you were my employee and you started looking at your phone when I was presenting a report in a meeting, you'd be on your way to being fired.

The right you think you have to use a phone when you want does not exist.

Respect the rules other people set when using their resources.

It's that simple.

  Finally, I find it highly disrespectful to call a student out for being on a phone in the middle of a lecture in front of all others

You are now experiencing the real world.  The one where people call you out to your face and in public for your errors.

Get used to it.  It's the difference between an adult and child.  All part of learning.

How disrespectful were you being by ignoring the teacher?   Did you think about that?

Immature is the right word.

Edit : regarding this and similar comments :

There are too many comments to address individually and this is as much effort as I'm willing to spend on this relatively small storm in a teacup.  My gut feeling is this won't make people who oppose my viewpoint any happier, but they deserve some kind of response.  But life's too short, so this is probably all I'll be doing on the subject.

Remember : Agree to Disagree is not ideal, but it's practical. :-)

  One thing which could improve this answer is an acknowledgement that the OP is paying the institution for certain services and - unless he disturbs others - it's not the institution owning his time and not their place to order him around. The OP is not working for the professor, the professor is working for him.

That's not how it works ( in the real world :-) ).

The fantasy that "the professor is working for him" is not correct.  What is happening is that for a fee you are permitted access to the resources (including lectures) of the college/school.  But that's not a one way contract - you are accepting the authority of the college/school and it's agents and their rules.  Typically that small print gives the lecturer rather a lot more power and discretion than you realize.

If the rules are really unreasonable (e.g. pretty girls/guys in front, stand all the time when there are seats, etc.) then you have two choices : dispute them in some legal way (e.g. contact the authorities or ultimately take legal action) or leave.

Now one of the most basic rules is that you pay attention.  It's not complicated.  It's nor strange.  It's not an infringement on your human rights.  It's an implicit (possibly explicit) part of your contract with the school.  It's the only thing you are required to do at a lecture beyond those other common sense things of not disturbing other people, dressing, not eating, not drinking, not talking - and so on..

And, yes, it can disturb other people when you start using your phone to text or whatever.

  OP just said they did put the phone down when the teacher asked

That's nice but the issue is the fact they should not have been using the phone in the first place.  The OP doesn't get this or the question would not have been asked here.

I've explained the OP needs to contact the authorities via appropriate channels.  That's all there is to it.

Many people seem upset by my post.  Fine.  They have a right to be upset if that's how they feel.  If it's any consolation when I was a young student I also thought every rule, restriction and law was personally aimed at suppressing my rights.  Maturity (experience) teaches you that it's not that black and white.  Some rules are necessary.

Inconvenience is not the same as being deprived of a right.

I am happy to encourage people who disagree to say so, but if you want change remember three things :

I can't change things.  You need to exercise normal legal political activity to try and get changes you want.  In normal political activity you do not always get what you want.  So contact your student unions, get a petition going, make a logical case to the authorities.  But be prepared to not win, because that happens.  Never start a battle you are not prepared to lose.
You can get more with a carrot and stick than you can with a stick.  Make a logical case why using a phone would benefit the college and lecturer as well as the student and you'll get a lot further than talking about rights you don't actually have.  That kind of approach will sound very naive to the authorities.
There are better battles for your energies that the right to fiddle with your phone during lectures.  Put that youthful vigor into something more useful to the rest of the world, please.


Choosing between PhD offers - top supervisor at my current institution or good supervisor at new university

A PhD starts a career, it doesn't define it.
There are benefits to moving, there are benefits to staying. Benefits aren't limited to now. You can seek those benefits later.
Move at some point in your career, not necessarily now.


What happens when a professor can't fund his/her own lab?

If there is no money, then there is no money. What happens quite often is that some of her or his colleagues help out by hiring deserving students instead till extra funding has been found. This has the advantage that it diminished the risk everybody faces because of uncertain funding, but it requires quite a bit of trust and good will in the department. So the worst case scenario, that the professor has no money and nobody wants to help her or him out, can definitely happen.

This also depends on the contract you have. In my case I got a 5 year contract to do my dissertation and some teaching. In that case, my position was safe: if somehow the professor's funding somehow failed the university had to come up with the difference, since the contract was not between the professor's lab and me, but between the university and me. This is in line with @IanSudbery s comment that, however much professors think of "their" lab as her or his private kingdom, it is only part of the university and not a separate entitiy. The fact that the university is finally responsible for paying the wages meant that the university required my professor to have guarantees for the funding for those five years before agreeing on the contract.


I used feedback from the code review SE for an assignment. Do I have to mark it?

Yes, you should ask the professor in advance and make sure he/she understands what CodeReview actually is.

More generally, you should know (and the professor should effectively communicate) what the parameters are for seeking help. I have doubts that very many professors would permit it, but some would.

The reason for assignments isn't because the professor needs the result. It is to cause a change in your brain that won't happen if you take very many short cuts.

Seeking help from the professor or an assistant is different, since they know the actual purpose of the individual assignment (in your learning) and can give hints that won't impede your learning, but help you deepen it. The contributors to CodeReview don't have the context (or usually the background) to do that properly. So you may be sabotoging your learning in pursuit of a better grade. Long term that's a losing game.

Making it functional first was a good step, but there is a lot to good programming beyond functional.

And if you haven't done so, then yes, mark it and point to the source of help. If there weren't already rules around the behavior there should be no reason to punish you and you might get better advice about seeking help from the prof. In fact, you should make the note pretty visible so it just doesn't get lost. Program comments may not be read without some statement at the top pointing to them.


How to handle an obsession about being 100% academically honest

Should I just accept that it's pretty much impossible for anyone to finish a degree with a 100% ethical standing?

No, I find that to be a rather unreasonable formulation of your predicament as well as a loaded question. What you should correct is not your notion that ethical behavior is achievable, but rather your unreasonable idea of how to achieve it, and your misguided view that there is some ideal level of "100% ethical standing" that is only attainable through extreme efforts of constant vigilance and constantly pestering your professors and TAs with annoying (and unnecessary, as you yourself seem to understand quite well) questions. In general in human affairs, trying to attain 100% of anything is an example of what is known as a category error -- the act of attributing a concept that is applicable to one realm of thought to another realm where it is no longer applicable. "100% ethical standing" is simply a meaningless concept.

I could go on and give a detailed answer touching on all kinds of philosophical issues and giving you a crash course on academic ethics, but a more lightweight approach seems like it will be more useful here. Basically, you just need to chill out. Relax, trust your instincts and common sense and stop worrying about this and you'll be fine, just like the vast majority of students who just want to complete their studies honestly and then go on to make use of the knowledge they acquired.


What is wrong with continuing to publish with my PhD adviser?

There's nothing “wrong” with continuing to publish with your (ex-)adviser. You have correctly identified the issue to avoid: after getting your PhD, the next step in your career is to establish yourself as an independent researcher. Thus, of course: depending on the context, publishing with your adviser might send the wrong signal!

So, you should continue to publish with her, but you should make sure that it's not 100% of your research (and publications). Another point that makes a big difference is if you can, maybe now or maybe after some time, take the lead in that collaboration.


Do researchers of deep learning understand the existing codes in detail?

Do researchers in deep learning understand the existing codes in detail? Or they just use the code as a module to execute?

A little bit of both. Some thoughts:

I only look at the code on a tiny fraction of the papers that I read. Most of the papers explain their "idea" well enough and have results on standardized tasks. So, there is no need to look at the code unless:

I cannot understand exactly what the "idea" is (and I am sufficiently motivated to continue trying to figure it out), or
I want to implement the idea myself.

In general, most of the codebase is the skeleton for ETL (extract, transform, and load), training, validation, tensorboard, etc. I ignore this. Instead, I look for the small part of the codebase where the new idea is implemented, and I study that in detail. Even if I want to run the code, I will generally add their new idea into one of my existing codebases, rather than running their entire codebase off-the-shelf.

Of course, new students will have different needs than more experienced people. After you've seen enough codebases, you can quickly distinguish between "the usual stuff" and "hmm, why did they do that?" When you are just starting out, everything will look unfamiliar, and you may need to go much more slowly to understand the different pieces. This is the same as any other discipline, really.

An added complication is that these papers come in a wide variety of languages. Recently, research papers have been converging on PyTorch, which I am very happy to see. But this is another difference: students generally get stuck on the software details of each language (which is reasonable, since their software engineering skills are less developed), while experts will only care about the underlying math.


What is generally the correct procedure for publishing translations of my own work?

If during submission, you clearly state that this is a translation of paper X, then I don't see an issue. It might however be a good idea to inquire with the journal beforehand whether they do publish translations of already published papers; not all journals might do that.
Also, you need to check with the journal where the English version has been published whether their copyright allows to publish such a translation in another journal, and of which version (e.g. the pre- or post-review version). Note that this might even be a point to consider when you want to post a translation on the arxiv.
Finally, there might even exist journals where you might be able to publish both the English and the translated version in the same journal, maybe even alongside each other; this might well alleviate those copyright issues.


How long is reasonable to wait for reply from an editor?

There are good reasons to expect communication with an editor to be slower than many other e-mail exchanges. Editors are busy, especially since editing may be a minor but time consuming part of their job. And responding to questions from authors often involves contacting referees, who may in turn be unresponsive.

I'd say that it's reasonable to wait a couple of weeks for a response to a timely request for a status update (two months after a revision strikes me as a bit early---I'd expect it to take longer---but not unreasonably early to ask for a status update). If it gets lost (for instance, the editor is waiting for a response from the referee, and hasn't remembered to tell you that's what's happening), a polite reminder and a few days to another week or so of waiting might be appropriate.

After that, though, you can rightly begin to worry that you aren't hearing back. If there are other editors, especially a chief editor, you can contact, I'd start there. I'd be very reluctant to unilaterally withdraw the paper, since that might cause complications if the editor returns and feels you resubmitted while it was still under consideration.  Before resorting to that, I'd try to talk to one or two senior people in the field for advice about the specific paper.

(Just to emphasize, I'm talking about communication with an editor about the status of a paper. Of course the refereeing process as a whole can take a year or more.)


How much does a student's ranking in their cohort matter for PhD applications?

Your letters of recommendation will be much, much more important than your class ranking. Spend your time on getting the strongest letters you can (and learning how to do this, if necessary).

Source: I have served on grad admissions for a top math department.


Should one avoid erudite vocabulary in statement of purpose?

Erudition and eloquence are useful tools for academics to possess.

However, excessively erudite writing can become opaque. That's not what you want to achieve in scholarly writing. Scholarly writing should be lucid, informative, and as direct as possible. Thus, using "five-dollar" vocabulary when "fifty-cent" words will do probably distracts from your writing overall. On the other hand, if that five-dollar word is exactly the word you need in a given situation, don't be afraid to use it. It's better, in my opinion, to moderately challenge the reader in a concisely written text than to be long-winded.


Where to publish a critical comment on an academic paper?

Do you know what is the best way to publish a critical comment on a paper published in top journal if that journal rejected the comment?

In another top journal. But your comment "have take a form of an independent paper" as Alexey wrote.

Check those two examples from Computer Science field. First (1) from ICSE, Software Engineering community top venue, where Monperrus offers a critical review on others' paper. Second (2), Arapakis et al. challenge the results reported in Bandari et al.

In my opinion, you should go for a peer-reviewed paper, which is a very noble form of scientific debate.


My professor is not teaching his online course himself, but uses publicly available videos instead. Is this appropriate?

If your instructor is available for questions, comments and discussions, then you can learn a great deal this way, potentially.

I recommend that you try to do just that.  If, after at least ten days of really trying, you have difficulties, or find yourself concerned that you may not be properly prepared for courses that build on the one you're currently taking, then I recommend that you reach out to a department administrator.  Present it as a problem you are having, not as a problem your instructor is having.  However, do lay out in as neutral a tone as possible, a description of the current course format, and if your instructor has been unresponsive to questions, do include that information.  Draft the email and sleep on it.  The next day be brutal and remove any trace of whining or complaining.  Just state the problem as a problem you are having.

Hopefully you will not have a problem.

Happy studying!


Correct name for experiment aimed at confirming an alternative Hypothesis?

If you are doing a bunch of hypothesis tests in the first phase, you are likely to detect false positives unless you correct for multiple comparisons.

In the second phase, you commit to a particular intervention so multiple comparisons is not an issue.

You could call the first phase exploratory and the second phase confirmatory. But, there is nothing special about the experiment. You are simply applying a intervention and comparing its affects vs a control group. Your motivations or hopes don't make any difference.

But maybe I've misunderstood your experimental design. You aren't very clear in your description. Specifically, I don't see how the second phase is "rigged".

Further, if you are being scientifically honest, the goal of the second experiment shouldn't be to confirm the alternative hypothesis, but rather to see whether the null hypothesis can be rejected. The experiment would be successful no matter what you learn.


Google Scholar sometimes counts different papers with similar names into the same publication (marked with an asterisk*) -- these usually add up the citations from multiple papers, which might or might not even belong to the same author. Some scholars also just rack up a lot of citations from spreading themselves out with quantity. It's just as possible that he's published a lot of papers with hundreds of citations.


Which among an LoR for startup work and a "good student" LoR, will be more effective?

If the startup is showing evidence of success (e.g., it's actually raising significant venture capital or making money from clients), then if it were me, I would absolutely go with the letter from the startup.  They may be have been undergraduates, but now they are a Small Business Success Story, and you are part of that story.  It will help you stand out as unique, capable of taking initiative, and capable of working on ill-bounded problems as part of a team.

If, on the other hand, the startup is still little more than a collection of nebulous hopes, dreams, and semi-finished software, the professor (who is essentially neutral as far as recommendation value goes) is a safer bet.


What does a university's acceptance rate indicate?

If the acceptance rate of a university is 90%, does that mean it accepts 90 students from 100 that applied?

Yes.

  Does the acceptance rate of universities indicate the quality of them?

No, not particularly.  For example, it's possible to get a good education at an institution with open admissions.  It's true that low acceptance rates are correlated with quality, for at least two reasons.  A university that is perceived as being of high quality will often receive more applications than it has space available for students, and being able to choose high-achieving students will help create an academically stimulating atmosphere and enable the university to offer more demanding courses.  However, this correlation is far from perfect.  Acceptance rates are essentially a popularity contest: you are measuring a combination of how many students apply and how many accept an offer of admission.  Like most popularity contests, they only tell you so much.

It's also worth noting that these statistics can be intentionally skewed by universities.  Because college rankings in the U.S. often involve acceptance rates, some schools have adapted by deliberately advertising to try to attract applications from students they have no interest in admitting (increasing the total number of applications decreases the acceptance rate).  This makes the acceptance rate even less meaningful than it used to be.

Added in response to Kimball's question about references:

I don't know of a definitive reference.  It's widely believed to be happening, but it's difficult to prove since who would admit it?  (Instead of saying "we're soliciting mediocre applications just to be able to reject them," any competent admissions director would say "we're casting a wide net to make sure talented students don't get overlooked.")  Certainly schools that are concerned about their rankings are trying hard to get more applications; see, for example, this story about Northeastern, which suggests but doesn't explicitly say that Northeastern is more concerned about the number of additional applications than their quality (the closest it comes is "The more applications NU could drum up, the more students they could turn away, thus making the school appear more selective").  See also this NYT story, which discusses attracting more applications as a form of ranking manipulation (but attributes this information to unnamed admissions directors and doesn't mention any concrete examples).  For comparison, seeking more applications is not so extreme: Clemson has been accused of far more dramatic forms of ranking manipulation.


Potential consequences for a PhD student using a cracked software

Usual disclaimer: I am not a lawyer and this is not legal advice.

Several things to consider here:

It is the university's responsibility to maintain their computers, including their contents. So if your friends have been using a computer provided by the university with cracked software on them, the vendor of the software will go after the university first. They just want to get paid what they're owed, so it's better to go after a large university than some broke students.
Normally, the university should have only provided students with user accounts, which do not allow the installation of software, which in turn is to be done by IT personnel with admin accounts. If they don't do this, shame on them, this is poor practice that warrants some fines here and there (and the cost saved with IT employees probably makes them insist on the poor practice).
If students had admin accounts to these machines, they have probably signed a contract/memo/agreement claiming they'd be responsible in such situation. Bad for them, but the vendor will prefer to go after the university first.
Part of grant money and department budgets are precisely meant to pay for tools required by research activities, which nowadays always include computers and software. There is no excuse for using cracked software over the long run.
To be clear, this is a matter of money, not of academic merit. As long as your friends behave during the process, they should expect to be fined, but not expelled. The university will come after them if they receive a fine from the vendor.
"Normal practice" (which I'm not endorsing here) when using pirated software for your academic work is to use it only in your personal machine and only if the department owns licenses for said software. In some large universities, they might even have "campus licenses" for software, making this ideia completely useless. The point is that you have the right to use the software, as your department paid for it, but instead of using it during office hours, you might prefer doing it from midnight to 6 am in the comfort of your bedroom.
If nobody has the license for the software, you might be in trouble to publish results obtained from it. But then again, you can first obtain results, then the license, then attempt a publication. You might even just ask for a trial license.
If these computers were owned by the university, there is no breach of privacy here. If they were owned by the students, IT should not have nosed around these machines without the students permission. And by the way, never grant someone the right to audit a machine of yours, specially if unsupervised. Everybody has secrets/nudes/browser history/work worth keeping private, all of which should only be kept/done in private computers.

My bet for the outcome (and please update your post in the future to inform us):

Students get away with a warning.
Advisor gets a warning and needs to spare budget to acquire the license, if the license is affordable. Otherwise, activities using this software will need to be dropped.
Story gets muffled, people will go around saying "It is yet to see what happens" until everyone forgets about the case. Then people will simply stop talking about it. This is to avoid having precedence of cracked software usage and preventing it from becoming common place.

EDIT
Just as an extreme example, there are software licenses that costs millions of dollars. Paying a fine over the value of license would warrant firing the professor who allowed its pirated use, as long as the university indeed pays the fine (unlikely) and had good policies to avoid it in the first place (further unlikely).

There is also software whose commercialization is restricted due to national security risks. Missile simulation tools come to mind. Here there is more than a "money problem", there is illegal usage of a controlled piece of software. But I'd hardly expect this to be the case.


How do I show others what I am capable of?

To apply for admission as an undergraduate at ... (MIT, Harvard, etc.) ... their web sites shows the steps you need.  There is an exam (SAT, Scholastic Aptitude Test) such applicants may take.  Probably there are opportunities to take it in your country as well, but maybe just in one or two cities, so you may have to travel there to do it.  (16-year-olds generally haven't published papers.)


Is Visa required to obtain a very short term research grant (15 days) from a US University?

If the grant is only to reimburse you for your travel expenses (airfare, lodging, meals, etc), then you should be fine with the visa waiver.  You are not considered to be employed by the host institution and do not need a work visa.  (Source: Personal experience - I've been responsible for arranging travel reimbursements for many visa-waiver visitors.)

You will probably need to document your expenses, so save receipts for airfare, lodging, meals, ground transportation, and so on.


Doing a PhD while being unable to travel due to disability

Conferences can be useful, both for presenting your work but also for networking.

Some conference organisers will be willing to let you present by videoconference, if you explain the reason. Others will not want to do that - perhaps for good reasons, perhaps for really bad ones which may or may not be legal. You can also have your paper presented by a co-author, which means that you can certainly get your work included at conferences and into proceedings - but if you don't do it yourself, you don't gain much recognition.

The networking side is much harder, as you can't do that by videoconference - at least, unless you or a funder invested in a telepresence robot or similar. Not being able to network effectively is certainly a disadvantage for your future career, but should not be an insurmountable obstacle, and should certainly not prevent you from doing a PhD.

You don't mention where you live, but in many jurisdictions having a sponsorship declined because of disability (where the disability does not prevent you from studying at PhD level) might be illegal. It certainly sounds deeply unethical to me.


Do arxiv moderators not work on Sundays?

Yes, arXiv staff are not working on weekends. They also do not work on major holidays in the USA.


How to Proceed: Journal Agreed to Publish, 6 Months Later Reneges

This is a very bizarre situation—I must admit that I've never heard of a paper being rejected because three words are incorrect. It seems that the level of response from the journal is not proportional to the level of the problem.

I agree with Nate's answer that you will probably need to publish elsewhere. Since the decision has been made by the editor-in-chief, the only appeal would be to the publisher, who would be reluctant to overrule a scientific decision by the editor-in-chief absent signs of foul play.

However, in addition to submitting to a different journal, I would definitely try to get in contact with the editor-in-chief to understand what's going on. If he's someone you already know, I would try to see if I could talk with the person directly on the phone, rather than just email. You might be able to get a better sense of what's going on with this rejection than just in an email. I would not try to force the editor-in-chief to change his mind; I would use this opportunity to figure out what caused the paper to go from essentially accepted to rejected in one step.

If you don't get any response, then you should escalate to the publisher. Such behavior is highly irregular, and should be brought to their attention. (Just state it as: "This is what happened and this is why I think it's unusual." But again don't expect a reversal.)


How to manage relationship with post-doc supervisor when applying for a tenure-track position one year before post-doc ends?

In my experience supervising post-docs the goal has been to get the post-doc into a tenure-track position.  I've seen post-docs apply for tenure track positions and get them before the end of our funding for the post-doc, and I've considered that to be a success, even though we had go out and find a replacement for the post-doc.

I would encourage you to discuss this with your current supervisor.  If they're not supportive then you probably won't get the kind of recommendation you would need, and there might not be any point in applying for the position.  If they are supportive then you can apply with some confidence.  Even if you don't get the job, you'll have some experience with the application (and perhaps interview) process.


How to ask someone to be cited in their paper?

Citations are mostly to establish and credit where ideas came from rather than to establish priority. Simultaneous or independent discoveries are fairly common.

It's appropriate to contact the other authors and let them know about your work. Be polite and friendly, you don't need to accuse and shouldn't request anything.

The script would be something like:

  Dr. PurpleElephant,
  I saw your recent publication in the Journal of Pachyderm Studies and thought you would be interested in our similar work last year published in Colorful Mammals (citation/DOI link). It looks like you found a more general case of ours...

And add whatever pleasantries or commentary is appropriate (for example, if you liked some aspects of their approach, or you want to point out something unique in yours). Hopefully you'll get a friendly letter back, maybe they'll be sorry they missed your work.

Note that this will almost certainly not get you cited in their current work which is already published (possibly it would be different for a preprint), but if they refer to their paper in the future they may also refer to yours. In case of some truly substantial simultaneous discovery, some other venue might be appropriate to draw attention to it, but that doesn't seem to be the case here: sometimes we end up on similar perches from standing on the shoulders of the same giants.


You don't need to drop out of the normal first-person-plural way of academic writing. You can write something like:

  Bob e.a. [1] theorize that (something you disagree with), but we are skeptical because (reasons you disagree). In this paper we offer an alternative hypothesis (your own ideas) and propose experiments to support it.

It doesn't matter whether you're a single person writing the paper or a team, you use the "academic we". That's just the convention.


How to Cite a conference talk / TED video?

A quick google "apa cite video" would give you lots of advice, such as http://www.easybib.com/guides/citation-guides/apa-format/youtube-video/ which notes:

Last Name, F.M. [Username]. (Year, Month Date). Title of video. [Video File]. Retrieved from URL.


Your description of being "allowed" to do research work in exchange for programming work sounds off to me. Learning and running experiments for a research project proposed by a supervisor is basically the job description of a research assistant. It's work in its own right that people are typically compensated for in some way, not a reward for doing other (programming) work.

The arrangement you describe is not common, and it might also violate U.S. labor law. Under U.S. law, it's illegal to let someone work for you for free unless they meet specific legal requirements to be considered a "volunteer" or "intern."

"Volunteers" according to U.S. labor law are individuals

  who volunteer their time, freely and without anticipation of compensation for religious, charitable, civic, or humanitarian purposes to non-profit organizations.

Your intent is clearly not religious, charitable, civic, or humanitarian in nature, so you do not legally qualify as a volunteer.

And to be classified as an "intern" you must meet the requirement that

  The employer that provides the training derives no immediate advantage from the activities of the intern; and on occasion its operations may actually be impeded.

(among other requirements). That is, the employer cannot expect to be dependent on your work for normal operations. I don't think you meet the requirements for an unpaid intern, though it's not possible to be 100% sure from your description.

The usual interpretation of the U.S. labor law is that an internship has to be part of a formal educational program (e.g., you are enrolled as a student and get credits for the internship, or write a report which you submit to your home institution) or a formal apprenticeship for it to be legally unpaid. In fact, if you search for unpaid internships in the U.S., you'll find that most listings say that only current students who can earn college credit are eligible. It doesn't say in your post that you are currently enrolled as a student somewhere.

This is not to say that there is no legal scenario in which a U.S. lab can allow you to participate in research there without paying you. (If the entire experience was supposed to be for your educational benefit - including the "help the lab with programming their machines" part - then my answer might be different.) But from your description, I don't think the scenario you describe is acceptable or normal.

I personally do not allow anybody to do work for my lab unless they are paid or doing a personal project (like a thesis) for which they earn academic credit. I've been told it would be legally problematic. For example: suppose I have an M.S. student working with me for academic credit. He graduates in May and has a job starting in September. I'm not allowed to let him keep working in the lab from May-September unless I can pay him (according to my university lawyers).

(Disclaimer: I am not a lawyer)


I need resources regarding the history & meaning of a PhD

You can see, breif history of PhD and a series of paper in Nature, Nature 1, Nature 2, and Nature 3.

Also, this paper is helpful, Changing PhD.


What makes securing faculty positions difficult?

One of the strange effects of faculty hiring (and graduate admissions) is that offers do not necessarily go to the strongest candidates.  Departments have limited resources to interview, recruit, and hire faculty.  Interviews are expensive; startup packages are really expensive; faculty job offers burn political capital even when they aren't accepted.

So hiring committees make strategic decisions based on the perceived probability that candidates will accept the position.  The University of Southeast North Dakota at Hoople would most likely not interview superstar applicants, because they don't want to waste their time interviewing someone who's "obviously" going to get offers from stronger schools.  As with any self-selection process, this assumption is partly justified and partly Institutional Impostor Syndrome.

So no, selecting an MIT grad is absolutely not a no-brainer for U-Cal-XYZ.

And yes, sometimes reasonable PhD students from very strong schools fail to get faculty jobs, or even interviews, because they don't quite have the research record to get an interview at the best departments, but their pedigree scares off weaker departments.


How is extra exam time for disability accommodation perceived by professors, especially potential reference letter writers?

(I will answer in the context of the U.S., but I hope others will answer for other parts of the world.)

  How is this perceived by professors?  Might some of them think that these students get an edge or advantage over other students unfairly?

The US Department of Education's Office for Civil Rights (OCR) has stated, "A test should ultimately measure a student's achievements and not the extent of the disability" (www2.ed.gov/about/offices/list/ocr/docs/auxaids.html).

If some professors are still playing catch-up, that's their problem.  Extended time has been settled legally for at least 15 years (see the Marilyn Bartlett case about accommodations in the bar exam, which was decided TWICE by Sonia Sotomayor, long before she was appointed to the US Supreme Court).

  If a student is looking forward to requesting a reference for grad school from a certain professor, would it generally be better for him/her not to request exam extensions for this professor's course?

There is no reason to have a tooth extracted without novocaine, i.e. there is no reason to sacrifice the needed accommodations, just because a professor might botch a letter of recommendation.  I say botch because it would be discriminatory for a professor to judge a student's exam results differently just because the student used a reasonable accommodation to achieve them.  OCR enforces the Americans with Disabilities Act (ADA) and the Rehabilitation Act, which protect the civil rights of K-12, undergraduate and graduate students with disabilities.

Institutions of higher learning and testing boards do not provide extended time and other accommodations lightly.  It is fair to assume that if the student has an approved 504 accommodation in place, it is in fact needed and appropriate.  College professors are experts in their fields.  We cannot expect them to also be experts in disabilities, and sit in judgment to decide which students truly deserve their legally binding accommodations and which do not.  It would be even more absurd for them to make such judgments without a careful examination of the student's documentation.  And if we did hand off this responsibility to individual professors... why would universities need to set up offices for students with disabilities?


Is improving a simple algorithm without beating the state of the art still publishable?

Sure this is publishable, but the real question is where?

The applied mathematical community, especially the one in which the state of the art methods are developed will probably not see the improvement of the simple algorithm as worth publishing in their venues. Why should they? They know that there is something better which they understand well. In fact, I know of at least one journal which states explicitly that algorithms published there need to beat the state of the art to be suited for them. But the community of practitioners who may be struggling with the nuts and bolts of the state of the art method and often fall back to use the simple method may be impressed.

So, choose you publication venue right and things should go well.


Is it dishonest to guess on multiple choice exams?

Should maybe we ask all students to do this [refrain from guessing on multiple choice exams]?

Some multiple-choice exams use negative scoring, where points are deducted for wrong answers. This discourages guessing, but introduces other problems.

One problem is that students who know the material vary a great deal in their confidence in that knowledge. If students are actively discouraged from answering questions unless they are sure they know the answer, students who lack confidence in their knowledge will be at a disadvantage. (I'm assuming you want the exam to measure student's knowledge, and not their confidence in that knowledge.)

  But is it cheating to mark something when you don't know the answer?

Not unless you're told "Don't mark something if you don't know the answer." Cheating implies deceit - there is nothing dishonest about guessing, unless it's forbidden and you do it anyways.


Need a thesis extension due to mental illness, but supervisor seems unwilling. How to proceed?

As you say, it sounds like your supervisor does not understand depression at all. Or at the very least, he or she doesn't realise that what you're experiencing is depression and not just typical thesis stress. That's very unfortunate, but all too common (in the general population, not just supervisors). You have every right to an extension.

However, given that you are depressed, you may not be the best judge of your own progress right now. Even students who aren't depressed have difficulty accurately assessing the progress of their research and thesis. Your supervisor has a lot of confidence in you, and seems to think you're "almost done". I'm reading between the lines a bit, but it sounds like your supervisor is a good supervisor apart from being clueless about mental health.

I think it might be worthwhile to have a meeting with your supervisor, and with someone who will be in your corner on the mental health issue (the Honours convenor, perhaps?). The three of you can then put together a plan to finish your thesis. Try to keep an open mind. I don't mean that you should let yourself be pressured into taking on more than you can handle right now. I just mean that there may not be as much work remaining as you thought.


GPA dropped due to a death in the family. How do I explain this on graduate applications?

You haven't said what country you're in, and the answer may vary somewhat.

From my experience in the US, I'd have concerns about an application with the kinds of grades you've described that didn't come with some explanation of the personal circumstances that caused the poor academic performance.  When I see bad grades with no explanation, I'll typically vote no on the applicant.

However, even with an explanation of why you did poorly in the past, I'd also have to consider whether or not you'd be likely to do well in the future.  If the personal problems that you've had are ongoing, then it's likely that you'll continue to do poorly in your academic work, and you'd be a high risk applicant.  If the personal issues are well and truly resolved, then I'd be more likely to vote yes on your application.

My advice would be to include a statement explaining your past poor academic performance, pointing out how you've done well at times when you weren't having these personal problems, and that you're confident that you won't have these problems going forward.

If any of your recommendation letter writers can also address this, it might help too- many recommendation forms have a specific question asking the recommendation writer whether the student's grades are fully representative of their performance or whether special circumstances should be considered.  .

You don't need to go too far into the details of your experience ("a family member died suddenly and I struggled with this during the xxx semester" is more than enough detail.)  What's more important is showing that when you aren't having such personal problems you have been a successful student and that these personal issues are no longer going to affect your academic performance.


In my area, software engineering, the criteria for having a paper accepted (which implies later publication) are usually listed in the call for papers of the publication venue (conference or journal). They typically include the following:

Novelty. The paper should contribute to the knowledge in its field. This could either include a new problem formulation, and a new idea to approach an existing problem.
Relevance. The paper should make a point in why the presented work is relevant.
Soundness. The work presented in the paper should apply a sound methodology. The argumentation presented in the paper (in particular, technical reasoning) should withstand scrutiny and be reproducible by experts in the field.
Presentation Quality. The paper should be logically organized, self-contained, use appropriate scientific language and writing style, and be free of major language flaws. In some research directions, there is a standard paper organization that should be followed (for example: Introduction, Related Work, Methodology, Results, Discussion, Conclusion).
Appropriate consideration of related work. The paper needs to depict its own contribution within the landscape of existing research. Closely related work has to be referenced and discussed.
Validation. (Only applies to papers that contribute some solution to a problem; a counter-example to this are empirical study papers.) The paper needs to validate the presented solution, for example, using a theoretical validation with theorems and proofs, or an empirical validation in which the solution is applied to realistic instances.

There is a lot of variation in how these criteria will be interpreted specifically. Some venues will have much higher standards than others, with top international conferences and journals on the one, and small national workshops at the other end of the range. Some venues will offer special paper types (for example, experience reports or tool demonstrations) that de-emphasize some of the criteria.


What are good argument against strict attendance policy, and university making it harder for students to maintain attendance?

A hard part of this is that it is not as easy as said. The vast majority of students are (while legally adult) not sufficiently mature, and particularly susceptible to peer pressure. Mandatory attendance (which our university doesn't have) attempts to address this. Fact is that students tend to be poor judges of the benefits of attendance (or prioritising the wrong parts - lectures over seminars or labs). With the right pressure many students can be taught more than if they are left to their own devices and from a student recruitment perspective it is seductive to put the protective measures into place so that the students will gain the relevant subject knowledge, understanding and skills (which are much more prominently assessed, and easier to assess than vague things like study attitude and independence).

Another problem is that when few students attend it is easier for other students to not attend. When students believe that they can pass the exam (that is due in 6/7 months) doing memorization a few days before the date you are fighting against a well established belief that has been reinforced through years of regurgitation exams in secondary (and primary) school. Anything helps.

At the same time, overworking students is also overkill, but in case that selection on entry is not feasible it may be a good way to quickly separate the wheat from the chaff. In many systems, withdrawals only count against the university after some months of study, so getting students who will quit (or are really not up to it) to quit early is quite important.


How to show the accreditation of a university abroad

Various countries have different accrediting bodies. Wikipedia has a nice overview.

From what you've written, it seems like they are looking for some information about what body (usually a private accrediting agency or a government ministry of education) your undergraduate institution is accredited by. To use a school near me as an example, I might say something like:

  Brooklyn College is accredited by the Middle States Commission on Higher Education, as stated here.  You can see Brooklyn College listed on the accrediting body's website, here.

In your case, you can point them to this page, which shows that the university is accredited by the Ministry of Science, Research and Technology of Iran (which is the government body that is responsible for accreditation of institutes of higher education in Iran).


It is difficult to see what other alternative the editor has; given that problems were identified in the paper by the original reviewer, the editor need to be confident that these have been adequately addressed, and a good journal should not base their decisions on the view of a single reviewer.  I'd say it is perfectly normal, and beneficial.

If the second reviewer has identified further shortcomings in your work, while that it perhaps not what you were hoping for, but in the long run I suspect they have done you a favour as it will strengthen the paper that is finally published.  I wouldn't be too concerned by this, just address the new set of criticisms as well as you can and resubmit.

What is not really acceptable is for a reviewer to give one set of comments, which you then address, and then for the same reviewer to give another set of criticisms about the revised version that they could have made in their original review.  However as this is a new reviewer, I don't think there is a real problem.


Are there published mathematics research papers that contribute a new approach for understanding a known result, rather than new theorems?

There are many papers out there that give a new proof of a previously-existing theorem. You can search for "a new proof of" in mathscinet (or even google) and find lots of good papers in respectable journals.

However, the new proof must provide new insight to be worth publishing. Two proofs can look different but actually be very similar, in the sense that they are relying on the same key ideas. This can be a bit subtle (and even subjective in edge cases), so it's a good idea if possible to consult with an expert in your field before making your findings public.

But if you manage to prove the result in a more elementary way than the original proof, that's a big point in your favor. It's always good to know that a result can be proven without appealing to a powerful theorem. If you go in the opposite direction (e.g. showing that a theorem from the 1950s also follows from Fermat's Last Theorem), you're less likely to impress people.


What license to choose for my PhD thesis?

CC-BY seems to be the industry standard license for open access papers, see Why CC-BY? for a discussion of the reasons. It's a well-known license, that allows various kinds of later use (including commercial), and hence it's a good choice for papers and (I think) theses as well. The BY part requires "appropriate attribution". For academic reuse you can pretty much count on the attribution coming in the form of citations.

Note, however, that CC-BY is not a "viral" license. That is, modifications don't have to preserve the license. If you want that property, there is the CC-BY-SA (share-alike) variant, but my understanding is that it can make it problematic to create repositories of documents. This is one of the reasons for recommending CC-BY for papers. However, you could always put a CC-BY license on the thesis, and a stricter one on the helper tools.

Just make sure that whatever you choose is compatible with any copyright policy imposed by your university. Places I'm familiar with just request non-exclusive distribution rights to put it in their online library databases, but I imagine other places can be more restrictive.


How would you ask your professor to be your supervisor?

To make the answer formal, yes, you should ask him. This is best done in person, and one of the best approaches is just what you say here about his skill and your common interest in a topic. Let him know that you think he is the best person around to do this, and you won't have a problem, yourself, if he can't be at the graduation.

What you need is his signature, I assume, and not his physical presence to approve your completion.

He might say no, but if you don't ask, the answer is certainly no.

Good luck.


Based on the amount of spam that I receive from them (mostly calls for papers in special issues), the fact that their automated emails do not feature a “unsubscribe me” link, and the fact that I did not manage to be removed from their lists after several complaints, I would say that they are not a respectable publisher.

I don't know how long they have been around, but most of their journals in my field (chemistry) were very recently created: see there for a full list, which you can sort by journal creation date. Their older journal, Molecules, has a less-than-stellar impact factor of 2.4. Its editorial board, apart from the occasional celebrity or two, is unremarkable.

As a conclusion: I think they surf on the popularity of open access journals, but I don't consider them serious players.


In writing research and teaching statements, I generally use past tense for activities that have been completed, and present tense for ongoing activities—the same way you would in standard "ordinary writing."

Statements such as these do not need to be signed, as they are not letters. (Your cover letter for the whole application is a reinforcement of this.)

As for talking about the position, it certainly seems like a good idea to me to talk about how your experience and teaching philosophy fits the specific position in the application, doesn't it?


How to prove episodes of academic misconduct?

If a professor wants to falsify data now, the professor probably falsified data in the past.  Look through previous publications by that professor for data that is obviously falsified.
Plagiarized images are the most commonly detected form of fabrication.  Not all image reuse is falsified data, but if two publications present the same image data as if they were recorded separately, this is proof of falsification.
People who falsify data are likely to engage in other academic misconduct, such as plagiarism.


This is mostly just a whole bunch of comments strung together.

First, I think you should look for advice specific to refereeing math papers, as refereeing in math is quite different than most other fields.  (Though it's perfectly valid to ask for general advice now, at some point you should want to know about refereeing specifically in math.)

Second, here are some places with advice:

Attributes of an ideal referee, Notices of the AMS
Refereeing a paper, from MathOverflow
How do I referee a paper, from TCS SE

One thing I would disagree with in the first article is the statement that "The referee is expected primarily to check the correctness of the paper."  I would say the primary job is to assess the importance of the paper, which includes correctness, though it is not always expected that the referee check every detail.

Anyway, since your question is rather broad, I suggest you read this and other Q&A's here and on MO, and then if you have more specific questions you can ask them separately.


How to decide which recommender to ask for LOR?

Go with the supervisor from your job.  The schools will have your transcript.  Unless there's something special the adviser can write, this is a no brainer from my point of view.

An example of a case where there is something special the academic adviser could offer would be if you have any warts in your transcript that you think your academic adviser can help you explain by way of the letter


How to check and correct editorial changes to a manuscript post-acceptance?

I've run into bad editing situations like this. In these cases, I've gone through the paper line by line, with a fine tooth comb. Yes, it is painful, but it is a  good idea even if the journal editors aren't obviously screwing up. (This can get doubly horrible if you have complicated formatting in your paper.)
You should bear in mind whoever is doing this is unlikely to actually understand what you are writing, and my experience of people doing this sort of thing is that they can be well-meaning and not too bright, so they can take it upon themselves to "correct" your manuscript, while not understanding what they are doing. Additionally, if you give them last minute changes to the paper, make sure to check they have applied them correctly. Are you the sole author? Can you get anyone else to help with this? It would make it less awful.

Your other ideas sound less viable. Asking for a list of changes assumes that there is someone there who actually knows what those changes are. My experience is that journal staff are often amazingly technically incompetent, and probably have never thought of using version control for example. though I'd love to hear about the exceptions. But you can certainly try to insist.

Your passive-aggressive ideas just sound bad. You don't want to withdraw your paper over an issue like that. And if there are errors in the paper, they will reflect badly on you, and nobody else will care.

At times I've thought someone should start a site like ratethisjournal.org where people could discuss their experiences dealing with different journals.


As an undergrad student, how should I ask a professor for an opportunity to do research with them?

Absolutely, with no qualifications, approach the researcher and ask what it would take to do research in his/her lab. As a first-year undergraduate student, it's very likely that you don't have the knowledge to contribute to the projects. So approach humbly, asking what you can do to prepare yourself. Ask for suggestions for a review paper or a few research reports that would bring you up to speed. Ask if you can attend lab meetings as a fly-on-the-wall to absorb the controversies and decisions being made day-by-day. The very worst possible case is that you're told, "no." If so, you're already there. Next worst is that you invest your time and get only an education out of it. That's not so bad. You'll be positioned very very well for next year.

Good luck!


How many graduate-level courses should one take to maximize chances of getting into graduate school? (PhD)

Graduate-level courses are helpful, but there isn't any magic formula that "X courses with a grade of A or A- will guarantee admission." Every case is different, and good grades are by no means sufficient for admission, if your letters of recommendation are weak.

If you're applying for a terminal master's program that is primarily coursework, then the rules are different, but for anything relying on research, your research experience and letters of recommendation will carry significant more weight than your classwork and test scores. What doing well in the graduate courses does is signify that you will be able to handle the coursework in your program, but it does not shed light on the rest of your abilities.

So my recommendation is to take graduate classes because you're interested in the subject and want to learn more about it, rather than just to impress an admissions committee.


How to handle unprofessionalism in academia?

In my limited experience this is the BS many have to deal with in academia, which is the main reason why doing a PhD made me change my mind about working in academia.

Universities are a place where bureaucracy thrives, however this can be to your advantage, when it comes to complaints procedures, which are taken very seriously (usually).

Find out the university's official complaint procedure (usually two stages, first stage is dealt by the school and if issues continue you may raise it to university level, at which point the supervisor, if at fault, will be dealt with in a biblical format ;).)

Make an official complaint, provide all of the evidence required (including emails unanswered), and it should be dealt with withing a couple of months.


Can I research and publish in my Masters field when my PhD is in an unrelated field?

If you can perform some research and write it up with the result that a journal wants to publish it, then it doesn't matter what qualifications you have, if any at all! Many journals do blind reviews which means their reviewers don't know the qualifications of any of the papers they review.


Should I talk about my poor academic performance due to financial situation in my SOP?

With a low GPA, your chances are already quite slim. You need a way to explain it. But it is even more important that you can explain why the institution can expect that you will be a success in the future. Your poor background doesn't help with this, no matter the reason. If your situation can be expected to continue, then it will be especially difficult to convince anyone that your outcomes will be different.

You have to make a case for the future, primarily.


How do I convince a colleague that plagiarism in a grant proposal is bad?

It seems that you have already tried to convince him, and it has been unsuccessful. I don't know what else you can do to convince him.
I would say that if I found plagiarism in any part of the work, the entire work, as well as the authors become suspect. It would very likely be automatically rejected.
My advice to you, is to stop working with him or, if you continue, to make sure your name is not affiliated at all with those proposals.


How to find all of the responses to a published research paper?

First, it may depend on your field, but at least in mine (physics and chemistry), it is rare for papers to generate comments or replies, and really extraordinary for a paper to be followed by multiple comments. (The editor usually lets the original authors reply to the comment, however.)

Some publishers provide links to the comments and replies on the webpage for the original paper. Otherwise, you can locate those comments using the following criteria:

they are published in the same journal, or in a preprint server (like arxiv)
their title includes “comment on” or “reply to” (or other such publisher-dependent prefix that you need to identify)

Finally, you should get the list of all newer papers citing the original paper, and check them out. If you're investigating a paper in depth, you’ll do that anyway :)


My master thesis supervisor refused to recommend me for a PhD

From what you've written, it sounds like your adviser doesn't think you know enough to be able to research a subject. Knowledge can always be learned. It's actually a very important trait for a PhD student to be able to sit down and learn what they need on their own.

There's no reason not to apply to PhD programs. It's going to be very hard to get into one without a letter from your adviser, but it's not theoretically impossible. The worst thing that can happen is that you spent some time and money and fail to get accepted anywhere. The best thing that can happen is that you get into a program and have the chance to follow your passion.

On advice from Pete L. Clark, I'm adding a caveat: You should be careful as to what sort of programs you're applying to and think carefully about whether those programs will lead to your desired outcome. Going into a PhD program is not something to be taken lightly. It will takes years of your life and be a potential drain on you mentally, emotionally, and economically. To land a decent academic position you need to graduate from  a top program and produce high level research. Afterwards you may have to put in more time and effort as a post-doc. Once you do finally get a position, you'll have to work your way through the tenure process.


What is the difference between aims and objectives in a research proposal?

This shows up generally in the English language, I've seen the exact same discussion in writing constitutions for not for profits, and similar answer applies.

Consider the context of a military plan:

Aim: Secure the northern boarder.
Objective: Increase garrison strength to 150 men
Objective: Assassinate the neighboring warlord: McBaddie
Objective: Rebuild border wall

Your aim is "What do we overall want" -- the what,
your objective is "What will do to achieve it" -- the how.
Once all your objectives are complete, then you should have thus completed the aim.
Objectives are also "whats" and so can be the "aims" for subobjectives.
Eg

Objective: Increase garrison strength to 150 men
SubObjective: increase recuiting in cities X,Y,Z
SubObjective: Decrease training times of recuits by increasing hours of training per day by 25%.

So for a research proposal:
say you are in the area of Sports science/mechanical engineering, working on bicycle design.

Aim: to produce the most efficient bycycle in terms of cadence to power ratio.
Objective: Develop a sensor accurately measure power that can fit into a pedal casing
Objective: Determine normal cadence rate for cyclists, and the level they can be trained to vary it.
Objective: Determine the most effective material to build gear systems out of.


Receiving a bad grade from close professor?

It is true that a good grade is worthy (every student wants a nice grade). However, it is not uncommon to score somehow “poorly” while you expect the best result. So, if your results are contrary to your expectations and if you have reason to believe that what you earned is not what you deserve (in the sense of your achievements in exams, presentations, written reports, etc), you may need to take some course of action as per your university’s rules and regulations.

I think, a useful first step would be to ask your professor to show you how you have been graded and what you did right and what you did wrong. That would also be a good opportunity to learn from your mistakes (if any). You may also have the opportunity to discover if there were any mistakes on the side of your professor in evaluating (correcting) your report. After talking to your professor, if you are convinced that the grade you got is what you deserve, then you have to accept that and learn from  the things you didn’t do well. If, with your discussion with the professor, you find out things necessitating revision of your marks (re-grading), that would be accomplished as per your university’s rule. If you still cannot resolve the issue after discussing with your professor, you may follow your university’s formal appealing procedures. But when you do so, have a convincing reason for why you are questioning your  grade. How much time you have devoted on the work or the fact that you need a good grade to pursue a PhD, I think, are not reasons strong enough to justify appealing. What is it that you correctly did but for which did not earn the deserved mark? Such things should be at hand. (I feel many things vary from university to university, but this is what I think you could consider).


Can a poorly done second degree ruin one's academic record?

Yes.

I think it is pretty obvious that if you provide the transcript for your second degree, a poor performance harms your chances.  This provides relevant information about your academic ability and/or work ethic, which a graduate program would consider.  It might even be weighed more heavily than your first degree, since it is more recent (and in a relevant subject to your planned masters').

So the question becomes can you just not tell graduate programs about your second degree?  I don't think this is a viable option.  A graduate program will expect you to submit information about all previous studies.  Not submitting a transcript for a second batchelor's degree will most likely be breaking their rules.  You would likely have to be deceptive in any application, interviews, and discussions with the potential graduate institution.  I think this is just wrong, but even if you don't have any moral qualms about it, you are placing yourself in a very bad position.  There is a chance you could get away with it, but you also might get caught, and that would have serious consequences.


Is it okay to keep on updating a published paper online?

Is it a good idea to upload a version of the survey on Arxiv and keep on updating it?

It's worth doing if you have the time and energy, but it's unconventional.  There are some continuously updated survey papers (such as the dynamic surveys in the Electronic Journal of Combinatorics), but the usual expectation is that a survey represents a snapshot in time.  As a career matter, writing a second survey on recent results a few years later may get you more attention and credit than updating your original survey.  Continuous updates can be especially useful if they are timely and the field is particularly hot, but they have their own limitations in a rapidly developing field (the original organization may weigh you down if you stick too closely to it).

From my perspective, the trickiest aspect is what to tell people.  If you silently update the paper, it won't attract as many readers as announcing that everyone should check back for periodic updates.  (And the whole purpose is to inform the community, so getting readers is important.)  On the other hand, it's difficult to commit to regular updates, and it's nice to avoid issues such as whether other authors should be unhappy that their latest results haven't made it into the survey yet.

  In that case, should the Arxiv version contain a note that an earlier version was published in so-and-so journal?

If you update the arXiv version of a paper after publication, it's critically important to be clear about how it relates with the published version.  Otherwise you risk confusing and upsetting your readers.

I would recommend against removing anything from the survey over time.  It would still be accessible via past versions on the arXiv for those who know to look there, but it's annoying to send a student to learn about X in Arani's survey and have them report back that it's not covered.


Is there any research on applying Agile/Extreme/Lean methods in academic research?

The paper Adapting Scrum to Managing a Research Group by Michael Hicks and Jeffrey S. Foster, describes the experiences of adapting Scrum to running a research group.

For those who don't know about Scrum, wikipedia has the following:

  Scrum is an iterative and incremental Agile software development
  framework for managing software projects and product or application
  development. Its focus is on "a flexible, holistic product development
  strategy where a development team works as a unit to reach a common
  goal" as opposed to a "traditional, sequential approach". Scrum
  enables the creation of self-organizing teams by encouraging
  co-location of all team members, and verbal communication among all
  team members and disciplines in the project.

  A key principle of Scrum is its recognition that during a project the
  customers can change their minds about what they want and need (often
  called requirements churn), and that unpredicted challenges cannot be
  easily addressed in a traditional predictive or planned manner. As
  such, Scrum adopts an empirical approach—accepting that the problem
  cannot be fully understood or defined, focusing instead on maximizing
  the team's ability to deliver quickly and respond to emerging
  requirements.

Scrum is built around the idea of a sprint, a short burst of activity. Again, from wikipedia:

  A sprint (or iteration) is the basic unit of development in Scrum. The
  sprint is a "timeboxed" effort; that is, it is restricted to a
  specific duration. The duration is fixed in advance for each
  sprint and is normally between one week and one month, although two
  weeks is typical.

  Each sprint is started by a planning meeting, where the tasks for the
  sprint are identified and an estimated commitment for the sprint goal
  is made, and ended by a sprint review-and-retrospective meeting,
  where the progress is reviewed and lessons for the next sprint are
  identified.

  Scrum emphasizes working product at the end of the Sprint that is
  really "done"; in the case of software, this means a system that is
  integrated, fully tested, end-user documented, and potentially
  shippable.

The emphasis is thus on highly dynamic, short cycles of work, and interaction between the team
members and the customer to get the right product delivered by rapidly ensuring that the development team is on target.

Now, returning to the paper: it  advocates 2 or 3 short meeting per week with the entire research group, rather than infrequent meetings between supervisors and PhD students. In these meetings goals, progress and achievements are reported on frequently. One outcome is that it helped quickly identify when a student was off-track, unmotivated or stuck.

I used the technique for my research group for a while. It was good for the various members to learn about what the others were doing, but as everyone was doing quite different things, in the end it didn't create any synergies I'd hoped for. Now that I am in a different institution and the new research group works on topics that are closer together, I think it could work, but we've decided to use a different approach to our research meetings.


Fifth year of my PhD and I hate my project. What should I do?

DISCLAIMER

I serve as a mental health 1st aid officer at my school. I received basic mental health training but I AM NOT A PSYCHOLOGIST. During this role, I have assisted many PhD students going through the same dilemma.

PROBLEM

I totally sympathise with you. One thing to consider, however, is whether you are feeling stressed and overwhelmed. PhD is a long and tough journey. The more you know the more you know you don't know. This is normal. This is OK. During a journey, the candidate suffers a lot, and many teeny tiny triggers can accumulate very quickly into pushing any PhD student over the edge. Some personal issues do contribute to the stress as well. Writing anxiety, home sickness, work-life balance and upsetting news overhyped in the media are all factors that can manifest into feeling insignificant and depressed.

I noticed you are working in mechanical engineering (last year). A common case I witnessed with engineers, is that they enjoy the technical work more than anything else (a.k.a writing). Building cool stuff or writing a fascinating and concise piece of computer software is just euphoric. There is a chance that you experience these feelings because writing is due. There is also a chance that you feel the thesis is sub-standard because you wanted to go back and build new cool things. Basically, you need your euphoric fix.

ADVICE

My advice to you is not to rush. Buy yourself some time to figure out what the root cause is. You can consult a therapist or a life coach (you should have access to this service via your university). There are few steps to rewire your behaviour into accommodating the current inconvenience until you finish.

Take some time off (1 week would do). Just treat yourself in doing what you love. No work stuff. Play video games, travel, read poetry, etc. Whatever makes you happy.
Do not feel guilty for wasting a week not working and do not let anyone to make you feel guilty about it. You needed this time off. The project needed you to take this time off.
Go back to your thesis with a fresh attitude (not feeling guilty or late).
If you are experiencing the same feelings and still thinking about quitting. List the cool research or engineering ideas you would rather do instead of working on that project you hate. Pick one that takes N days and do it (don't work on weekends). Maybe you just need that euphoric fix. Set N=4.
Go back to your thesis again. If you still hate it, this time work on the project for at least 5-N days.
Repeat from 2 with N=N-1.

IMPORTANT THINGS TO NOTE

a. Your post-grad degree is just that. A degree. You have your entire life ahead of you after you finish.

b. The steps I listed above are from my supervision experience. While I consulted with a psychologist in designing these steps, they do work on case by case basis and are not scientifically tested. Think of these steps as a life hack.

c. If you feel like not getting from bed in the morning for two days in a row, seek medical help. It is probably nothing or just a dietary deficiency but you better check.

d. If you are an international student, explore the possibility that you may be feeling homesick. Do not get defensive or shy to admit it. It is real and it happens to almost everyone.

e. I am not advocating sticking in a program that does not work for you. There is no shame in quitting. However, if you are quitting I advise you to do it for the right reasons. Please be careful of the legal consequences, if any. Also please consider the career interruption period (5 years) on your CV.


What can be an exceptional record of teaching?

The following points would contribute to a good teaching record:

List of courses that someone has given. Note that this shows the quantity of teaching, but not the quality. Still, I would consider it the key part of someone's teaching record, and to some extent quality might improve with quantity in this case.
Undergraduate and graduate student theses that one has supervised. Some measure of teaching quality might be how well the theses were done (e.g. prizes/publications), even though this says more about the student than about the teacher.
Teaching evaluations from students. That's probably the best way to really assess the quality of teaching.
A formal teaching qualification and any teaching prizes will be a nice bonus, of course.


Trouble choosing an appropriate arXiv category for a paper

This question may be considered too specific for this site, but I'll try an answer anyway.

As someone who works in numerical linear algebra and has used M-matrices extensively, I think a submission with this topic would be welcome in math.NA. Math.RA would be my second choice, followed closely by Math.PR (probablity) which you haven't considered. One of the main results of your paper is an algorithm, and it must be an algorithm which is (at least partly) numerical in nature if it can recognize M-matrices. As you correctly note, M-matrices and algorithms involving them are a first-class citizen in numerical analysis, and they are featured in articles appearing in journals in the field. Even abstract properties of them would be on-topic, because their main use is (probably) going to be proving the properties of algorithms.

I must say that the arguments you list in favor of math.FA and math.RA seem quite vague to me; they would apply to almost all of numerical linear algebra. As for cs.DM, as I said earlier, your algorithm necessarily is not entirely discrete, so it seems less appropriate.

Anyway, you probably won't go wrong with any of NA, RA or PR. Arxiv's categories have some overlap. As Pieter Naaijkens's answer suggests, you may get slightly more visibility from the people in your field if you go for NA.


Over the course of learning (i.e. your life) you learn strategies for problem solving. When you encounter a new problem you go through your known strategies to find a solution. If one occurs to you, fine. If it doesn't, perhaps a reasonable modification of one of your strategies will work. But if that doesn't get you home then you need help. So ask.

But you will do better if you do two things. Don't ask for the answer, but, instead, for insight into how to find the answer. And then, incorporate what you learn into an expanded set of strategies.

In programming, many of the strategies are well known. Testing, edge cases, etc. In other fields there may also be well known strategies. Quite a lot of education is to expose students to these various ways of looking at problems.

But in general, it is better to ask than to thrash. And there is no reason why it shouldn't be the teacher he or she may actually be the best person to give you the minimal hint that lets you get yourself over the block. Other people are more likely to just give you an answer that will advance your thinking power much less.


Is it okay to ask a professor what they expect in a grad student for a research assistantship position?

You should definitely ask him. But at the same time let him know that you have gone through his course details online. In your conversation with him ensure that you are not asking anything which is readily available on the university website. In other words, you should reflect in your actions that you are sincere about your queries and not wasting his time.
You should definitely ask the previous students. You can glean from their experiences to find out if this position is suitable for you.


At this level of generality, I think all one can say is the following:

Look for programs that do not have a GRE as part of their admission requirements.
For departments that do require it: if you have some specific reason for being unable to take the GRE, or for not having scores that meet their criteria, contact someone at the department and ask how to proceed.  (Admissions information normally includes the email address of a contact person.)  In many cases, you will include some explanation in your cover letter or statement of purpose.
If a department requires the GRE, and you don't have a compelling reason for not taking it, or for doing poorly: don't apply to that department.


Can I scan data from a paper for my own research?

It might be helpful to consult some legal assistant at your university, because there is a bad relationship between our group and their group, so if they are really determined, they might want to make problems, so it would be good to have a backup plan, or just be sure that you are really not breaking any laws, and that your party will stand by your side in case things from the other group's side become dirty. (This is an awful situation, though.)

But that aside, the line of reasoning is quite straightforward: anything one publishes becomes publicly available and viable for research by others. I understand that they didn't publish a table with numerical data, but if you think that recreating it from a plot is methodologically fine, then in your paper you should just describe the method and of course give credit to the source.


Can you reject a postdoc offer after the PI has paid a large sum for flights/accommodation for your visit?

It sounds like you are in the interview phase with no stated commitment in the form of having accepted an offer. Having your travel expenses reimbursed for an interview is not in any way a commitment to accept a position should it be offered. This is a completely normal expense that's part of finding good candidates. It is not expected that everyone they offer a job to will accept.

As long as you approach the interview in good faith, meaning that you haven't already accepted a job elsewhere, and that there is some reasonable non-zero probability that you'd take the job if offered, you shouldn't feel bad about having your interview expenses covered because of the possibility you might not wind up there.