Is it possible to withdraw a conference paper after the rebuttal period?

I suggest that you write to the chair of the program committee, explaining that (1) you agree with the reviewers about what was missing from your paper, (2) you've revised the paper to correct the problem, (3) you realize (or at least believe) that it's too late to modify your submission to this conference, (4) you would therefore like to submit the the revised version elsewhere, and (5) you would therefore like to withdraw your submission to this conference.  I would expect a reasonable program chair to let you withdraw the paper; after all, the conference gains nothing by forcing you to wait for an official rejection.

I'd also suggest mentioning that you're grateful to the reviewers for pointing out the problem.


Which articles don't need experimental results?

In all the work you are giving as examples, you are essentially developing methods. Not giving any experimental or very strong theoretical evidence that those methods do what they are supposed to do has many negative effects:

It strongly diminishes the value of your work to the extent that you may have trouble publishing work that you could otherwise publish it in a high-ranking journal. Peer reviewers may very well demand that you report on the results of applying your method to some data and may reject your paper if you have no very good arguments for not doing so.

Publishing methods without giving such evidence is the exception and usually only done, if deriving and explaining the method makes for a whole paper and applying the method is done in a follow-up paper or if the method paper and the experimental paper are better published in separate journals. And even then, there is usally some short application to (often artificial) example data in the method paper.
It makes it much less likely that people ever use your work, build upon it or cite you. If I read a paper in which the author proposes a method but fails to show any application, I would strongly suspect that this is because they can’t, which in turn hints at something being very wrong with the method. I would be very skeptical about such a method and would be much less likely to use it.
It will be harder to get funding for your work or justify that you spent your funding well.
Whether you publish it or not, applying methods is one of the best ways to learn what demands and problems occur in reality, which allows you to develop better methods.
If you repeatedly do something like this, you may obtain a bad reputation due to the above.

How bad all this is, eventually depends on your field’s openness to theoretical work and how difficult its is to apply the methods and properly evaluate them. But as far as I can tell from my limited insight into the computer-science literature, I would consider the impact to be rather strong in your case.

Given the nature of your work, I expect it to be impossible to provide convincing theoretical evidence that your methods work. For example languages are notorious for exhibiting weird behaviour and having tons of exceptions. Thus only by applying your method can you demonstrate that your it isn’t rendered useless by peculiarities or special cases you did not account for.

So, to sum it up: Yes, it may be possible to publish your methods without experimental evidence that they work, but I would strongly advise against it.

If you strongly despise experimental work, I suggest that you team up with somebody who does this work for you.


The first part of your question suggests that you want to find resources on how to find jobs in Asia. That's easy. Googling "Academic Positions Asia" found me this website (www.unijiobs.asia), (on the first hit) which claims to be "Asia's University Jobs Portal."

This seems to be what you are looking for. The site seems to have a fairly comprehensive set of search tools, with the ability to do keyword searching or to search by position type, by discipline, or by location.

The end of your question suggests that you really want to find people to fill positions that you have. Listing on sites like I just found and like what you found will help, but in general, you need to advertise. The best advertising is to be had in the publications or on the website(s) of the professional organization(s) relevant to your discipline.


Motivating myself to continue being a very good student?

Here's just an outside impression. It doesn't look good to me that your motivation, your love for your subject, is affected by the fact that most students around you are weaker. Actually this is a situation in which "the best" regularly are, just by being the best. And if they are really the best, it will not drag them down. Why do you even care whether some others who are not as good as you also can graduate? You have stated that actually there are students and lecturers from whom you can learn, so stick to them.
I think you should not assign responsibility for your lack of motivation to fellow students or your institution. You have to ask yourself seriously whether what you do is right for you, and if it is, how you can change in order to keep your motivation up. (Of course it may be true that there are better universities and top groups, but if you are really cut out for doing something good in the field, you should be able and motivated to start doing that as long as you are still in the place you are.)


Working with a professor who does both mainstream and non-mainstream physics research

A well-established researcher usually has multiple research programs that are loosely united under one common theme. As such, they will have different reputations in different circles of academic research. A professor, for example, may be well-regarded in computational chemistry, but his work in biological modeling may receive little attention. Since a researcher in computational chemistry will probably not follow the literature in biological modeling very closely, the computational chemistry community may actually know little about the said professor's work in biology. Thus, to answer your question, how you will be judged depends on which of the professor's research program you are associated with. If you are really concerned, then you can simply stay away from the non-mainstream research that the professor is working on.

With that being said, I want to push back a little bit on the assumption of your question. It is sometimes joked that the sign of senility in a biologist is that s/he starts to work on the problem of human consciousness, which for a long time was not regarded as proper research subject in biology or psychology. But if the "non-mainstream" research that you are referring to is not downright unscientific, your concern may not be well-founded. Sure, as a young scientist it is not wise to work on unpopular subjects, but the popularity of a subject and the fad associated with it is not always correlated with the soundness of an area of inquiry. Sometimes good science is just not popular (such as Mendel's work that laid the foundation of classical genetic analysis).


On understanding the "code" of recommendation letters

I am writing from the perspective of mathematics in the United States.

To the best of my knowledge there is not really any "code" for recommendation letters.  However, there is a quite large amount of inflation, enough so that writing without an awareness of the current levels is a bit like Dr. Evil holding the world ransom for one million dollars.

The process abets this inflation in many ways.  Many grad school recommendations have a bunch of questions asking for the candidate to be numerically rated on a bunch of different metrics -- including things like "honesty", "integrity" and "leadership" -- and you can say things like "The best I have ever seen," "In the top 2%," "In the top 5%", and so forth.  It's more than a bit silly, but having both written the letters and read them I can say that most successful candidates are getting top or nearly top marks in every category...no matter the fact that in most interactions with students, things like honesty and integrity are more conspicuous in their absence than their presence.

To get a sense of the inflationary regime it is very helpful to compare letters written by (many) Europeans to letters written by (most) Americans.  Recently someone whom I have a substantial professional relationship with applied for a postdoc at my institution, and afterwards (he didn't get it, but he got a good one elsewhere) he asked for feedback.  I told him that one of his letters was essentially only one paragraph long (and I told him which one!).  That paragraph was uniformly positive, and I can't point to any specific, factual thing that was missing from it.  However, at the current state of inflation, most letters are two to four pages long.  A one paragraph letter just won't do.  It is not necessarily code for "the candidate sucks".  It might also mean: "I am too busy/selfish to write the letter that I know the candidate needs", "I am not familiar enough with the current state of inflation to write an appropriate letter" or even "In my part of the academic world no one natters on for pages at a time; is it different in yours? What's wrong with you people?!?" In this case, I would suspect the latter.

Added: Inspired by some remarks in @David's answer, let me mention that there are certainly things that will be read in ways that may not be what a naive writer would intend.  I wouldn't call this "code," but others might.  Some examples:

A good letter must explicitly mention that the candidate is both intelligent and talented.  In the absence of this, any other praise may be read as a nice way of saying that the candidate is not intelligent and talented.  Saying that someone is a hard worker without saying they are bright will be read be many as meaning that they are only a hard worker.
Praising someone's teaching must be done carefully, lest it sound like you mean to say that the candidate does not take their research seriously or even does not intend to further pursue their research at all.
Female candidates are often praised for being team players while male candidates are often praised for being brilliant, individualistic and perhaps even iconoclastic.  You should keep this in mind when writing and reading letters for female candidates.  When describing a strong female candidate I make a conscious effort to use the "good male words" like brilliant, gifted and so forth...and also to back them up, of course.


Dealing with potentially bad response from supervisor upon leaving with MSc for different PhD program

This is all opinion, so it is only worth what you pay for it, of course. But I would first consider how long it will take you to finish your current degree. It is pretty miserable being miserable for three more years, but if it can be done in a year then it might be best to just tough it out.

There is no reason, in principle, why you can't change fields later, either gradually, from a paid position, or abruptly. If the fields are different enough you may need credentials there, of course.

If you do complete the doctorate, then your old advisor's opinion about switching won't be of concern, only his/her opinion about the quality of your work.

However, another alternative, if you have picked out a different university, is to quietly explore with them the possibility of switching. If you can find a compatible potential supervisor there, the current situation may not be a detriment to switching. Personal contact is probably best here as it enables you to make judgements about how much to reveal about the current dilemma.

But if completion is a long way off, then quality of life would seem important enough to make a break, even if not all of the consequences are positive. But only you can balance the forces.


Should PhD students pay out of pocket for their PhD expenses?

"Should" is a hard word here. I certainly never paid for these things, but my supervisor was well funded, and so I didn't have to worry about it. At the other end, I think a student certainly "can" pay for these things out of their own pocket. My recommendation for travel would be to avoid this by pursuing departmental, university, and conference-specific travel funds.

I can't imagine it being reasonable for a student to purchase lab equipment. It's often expected that you'll have your own laptop, but workstations, servers, and compute clusters should be provided by someone else. Same for microscopes, reagents, glassware, and everything in between.


What is expected in a masters thesis for Phd admission in Europe by admission committee in Number Theory

From a Finnish perspective (the department was focused on analysis, not number theory):

No, it is not expected for you to have original publications from your master studies, but if you have them, great! I am not sure how a publication in a predatory or very low quality journal would be taken; in the spirit of being careful, I suggest not publishing unless you are certain it is a decent result and a decent journal. Or maybe only publish a preprint.
A good master's thesis need not include original research, but it might. It shows a clear grasp of mathematical thinking and good and non-trivial proofs. An excellent thesis has original work, or does the same as a good one in a very demanding subject.


Start immediately, accept as late as possible when you are happy. If another offer comes in while you are negotiating, that's fine. You can work on negotiating that, too. You may even have to tell the first school that you are negotiating with the second school and vice versa. There's no point in delaying the negotiations, just the acceptance. Of course, as soon as you accept an offer (and it's confirmed), you should immediately withdraw all other pending applications.


Adding a citation after paper is accepted

Of course it's ok. Even if the paper is accepted, but some minor corrections are required (I guess the reviewer noted that after these corrections the paper can be accepted without sending the revised manuscript to them again), your work on it has not not yet finished, and you are free to make modifications that you consider appropriate - not only those that the referee asked for. So if you found something that the reviewers didn't ask for, but adding it to the text improves the quality/completeness/etc. of the paper, you definitely should do it.

Talking in general: in the meanwhile you could obtain some new data, could perform the experiments on different equipment, apply another method to confirm/strenghten the results, or some of your colleagues pointed out you have some minor error or that some part is unclear, or you found some other relevant works that you want to compare your results to - all of this can be done even in such an almost-accepted stage.

Finally, it could also happen that you'd need to add some extra sentence to keep your overall style consistent after the requested corrections, or to make a more natural transition between two parts of the text; this would also be perfectly fine, even if - strictly speaking - that's not precisely what the referee asked for.

Overall - aim at the highest quality of the article that you can achieve at the moment.


When citing an arXiv paper, what year should one write?

I would cite the exact version you are referring to in your work. Therefore the year should be the year of that version. You should also use the actual arxiv identifier in the citation. This is to minimise the effect of potential changes in the cited work on your paper. Moreover, your goal is to provide the reader with a precise pointer to the cited work so that they can easily find it.


Can I write a template just like the Elsevier LaTeX template?

If you check it on Elsevier web page, it clearly states that modification of the manuscript template is totally ok and they provided the download  link.

On the other hand, there are also some other templates that are specific to a journal that is stated to be ethical if you ask the editors' permission.

Check the page out to get more instructions and useful information.


Sharing assignments with a potential employer

I don't think you need to worry about school policy or copyright here: you're privately sharing these documents in order to allow somebody to better evaluate you, not attempting to transfer ownership or widely distributing them.

As such, the question of who owns the code is irrelevant: you are not claiming ownership, you are claiming that the portions you wrote provide evidence of your skills as a programmer.  The company should be expected to treat it as a confidential part of your application process, just like all of the other personal information that you have given them.  If they do not, any possible fault and liability lies with them, not with you.


Benefits of being a guest editor of a journal?

Disciplines are typically organized in loose groups around a fairly small number of persons. They organize conferences, are editors, are on boards of professional organizations, etc. They are always looking for the next generation, new researchers who could take over when they retire. Being a guest editor for a journal, organize a workshop, chair a session, etc. signals that you might be the next generation. Having a reputation of being the next generation won't hurt when you aply for your next job. It is also good practice for when you become a regular editor.


How do I recommend a student requiring extended deadlines?

You were already required to evaluate this student's work under the assumption that they performed under the same circumstances as everyone else, so why suddenly stop doing so at a recommendation letter?

That said, this quickly becomes a legal matter, and we have few true legal experts (for any jurisdiction) on this site.  I'm certainly not one of them, but here's my opinion and understanding...

The companies are not allowed to discriminate based on disabilities, and are required to make "reasonable accommodations" for them.  As such you can reasonably assume that whatever job is being applied for will already have this in effect, and that the disability is therefore irrelevant.

If, for some reason, the student is hiding their disability from potential employers—or, worse, had been faking it with the University—, then that is their responsibility, and the responsibilities of whatever (medical) professionals were involved in the evaluation, not yours.

If you remain in doubt—it would not be unreasonable to be confused on whether certain things you know about the student fall under "protected disability concerns" versus "legitimate, non-protected concerns"—, contact the very office that handles these disability arrangements, and possibly arrange to have a meeting where you can discuss these matters at length.  They should be able to provide you with guidance on how to faithfully execute your duties vis a vis recommendations while remaining in compliance.  You can even contact a lawyer for yourself, though you will likely have to pay for this.  The disabilities office will be inclined to advise you to act in whatever is most convenient for them and the university, which may be more strict than is legally required and enforceable, but in a case like this I would suggest you follow that because of:

The golden rule of writing a recommendation letter is: if you feel you cannot write a good recommendation letter for the student then reject their request to write one, and if you feel you cannot write a strong one then tell them so, so that they can decide if that is acceptable or not.

If you feel that these will automatically apply to you with respect to students with disabilities, you may want to (preemptively) arrange to speak with someone in the disabilities office, or a personal lawyer (this may be more strongly advisable in this situation), about writing letters for students with disabilities.  This would be to head off any potential concerns about you acting discriminatingly towards such students.


Is it unwise to repeat portions of a successful grant proposal?

Ask the program officer (PO), because he/she will be able to back you up if the permission comes from him/her, should the reviewers criticize so.

However, slightly recast your question. For instance, ask if the proposal will be reviewed with your previous proposal side by side or by the same reviewers. Tell the PO that you ask because you intended to frame the background with some similar information you presented in the last version, but worried that it would create redundancy. And emphasize that you will be more than happy to transfer the background to the continual application if that would make the application process smoother.

In the mean time, evaluate the magnitude of the intended cutting and pasting and what information is being transferred. Historical findings are unlikely to change and can understandably be worded similarly; but if what you want to paste were things that you would set off to explain/learn, and after three years the unknowns remain, then it probably will not go too well. Also, critically review the literature. If the parts to be cut and pasted are more contemporary literature review, it's hard to believe nothing can be added in three years. Anyway, don't use them just because you don't have time to revise the background and the last one seems still pretty good.


This sounds like an incredible botch-up, to the degree that it has me seriously questioning whether the journal you submitted to is the one that you believe it is.

Most reputable journals now use paper-handling and review systems that are highly automated, such that it would be extremely difficult to get a paper attached to the wrong reviews (like, beyond incompetence and into active interference with the systems). One reviewer sending in the wrong review I can see---two that are clearly referring to the same wrong paper is unlikely to happen unless something much deeper has gone wrong.

At this point, the appropriate course of action is not dealing with this handling editor any more, but escalating to the editor(s) in chief (EIC).  They should be responsive and able to sort this out quickly.

If you do not get a satisfactory response out of the journal leadership within a week, I would start to wonder whether you are really dealing with the journal that you think that you are. The behavior that you are describing sounds more like that of a predatory publisher: sometimes journal websites are hijacked or reasonable people (like your colleague, assuming you trust them) are tricked into supporting predatory enterprises with names designed to sound almost identical to reputable ones.  It is also the case that journals, like any other organization, sometimes collapse and fail, and it is possible that you might be witnessing the last stand of a formerly respectable institution.

In any case, if you don't get a satisfactory response from the EIC within a week, I would suggest withdrawing your paper and sending it to a different and more trustworthy publication venue. But first, if your field allows it, publish a preprint somewhere like arXiv as a precaution against possible plagiarism or refusal to accept your withdrawal.


use of of 'unlicensed' github code in research paper

This topic is treated in this answer on Open Source Stack Exchange. I reproduce it here because it might also be relevant for Academia. The Open Source.SE answer points to GitHub's "No License" page:

If you find software that doesn’t have a license, that generally means you have no permission from the creators of the software to use, modify, or share the software. Although a code host such as GitHub may allow you to view and fork the code, this does not imply that you are permitted to use, modify, or share the software for any purpose.
Your options:

Ask the maintainers nicely to add a license. Unless the software includes strong indications to the contrary, lack of a license is probably an oversight. If the software is hosted on a site like GitHub, open an issue requesting a license and include a link to this site. If you’re bold and it’s fairly obvious what license is most appropriate, open a pull request to add a license – see “suggest this license” in the sidebar of the page for each license on this site (e.g., MIT).
Don’t use the software. Find or create an alternative that is under an open source license.
Negotiate a private license. Bring your lawyer.

Note in the second line that you do not even have permission to use the software. Unfortunately, this means that, in order to be safe, you should either wait for the developers to reply to you and add the license, or write your own code.


Is it appropriate to summarise and paraphrase complex reviewer comments before providing my answer?

It’s always better to quote the reviewers’ text directly. That way, there is no ambiguity as to what you’re responding to. (Moreover, many journals expect you to quote directly!) However, there is certainly no requirement that you must proceed step-by-step and quote everything in the reviewers’ responses exactly as presented. If something is mentioned multiple times, you could list the different references together, and provide one response for the group.


Found an error in a paper I presented at a student engineering conference. Should/can I talk about it in my MS applications?

Reading your background, it seems that everything about the work was correct except for a mistake in translating the algorithm from code to pseudocode.  Moreover, you've done your best at correcting the mistake.  Mistakes happen in science, and especially when it comes to the dread pseudocode (personally, that's why I always include actual executable code whenever I can).

From what you've presented, I think you have every reason to be proud of this work and none to be ashamed. Talk about the work in your applications.  Talk about the paper.  Talk about the experience in getting it corrected.  Anybody who you'd actually want to work for will see all of these as strengths and not weaknesses.


Should I justify an average GRE score with a good excuse?

I don’t think you need or should mention it.

First of all, 4/6 is not a bad score, even for a PhD application. Moreover, Writing is probably the least important section of the GRE test, at least for a physics major.

Second, the professors who review your application would expect to see other more meaningful indicators of your research potential, and thus, explaining why you don’t have a higher score will make you look petty. In fact, try not to talk about your Writing score because the reviewers might not care about it at all, unless you mention it.

After all, the rule of thumb is to focus on the strength of your application instead of explaining the weaknesses.


A confusing reply from potential supervisor

It's "standard" (depends on where you are applying to) for graduate students to be paid a stipend. The money comes either from the department or from the professor's own funds (this in turn is part of the reason why professors apply for grants - to hire students/postdocs).

The professor is asking you if you've applied for any external fellowships or scholarships because:

If you have, you've shown some knowledge of how academia works, and you've made some effort to secure funding for yourself.
If you were successful, you'd effectively be "free" - the professor doesn't need to use his/her own funds to pay for you.

It goes without saying that if you can say "yes I've applied", or even better "yes I've been awarded", it boosts your chances of the professor agreeing to take you on. Conversely, if the answer is no to both, it will definitely not help your application, and it's possible he cannot take you on if he doesn't have enough funding.


Should I inform my referee about my applying result even I get rejected?

You should tell them the result of your application. If the result happens to be negative, briefly tell them about your next step (e.g. will you apply to the same thing again in the future? what do you plan on doing until then?). They may even suggest a next step.

If you don't inform them of a negative result right away, they will find out if you eventually ask them for a second reference letter. Furthermore, since they explicitly asked you to tell them the result, it would be impolite to not.


Leaving postdoc after less than one year with no reference letter

I would apply to new postdocs using the professors at your former doctoral program as references. If there's someone at the postdoc school that you worked with and can speak positively, you could use one of them instead of one of your former profs, but I'd keep the ratio 2:1 or 3:1 in favor of your former professors.

The good thing is that you're in your first year of the postdoc. Sometimes there are just fit issues -- in terms of personalities or research topics or both. Everyone in academia is aware of this and we're aware it's not always the fault of the applicant -- especially when it comes to "big names" (== big egos). I think you could apply to new post docs referring very briefly and obliquely to fit -- and using the materials and references from your doctoral program.


How should I handle poor English in reviewing an article that claims to be proofread by two native English speakers?

You should not email Textcheck about the article. The journal review process should be confidential, and you should not take the liberty to violate it. You should put the quality of the writing in your review. If it's still bad even after review by this company, then those are the breaks. It sounds like it still needs some help.


Where to Address Issues With Bad Class Formats

TL;DR: you could write a letter to your program director. However, success may be elusive, since the situation may be constrained by forces outside of the control of you and your lecturers.

It is worth addressing. The official course evaluations are the appropriate place for this, so you have taken the right approach. However, depending on the situation at your university, it may be the case that nothing you can do will make an impact on the situation. This is because the situation may be forced upon the lecturers through circumstances beyond their and your control.

Consider the following example. I am the responsible lecturer for a data mining course at my university. Teaching is 30% of my job, with 50% dedicated to research and 20% to project management. I am teaching this course in the traditional format, which I would prefer to keep doing. Last year, 134 students followed my course, and I survived (with positive student evaluations). This year, 312 students showed up, and I am barely hanging on (with student evaluations pending). Purely trying to keep up with the barrage of student questions in my inbox is eating up all my time. If I keep the course format the way it was, there will be absolute zero time for me to fulfill the non-teaching 70% of my responsibilities.

At my university, I am forced to write a formal reply to the outcome of the official student course evaluation, explaining how I will address the comments in next year's edition of the course. Hence, these evaluations matter at least a little. However, if I decide to refer to videolectures instead of ever teaching a plenary lecture again, the following will happen. My student evaluation grade will go down. The extra time I free up by eschewing lecture preparation, I will dedicate to writing another grant proposal. If the proposal gets the funding I request, I will get tenure. If I don't get that funding but my student evaluation grade remains high, I might get tenure. My situation simply does not provide me with any incentives to keep students satisfied; in fact, if I were to keep students satisfied, I actively reduce my tenure probability.

If your lecturers have mixed responsibilities like I have, it may be the case that their job parameters are set up such that student evaluations are not relevant enough to them. If not, then your success still depends on what value your university attaches to course evaluations. No success is guaranteed.

So what can you do?

definitely keep filling out those course evaluations. This builds up to a paper trail of things being wrong in your programme at large, rather than being a problem of individual courses;
ensure that you get the education you desire. If the course doesn't provide you with the education, you should use your time at university to get it yourself. Form a study group with your friends, acquire the books or other materials to teach yourself the subject. It is of course far from ideal to have to do this yourself, but if your university does not develop your skill set, you can still develop your skill set. Acquiring this optional text book you talk about, for instance, is a good move;
if you have a set of coherent complaints, showing consistent shortcomings across multiple courses and lecturers, and these complaints are shared between a substantial number of students, bring the complaints to your program director, as a group. The program director should address problems with your program as a whole, that span beyond a single course.


How generous should I be with citations?

Even things that you aren't directly using may be quite relevant for establishing context.

The only thing that ever keeps me from being generous with citations is page limits.  Otherwise, any citation that fits well with the flow of the scientific narrative and helps place your work in the context of related work is good for everybody involved, and I see not reason not to err on the side of inclusion.


how can i know the journal still covered by Scopus ( include 2018 year )

To check if the journal is currently indexed in Scopus, follow these steps:
1- Go to https://www.scopus.com/sources
2- Search for your target journal by title
If you find no results, then the journal is not indexed by Scopus
If you find your target journal, click on it to see the coverage years; if the coverage years are from 2008 to 2018 taking into consideration that we are now in 2021, so the journal is already discontinued. If the coverage years are indexed till present, so the journal is currently indexed.
I have shared a copy of the title list of Scopus journals here (last update October 2020)
https://drive.google.com/file/d/146wsDZcQyFenVQGYcTHs_PiRNw9Z-otm/view?usp=sharing
Resources:
https://www.scopus.com/sources
https://blog.scopus.com/posts/titles-indexed-in-scopus-check-before-you-publish
https://www.rasayely.com/how-to-check-if-a-journal-is-indexed-in-scopus/
https://www.ilovephd.com/how-to-identify-isi-scopus-or-scimago-indexed-journals/


SPIE does require the multi-page abstract as far as I know - in fact, this is one of the reasons some of the groups I worked with don't publish there, because it's a lot of work for a paper that isn't in a formal journal.

The technical answer to your question is that your submission could be withdrawn if you don't submit the abstract, as per their guidelines:

Conditions of Acceptance

By submitting an abstract, I agree to the following conditions:

An author or coauthor (including keynote, invited, oral, and poster presenters) will:

• Register for the conefrence & pay the fee.
• Attend the meeting.
• Make the presentation as scheduled in the program.

• Submit a manuscript (6 pages minimum for LASE & OPTO; 4 pages minimum for BiOS; 20 pages maximum) for publication in the Proceedings of SPIE in the SPIE Digital Library.
...

However, your main question as to what really happens if you don't submit the abstract?  Here is my guess:
I have tried to access various presented papers on the SPIE online proceedings after the conference, only to find them missing the full 6-page abstract (only having the 1-paragraph abstract).  This implies that they do not retract/adversely alter your submission's status if you fail to turn in this full six page abstract. I don't have any better evidence than this though.  (These were not invited papers either, but usually papers from companies who may not have wanted to divulge too many details in a full 6-page abstract.) It's possible that they submitted the full paper after the conference and I just didn't check again later.

Also, if you've already published the work in another high-impact journal, then I'd have thought it would be pretty easy for you to put the 6-page abstract together, and it won't impact your future publication plans too much. You can include new material in your presentation but omit this from the 6-page paper to prevent jeopardizing future publication plans.

Lastly, in case you do want to include new material in the paper, sometimes journals will accept papers that have previously been submitted to conferences, with the understanding that much of the work has been published before but at lower quality and usually lower standards than the Journal. One often does more rigorous analysis, includes additional details and work (measurements or simulations) for the subsequent journal pub. I often find conference papers with accompanying higher-quality (often longer) journal papers by the same groups, on the same subject, but with additional info/rigor in the Journal paper.

Update:

I spoke to an SPIE rep at the conference, and he said that you can indeed submit "anything you want" (my words) in the submission, and that even if the paper was too short they wouldn't penalize you in any way.
He did say that if you did that all the time they may become concerned, but in general the page numbers were a "guideline", not something to have your presentation rejected over.


Is publishing in open access journal a good impression?

It depends entirely on the journal. There are good and bad open access journals, just as there are good and bad closed access journals.
For example, in biology Nature Communications, Cell Reports, eLife, PLoS Biology and Genome Biology are all open access journals with excellent reputations.
PLoS One, BMC genomics, PeerJ, Scientific Reports are open access journals that have a reputation (earned or not) of publishing work which is sound, but maybe less exciting.
And then there are various lower quality open access journals that people might be suspicious of.
This is no different from closed access journals.


Is it ok to give your Old Assignments to others?

There is no single right answer here. The answer depends from university to university, and even from faculty member to faculty member. For example, one professor in my department believes everything should be sharable, while another believes that it's wrong to share old materials.

So you'll need to see what the policy of the instructor teaching your friend's class is.


Can we use the same picture across multiple chapters of a thesis?

The reason why we have figure numbers (or for that matter, equation numbers) is to ensure that calling these numbered objects becomes easier, you can identify these things with their labels. In fact, if you keep pasting the figure over and over again, whenever it is needed in the text, you will unnecessarily lengthen your thesis, and confuse the reader, who will scroll back to the earlier instance to see what is the difference from what he/she saw there.

Simply identify it by the figure number, and refer to it as Fig. 1.1 (or whatever it is, more generically,

  Fig. \ref{figure_label}

if you are using LaTeX), in all later instances when you feel the need to call it. This befits clarity, conciseness and convention - all three of them.


What are the differences between these levels of study?

A Phd is a three or four year degree awarded following research and a thesis.
A Masters course is a taught postgraduate degree usually of one or two years duration.
A Masters thesis is a research degree of one or two years duration awarded following research and a thesis.
A Post-Graduate Diploma is usually two-thirds of a taught masters and is awarded to someone who did the examination component but did not complete a dissertation.
A Post-graduate Certificate is usually one-third of a taught masters and is awarded to someone who left after completing half of the course credits.

These terms would be used in areas based on the British University system, but all have analogues in the Bologna Process.


It is very hard.

A few years ago, a professor I had had told me that he advises students to aim to get a job at a school a tier or two below where they went to grad school, as a general rule. The reasoning is simply that there are far too few jobs. How many graduate students are in a cohort at Columbia? Now compare that to the number of new faculty they hire each year.

The math is straight forward: If every university hires one new faculty a year, that means that you need to be (on average) the best at your university to get a job at an equivalent institution. Most universities have more than 10 incoming graduate students. I don’t know how many new faculty top math universities hire on average, but I would be shocked if the answer was greater than 2.


How to get in a Master program in Applied Maths coming from a Physics Background

Because of your financial situation it sounds like you will need to either gain full time admission to a masters program that includes a scholarship offer

or

Attend part time while you work

Many admissions officers will not be familiar with the Brazilian grading system. In addition to enclosing your transcripts and cover letter, submit proof (if it is not already on your transcript) of your impressive class rank. Use your cover letter to further explain you academic history.

You may need to prove some of what you learned as an autodidact in order to demonstrate your preparedness for the graduate programs you apply to. Either produce research or find a relevant test that you can use to prove your knowledge. If there is not a standardized test relevant to any alleged deficiencies in your knowledge base (judging you based on transcripts) ask the school you are applying to for the right to take a final exam of a capstone bachelor level math course to help prove your knowledge base.

You will have to prove to the schools you are applying to what you learned as as autodidact. If you can do that you may be able to gain admission without the need to take more undergraduate coursework


Yes, this can be done in a number of ways:

In Google Scholar, you can set up an "alert" for citations of any paper that you're interested in.  Scholar is very broad in its collection of data, so this will include citations not just in peer reviewed journal articles but also citations in ArXiv preprints, theses, conference proceedings papers, and all sorts of "grey literature."  Google Scholar alerts are free.
In Thomson Reuter's "Web of Science", you can have saved searches that generate alerts that are emailed to you.  In comparison with Google Scholar, Web of Science indexes a much smaller set of publications, so the coverage is not as broad.  Furthermore, you (or your institution) need a subscription to the service.
Elsevier's Scopus database also offers alerts.


Should I mention my reference's university role (administrative) when listing?

The thing to remember here is that your reference letter writers will be providing official letters, and therefore will be including their full titles (presumably the letterhead will list this). In such a case, it doesn't really seem to make much sense to "hide" the status of the person writing the letter. Moreover, if the position is one which will include some administrative duties, a letter of reference from someone doing university administration might even be a plus.


What is the reason that once a student has passed a university course, the student cannot take the course again?

In the United States, institutions that have such a rule do so primarily because of the requirement of satisfactory academic progress, or SAP, that is imposed by some, perhaps many, forms of financial aid.  "Progress" means accruing the credit hours necessary to earn one's degree, and students who repeat courses for which they've already earned a satisfactory grade are not progressing (as fast) toward graduation.  Students who do that more than a couple of times may have a high GPA, but unsatisfactory academic progress, and may lose their financial aid.

Edited to add: Sadly, and to me astonishingly and dismayingly, the subtleties of how financial aid works seem to escape many students.  They overlook the SAP requirement entirely or decide they will somehow "catch up later."  In the United States, it is difficult or impossible to have different rules for similar groups of people, so we generally can't have one rule for students with financial aid and another for those without.  The result is that, even if it makes no difference to your financial situation, in many institutions you can't repeat a class in which you've earned a satisfactory grade.


Method/tactic to extracting information from articles

For your specific example (introductions), I generally need to get through lots and lots of papers to sum up the state of science on a topic, so I read the abstract and the conclusions to make this time-efficient. The abstract should have the main result of the paper with statistical values to back it up, while the conclusions should have statements about the implications of the study and calls for future research. If something doesn't seem right about either, one could investigate the meat of the paper to decide whether to throw it out or save it for reference. Then, I use a program like Endnote and keep notes for how I would cite the paper. This helps me cite while I write.

As a big disclaimer here, there are some papers that might be considered seminal or groundbreaking in a field... these should be read from beginning to end because they represent major advances or shifts in knowledge, approach, etc. That's my take!


Advantages of doing a research-based Masters (e.g an MRes) before the PhD:

learn research skills
explore your subject
refine your research question
get a big chunk of your literature review done in a structured setting
work out if taking a PhD is really for you - whether you've got the aptitude and the interest


Are mathematics REUs absolutely limited to undergraduates?

I quote from the NSF REU guideline (emphasis mine):

  Eligible Student Participants: Undergraduate student participants
  supported with NSF funds in either REU Supplements or REU Sites must
  be U.S. citizens, U.S. nationals, or permanent residents of the United
  States. An undergraduate student is a student who is enrolled in a
  degree program (part-time or full-time) leading to a baccalaureate or
  associate degree. Students who are transferring from one college or
  university to another and are enrolled at neither institution during
  the intervening summer may participate. High school graduates who have
  been accepted at an undergraduate institution but who have not yet
  started their undergraduate study are also eligible to participate.
  Students who have received their bachelor's degrees and are no longer
  enrolled as undergraduates are generally not eligible to participate.
  For REU Sites, a significant fraction of the student participants
  should come from outside the host institution or organization. Some
  NSF directorates encourage inclusion in the REU program of K-12
  teachers of science, technology, engineering, and mathematics. Please
  contact the appropriate disciplinary program officer for guidance.
  Within the framework of the basic eligibility guidelines outlined
  here, most REU Sites and Supplements further define recruitment and
  selection criteria, based on the nature of the particular research and
  other factors.

So this means that (a) your host will not be able to receive funding for you from the NSF if s/he accepts you into the program (b) on the other hand if you and/or the PI of the grant is able to secure funding otherwise, there's generally no rule saying that a student in your position cannot be involved in research in some way.

You will need to individually contact the REUs you are interested to find out whether they'd be willing to grant you the leeway.


Project management techniques applied to research

A number of things spring to mind.  The first is communication of goals and time lines, and I'd just point to Gantt and PERT charts.  Each has advantages and disadvantages, but the key is to make sure that everyone knows and understands what needs to be done, when it needs to be done by, and who is responsible for what.

The second is the amorphous management trees that come up in research environments.  A great discussion and treatment of this is in Project Management, by Heerkens -- https://www.amazon.com/Project-Management-Second-Briefcase-Books/dp/0071818480.  It doesn't  speak to research, but projects in general, and a project is a project.  I really like his treatment of the "accidental manager", where you find yourself in a position of responsibility managing people who you have no real control or influence over.


Forth year PhD student having trouble with his supervisor

Well, in CS I know many people using the same approach. It works well for some students, for others it is terrible.

One thing really went wrong: You wrote several papers which got rejected - this is something a supervisor should avoid by giving feedback beforehand. This feedback could have helped you finding your way in the scientific field. Did you involve your supervisor in the paper development process?

One thing is strange about your situation: You worked for four years right now, he is paying you and he wants you to finish. If you really did not achieve anything, I would have tried to get rid of you and hire someone else. So there might be something in your work you are not aware of at the moment. Or your supervisor is very lazy. Or he just trusts in people.

If you are hired to work on a specific project: Is this project related to your PhD? Or are you just working on your PhD topic?

I would suggest to really use the christmas break to

Build a mindmap of your field / your work. Indicate all items which are mandatory for your PhD.
Honestly try to figure out why your papers were not accepted. Try to figure out if you are having any chance to change thr source of the problem.
Build a work plan consisting of simple steps which will lead you to a "just-made-it"-PhD. You can improve it later on
If you feel you are lacking skills (e.g. programming, paper writing, ...), find a way to adress them. Train the skills. It's worth the effort.
...and take a break. It sounds like you need one...


On math papers and general questions they need to address

Yes you do have to answer these questions, and math papers do.  But you may not have noticed it as a non-mathematician, because math research is extremely specialized, and the broader picture will still be incomprehensible to you (or to most mathematicians).
Suppose I wanted to read Wiles's paper providing the final piece of the proof of Fermat's Last Theorem.  I would have to spend about 2 years of intense study to get to the point of being able to even understand what the basic theoretical constructs of the paper are, and I'm closer to this area of mathematics than 70% of mathematicians.
I might add, as is customary for more important papers, Wiles's paper pretty extensively addresses the bigger picture.  Less important papers will have a smaller, more specialized audience, and there is no need to explain the picture as broadly.
One does not choose research questions in math; one chooses research questions on Glauznov operators on Tchaikovsky cohomology of Rubenstein spaces (example completely made up using names of Russian composers).  Naturally, one explains the motivation for one's research for (the 10) other people working on Glauznov operators on Tchaikovsky cohomology of Rubenstein spaces, and the papers that introduced Glauznov operators, Tchaikovsky cohomology, and Rubenstein spaces all explained the motivations for these ideas.  If you think your paper is important, your introduction will also explain the implications of your work for the overall study of Tchaikovsky cohomology of Rubenstein spaces.
I've done a cursory look into the historical chain of ideas that leads to my research.  It's about 15 layers of theoretical constructs from something a non-mathematician might think about.  About 200 years ago, some mathematicians took a naive question and created a theoretical construct to help understand it.  They found some facts about this theoretical construct, and some other mathematicians created a further theoretical construct to understand these facts about the first theoretical construct.  Repeat about 15 times to get to my research.  (Take a different chain of about 25 layers of constructs to get to Wiles's proof of Fermat's Last Theorem.)


I've always used the following in ALL of the classes I teach:

What did you like most about quantitative basket weaving? [free text]
What would you most like to see changed for quantitative basket weaving? [free text]
How valuable do you feel your time has been in quantitative basket weaving? [1-10]
Do you have any other comments about the module?

To these I will often add 3-5 other questions which I'm curious about. Sometimes it is to test the waters on new things I'm planning on trying with them or future classes.

The key is to keep it short. ~5 minutes is way too long. If you take more than 1-2 minutes of students' time, you are very unlikely to get many responses.

I usually ask these questions at mid-point and after the final class. However, if you want more frequent feedback, I'd suggest the "one minute paper" where you ask two simple questions (paper, electronically, whatever fits):

What do you think is the most important thing you learned today (or this week)?
What did you find the most difficult point to understand?

One minute papers are useful for constant course corrections while the earlier questions are more to find out how to change the design of the module next time (or next half).


Whether to italicise the name of government program in APA style?

APA requires the use of italics for:

Titles of books, journals and periodicals, films, and videos
Introduction of new key technical term or label
Anchors of scale
Words, phrases, or letters presented as linguistic examples
General/scientific names, species, and varieties
Letters in statistical symbols or algebraic variables
When a reader might not see the intended emphasis or misinterpret the use of a word in a sentence.

The name of a government funded program does not belong into any of these categories. So the answer to your question is no.

For sake of completenes, here is when APA forbids the use of italics:

Emphasis
Foreign phrases common in English
Greek letters
Nonstatistical subscripts to statistical symbols
Chemical terms

By the way, I found this information simply by googling for "APA italics".


How can I encourage my advisor to adopt better work practices?

Turn the tables.  For your next paper, you maintain the master copy.  Make sure all the infrastructure is in place, including a fairly solid draft of the paper, before you involve your advisor in the writing process at all.  Use whatever version control and reference system you find most useful.

Your advisor may simply refuse to use your tools; fine, you can still incorporate their emailed inputs.  Or they may just need someone else to figure out the infrastructure and teach them how to use the tools, instead of figuring it out themselves from the manuals.  Either way, you'll have some extra work to bring your inexperienced (and possibly resistant) coauthor up to speed, but that's a standard part of the student-advisor relationship.

In the worst case, your advisor may simply refuse to give up control of the master copy.  (Never mind that it's already too late.)  In that case, you may need to encourage them to look for another student.


Expectations for a research student at a Japanese university

I was a research student at the University of Tokyo for one year.

As the answer to the other question states, a research student has literally no responsibilities whatsoever. The apparent point is to allow foreign students time to study for the entrance examination for the formal graduate program. They might give you as little as four months (roughly) or as much as a year before the exam is held.

Your advisor may or may not recommend that you sit in on classes and learn how the university works. If you are in the sciences, there's a good chance that you will be assigned to a research team in preparation for entering the college. If you are in the humanities, it's likely that your only responsibility will be to try to pass the examination. If you are already familiar with your field, you will have an extreme amount of free time.

"Research student" is actually kind of a misnomer. During my pre-acceptance year I did independent research on my own initiative (mostly because I was bored) and had two papers accepted for publication, but my advisor did not ask what I was doing, and my office did not know I had published papers until after I was accepted as a masters student.


GRE: how important is it to get it in time?

Three things:

the application deadlines for you are several weeks earlier than the dates that decisions on the applications are made, so even if the scores arrive after the deadlines, they may still arrive in time to be taken into consideration.
different U.S. disciplines (and to a lesser extent, different departments in the same discipline) have radically different views on how much the GRE is worth. So the answer to your question really depends on what subject you're intending to study, which you haven't told us.
bureaucracy at some institutions may prevent your application from being considered, even if the faculty thinks the GRE is unimportant.

The best thing to do is write the schools you are considering and ask. You may have taken the GRE in time for some of them, and I expect others will consider your application even without the GRE.


Is it better to choose recommenders by discipline or by familiarity?

Ideally you want someone who is well known to people on the hiring committee.

It sounds like you already have letters from two people who are very familiar with your work.  If you can get a STRONG letter from a "big shot" in the field (math?), you should go for it.  That person doesn't need to know you very well, but he/she should be able to put your work in context and explain why it is important/interesting.


What are the chances of an article to get published if it got minor revision comments, and a single optional major revision comment?

I have had this on a couple of papers. When I first had this, my advisor at the time told me that this is not usually something to be overly worried about and that it presented an opportunity. Specifically:

It is optional, as @FuzzyLeapfrog said in her comment:

  Thank the reviewer, let him know that you are aware of the benefits of using data from other locations, add a paragraph on this in the outlook part of your paper as "future work to do" and mention this in your response to the editor/reviewer.

It is also important to state in your 'response to review' document that the time taken to obtain the additional data will be prohibitive.

Additionally, take this optional revision as possibly the impetus for you to do another paper based on the suggestion.

In regards to the editor's decision of 'Major Revision', reread the message to check to see if this optional revision is in fact the reason. If in doubt, be sure to make contact with the editorial team to clarify.


I don't think this case warrants authorship. Your advisor did nothing to contribute to the new work, helping you with a prior paper says nothing about future papers.

You should absolutely cite your thesis (or whatever paper used this dataset) in your new work, and make sure that the dataset is not protected in some way (say, if it's a clinical dataset that is restricted in use via an IRB you might not be able to use it).


Ask professor if she is 'still' willing to write me a LoR?

There's no reason why you can't ask:

Dear Prof. X:
I was a student of yours for class Y in term Z. While I was still an undergraduate, we had talked about the possibility of you writing a letter of recommendation for me. At the time, I did not end up applying to graduate schools at the time, but will be doing so . Would you be willing to write a letter for me now? I can provide you with an updated résumé/CV.

with appropriate modifications.
You can definitely mention that she previously agreed to write a letter—you might be refreshing her memory, in case she gets a number of requests for such letters!


Are there areas where only some universities pay their sports scholars?

In the United States, many (perhaps even most) institutions do not give sports scholarships.

For example, I went to MIT, which gives only need-based funding (0% sports scholarships), but has a quite high NCAA varsity participation rate because, well, sports originally exist because people enjoy playing them, especially in the company of others. That's certainly why I was a student athlete (even captain of my team).

What institutions without sports scholarships tend to lack is not athletes but audiences.  At MIT, for example, the varsity football games were infamously said to be better attended by the band (who loved chances to play) than by anybody else, though I can't verify this because I never bothered to go myself.

By contrast, the institutions that do give sports scholarships tend to have big crowds and be the high-visibility teams that you see on TV, thus exaggerating their apparent frequency.

Given the wide mix of public and private institutions with varying philosophies and missions, I expect you'd likely find this contrast in every major US city.


Until you have your PhD officially, your CV should list "PhD Candidate" or "PhD Student," depending on your proper status. In your education section, you should list the month you expect to graduate (and you should say "(expected)" or similar next to the date).


Is there a list of countries (or universities) showing which prefer direct communication with referee?

Well, many good answers are already included in the comment section, but Let my try to summarize and extend this a bit:
First of all, there are good reasons for not involving the student (you can be more honest, the student can not pre-select). To my knowledge, ther eare at least three different submission types:

Student sends in recommendation which is written openly
Students has to submit letter of recommendation, but it must be enclosed in a sealed envelope
letter of recommendation has to be sent directly.

The chosen method might not only depend on the institution, but also on the funding scheme if the student gets financial support. The sheer number of possible combinations, combined with funding schemes which might vary from year to year makes the existence of a complete list extremely unlikely.
I would suggest to  follow the advice given by Stephan Kolassa to let the student figure out how the process works. It might be good to tell the student that if there are several options, you would prefer to send in the letter directly.


Academic Freedom for students re: advisors and solo papers?

Going back to Wikipedia's source, we're told that

  Strominger has since moved Pasterski, as a second year graduate student, into “Mode 2,” where she is given the latitude to work without his direct supervision on any topic of her choosing with anyone she wishes.

In other words, Pasterski seems to have quite a bit of independence to choose the direction of her work and collaborators. I suppose this represents academic freedom in the sense of "freedom of inquiry", but as far as I can tell neither "mode 2" or "given academic freedom" are formal designations at Harvard. As such I suspect they are not associated with the kind of protections that the academic freedom of professors can have (i.e. tenure). That is, in this case, it appears to be an agreement between advisor and student on how to handle things.

Since the original source calls it "mode 2" it seems likely that the phrase "given her academic freedom" is just a turn of phrase in the Wikipedia page. After all, freedoms are generally not granted by or from an individual. The notion of student academic freedom is generally defined in policies that would apply to all, not as a prize to be won for jumping a hurdle. Of course, I cannot prove a negative, so the latter might still happen somewhere.


Is it a good idea to write to some researchers for some help on my own research?

I would ask your professor first. Not to arrange a meeting but rather for advice. Maybe he thinks it would be best if you write yourself, maybe he thinks it would be best for him to establish a contact.

Next, remember that professors don't have infinite time, so be properly prepared. You claim that there is an error in the algorithm. So work it out exactly, have multiple examples ready to show that for these examples, the algorithm produces the wrong result, have proofs ready to show what the right result is, etc. You might not need all of it, but it is always better to be able to say "yes, I have it right here" instead of "well, I didn't think of that, maybe I will look at it...". On the other hand, don't send everything in your first email, if the prof thinks he has 20 pages to read to understand your problem, he will most likely not.

All in all, it is not a bad idea. Worst thing that could happen is that the professor has no time for you or doesn't answer your email, then you are at the same point you are right now. So go get some advice from your supervisor on how to best contact him, what to prepare in advance, etc. and write him a message.


Change of author sequence after accept with shepherding

Presumably you know the shepherds and can ask them. But I suspect that if the authors all agree on a change the conference won't object provided that it doesn't come so late as to require changes to websites or proceedings. But in general, order of authorship should be up to the authors.

I might change this opinion if shepherds had made specific advice about authorship, but I've never seen that done. But still, the paper belongs to its authors.


Should a graduate student accept random offer to be a reviewer for IEEE Transactions paper?

It is probably a good thing to do, just for the experience. It will also get you on the good side of the professor.

However, make sure, in accepting, that the professor and others know that you haven't finished your degree yet. That might cause them to withdraw the invitation, of course, but it should be made clear.


How to deal with an unhygienic human subject?

Just put up with it.

It may be an unpleasant situation for you and others in the lab, but you haven't mentioned any significant negative consequences of his lack of hygiene; nor can I think of any.  I would just tolerate it.  If necessary, clean any dirty surfaces in the lab after each session.  You could also warn others to vacate the area when he is around, if it is harming others' work environment.

Your research is dependent on the subject's good will and participation.  So I would not do anything that risks his ongoing involvement.  Keep in mind that this is unlikely to be something that can be solved easily--this person is already causing unpleasantness to everyone else around him and yet persists in this behavior.


A question regarding renewal of postdoc fellowship, and the mentor not making the picture clear

I find "I'd first like to work with you and see how you do" perfectly reasonable and that's probably his actual position on this issue. What he said during the interview ("depend on the results of his next grant application") is probably also true, just not the whole truth. He wanted you to accept the position after all. As you know, until a contract is signed you have nothing.

Try setting up regular feedback meetings so that you know "how you do" and can try to improve your performance (and his perception of it) and can adjust your search for the next position accordingly.


Should a marker TA handle students' marking issues by email?

Part of the rite of passage of being a graduate student is having to deal with insistent students in person.

If students ask for more marks, you can firmly but politely state that marks are not subject to negotiation, but that you'll gladly discuss the contents of the answer.

Aside: learn early to be firm for otherwise word will spread you are soft and you will invite more headaches.  Being firm can lead to awkward silences as you may rapidly reach a point when there is nothing more to say.  If you reach a dead end you can always close by firmly but politely ask if there are other topics to discuss.


How long should one wait for a reference before writing to the course convenor?

I'm going to answer this question myself for the benefit of people who may stumble upon this in the future.

In the end I didn't email the convenor, but I phoned the Prof in question. I initially thought maybe I needed to give it longer than three weeks and I was being impatient, but it turned out that they totally understood and said they had been very busy but of course they would do it. They ended up submitting the reference the same day. To those people who may be in a similar situation: don't be too shy about phoning or visiting your professors for this reason. They understand the necessities of getting it done and done in good time, but understandably get waylaid by priorities.


What steps can US undergraduates take to reduce the frequency and severity of assignment of unearned grades, as from grade inflation and cheating?

Grade inflation is not happening because of academic misconduct.  That has zero to do with it.  Most of us are surprisingly good at spotting plagiarism and we give out a depressing number of zeros for that and other forms of misconduct.  Trust me, very few of those students are contributing to inflation.

Grade inflation is a long-term slow trend.  Most instructors try to grade "about like" their colleagues in the department.  But few of us want to seem unfair, so we err on the side of being a bit generous. Over time, you get inflation.

But go for it.  If you came to me, pleading for a tougher curve and a lower grade, you'd definitely be my first.  I would certainly remember you.


Dealing with unsupervised research as novice researcher

Networking would be my run-to. I'm sure you can find someone that knows enough on the topic to help guide you.

I had a research paper that I had to do for my programming degree and I had to research programming for different platforms, in my case, web flash games in comparison to mobile game development.

I knew nothing about the software, code language, or how the 2 different platforms varied in the game industry so instead of just reading other papers, textbooks, and videos I went on to website where these games were found and left comments asking for the Devs to contact me, I contact the site owners themselves about getting into contact with one of their Devs, and I even posted an ad on Craigslist (I did actually find someone that taught courses in the subject though Craigslist and he was the best source I found).

You really just need to ask around and it's easier to find people than you may think as long as you put effort into it.


How to cite a reference which disappeared?

I personally think this is not your responsibility to control the sources availability over time. If the official provider's URL is added, it's usually enough. There are numerous means to retrieve the metadata; the easiest one, as mentioned by @JeffE, is WbM, also there is Google cache.

BibLaTex supports a urldate = {YYYY-MM-DD} field, which adds "visited on MM/DD/YYYY" info to the reference in bibliography, assuring the reader which date can be used to restore access if the link is dead.

More technical aspects regarding handling external data sources with BibLaTeX are discussed on TeX.SE: URL of cited web site in bibliography


How to start doing significant research?

What you are describing is certainly not good advising, unless you have cherry-picked some particularly negative quotes and taken them out of their context.

It is true that monolithic and groundbreaking theses are regarded higher than "stapler theses" (3-5 papers combined into a thesis), but your reputation will most likely not hinge on your thesis -- and writing several papers early is most likely better for it than writing a really good thesis. (Keep in mind: You will be applying for jobs before your thesis is out! And while those jobs will not be permanent ones, it is still very important to catch a good one, since it will influence your ability to do good research in the postdoc period. In your application, a written paper counts more than an unwritten thesis, no matter how important the latter promises to be.)

Another downside of "one big project" theses is that they are more likely to fail. If 1 of the 5 papers in your "stapler thesis" is revealed to be non-novel (and that happens in most active fields, particularly when different schools use different notation and don't communicate well with each other), your degree probably won't be delayed. If the main result of your monolith thesis turns out to be non-novel, then it may be a serious problem. And that's all assuming that you do win your bet and get that one really good result.

I have written a "stapler thesis" myself (actually the worst kind, without even a Chapter 1 that connects everything; admittedly I do a lot of exposition in my papers). I have seen many "stapler theses" from MIT students who went on to do great work. There is no stigma in them; you can do better, but someone can always do better.

As to this:

  My advisor does not like to suggest ideas/problems to me because he said he doesn't know what would be ground-breaking either or else he would do it himself than gift it to me.

The honesty is refreshing, but perhaps he should not be suggesting you to fend on your own then? Graduate students are usually not very good at recognizing which directions have promise and which are stale. This is an advisor's job. If the advisor cannot do that, he should then give the student something more concrete and incremental to do.

  My advisor said it may be good to read quantum physics as he himself is reading that and sees "lots of potential" in cross-disciplinary investigation.

This is a very dim and faraway lighthouse to steer towards. If your advisor is not offering you anything more concrete (at the very least, some reading, and not just introductory textbooks), then you can just as well ignore it for your thesis. Everyone and their dead cat knows that quantum physics is connected to probability; this is not exactly a hot scent.


Why do professors give talks on published work without their coauthors present at the seminars?

An incomplete list:

Because they're invited to give a talk, and their coauthor(s) aren't.
Because their coauthor(s) can't afford to travel to every talk they give on that piece of research.
Because their coauthor(s) are busy with other things.
Because this way they and their coauthor(s) can disseminate their ideas more widely, by giving more talks for the same overall investment of time.
Because the work is interdisciplinary, and the conference at which the work is being presented is devoted to some of the disciplines involved but not all of them, so attending would be irrelevant for the coauthor(s).

(Thanks to the commenters who suggested further additions.)


Transferring Computer Science graduate school

It isn't usually possible to "transfer" to another school, but you could always apply to a different program and terminate your current program. In this case, to answer your questions:

Yes, you will need to apply to any new schools you'd like to consider. They are independent institutions, so they need to evaluate you according to their own standards.
You will have to ask the school you apply to how they will take transfer credits. There is often a credit limit, and you might need to take an exam or by some other method prove your competency.

Note that you may need to provide reasoning for why you are switching programs when you apply to an alternate program. It may be harder to get into a program given this -- schools may not want to take a risk on a student that quickly exited out of another program.


What language should my poster for a national convention be?

"The conference language is native language, but english
  contributions are welcome as well.

The conference organizers have made it clear that both native language and English are acceptable and welcome for your conference materials.

That means it’s entirely up to you. If you have strong feelings about supporting your local language, you can feel completely free to use that language for your poster. I am sure many of the native speakers present would find that an agreeable decision and would be somewhat grateful. On the other hand, there will likely be some foreign participants who would find your poster unaccessible and will miss out on learning about your work. Perhaps some of those people are academics you will be interacting with further down the road of your career (e.g., if you end up applying for postdocs overseas).

If you just want your work to reach the largest number of people and don’t care about anything else, I’m guessing English is the way to go (assuming you are in a country such as Germany with a very high proportion of English speakers).

It is a choice to make; neither option is any more right or wrong that the other.

And if you really can’t decide, how about preparing a bilingual poster?


Should I follow-up about poorly answered questions in an interview?

My advice is to take a deep breath, what happened in the interview room is now a closed book. While I am sure that we would all like to sometimes be able to change the past. The past is a sealed land.

I suspect that as it was your first interview that you messed up royally in some way, do not be disheartened. Learn from what happened, chalk it up as experience.

I am an associate prof, I went through a lot of attempts to get my first academic post. Each time I failed in an interview room I failed less bad than the last time. I would use your interview failure as a chance to try to identify any training needs you have.

If you act in a sensible way on these then you can make yourself into a better academic.


Potential repercussions from overlapping university appointments?

From the standpoint of the law it should be fine. Most (close to all?) countries allow you to hold several appointments in the same month. If not, some part-time workers (think waiters, bartenders, etc.) would have a hard time making ends meet.
The other legal factor is the employment contracts. These could require you to seek authorization from the current employer before starting outside employment.
It absolutely is a conflict of interest, but one that should be possible to solve by disclosing the situation to both employers. The actual solution might be the one-month leave you mention, quitting the first position earlier, getting a thumbs up from the current employer, or doing a 50/50 time split the first month. Either way, the current institution deserves to know if you begin to work for, and earn money from, a new institution - whether you intend to leave your current job or not.
Note that the possible conflicts of interest don't just concern the pay - if you use resources from the first institution to benefit the second it can also be bad. This isn't really solved by a leave, but by disclosure and then handling the resources responsibly.
I don't really see any professional issues, assuming you handle the conflict of interest issues professionally (i.e. disclose them). After all, it is rather common in academia to have more than one affiliation. Of course, one also needs to be professional in choosing which affiliation to put on papers.
Another consideration, especially in the US, would be benefits and medical insurance. The easiest way to handle this is probably to waive those benefits for a month at the new job. And if the two institutions are in different jurisdictions you might have a fun time figuring out how to do your taxes correctly...

Another benefit of disclosing the situation properly is that you can then ask HR (at both institutions!) if there are other relevant issues in the specific case. Ultimately, it's their job to know how to handle these things, not yours.


Are university salaries public information in Sweden?

Yes, individual salary information at Swedish universities fall under "offentlighetsprincipen" (the principle of public access to official records), unless they are explicitly classified, which would be very rare. (See for example this document from Stockholm university describing how "offentlighetsprincipen" applies to university matters.)

The easiest way to obtain them is probably to contact the HR department (personalavdelning) at the university/faculty in question.


Citing an unpublished paper? plagiarism?

There is no particular problem with citing unpublished work. Just list it as such. There is no problem with citing work that will not ever be published in fact. Just name the author and list it as "private communication". Give a title if appropriate, or a description.

In the case at hand, it seems wiser to cite A within B as it is likely to be published first, but since you don't have the final version, it could be listed as "unpublished, in preparation".

Talk to your advisor, of course, about what he/she recommends here. I think in most cases the rules on a thesis can be, with permission of the advisor, a bit looser than for formally published work. You need to cite, in any case, but the fact that things are a bit tentative can be finessed.

As for plagiarism, cite your own work, whether joint or not, just as you would the work of another.


The person who created the application I used for a study wants to help analyze the data

I don't see a problem. Many people create a tool, use it to analyze something, then publish the results. Many companies that produce products publish papers that try to put their products in a good light. It is the job of both the authors and the reviewers to do all this in a rigorous fashion, but it doesn't mean such papers are disallowed.


Post physics PhD, how could I go about working in ecology, environmental science or earth sciences?

How likely is it that I could make such a large career shift?

It is very common for people who studied physics to end up doing something rather different.  Studying physics is great preparation for many different endeavors.

  How do I go about finding out more about what research is out there and what I might like specifically, given the very large quantity of research that exists??

Fun ways to do this are to attend seminars and take a look at journals in the target fields.  At this point you're mainly getting your feet wet and getting a few ideas about what's out there, and what the culture of those other disciplines is like.

  Does anyone know of any examples of people who have made similar shifts? (Partly just because right now I need the inspiration and belief I am not trapped!)

My advisor, Akira Okubo, is a good example.  You might enjoy reading this tribute and overview of his life and work: http://www.yen.biology.gatech.edu/papers/Okubo%20tribute.pdf

  What sort of things might I do directly after my PhD to build experience/learn more? Is trying to get field experience a good idea? Should I start to consider Master's programs?

Perhaps the shift would be less drastic if you started out by making a slight sideways move into environmental science.  But that might not even be necessary.

I think you can go straight into a two-year postdoc after you graduate.  As long as you choose the right sort of person or group to do it with, I don't think you'll need to do another degree or more coursework first, because of your undergrad broad span of sciences and the lab biology projects.  If you find you have some gaps, you can fill them on your own or by auditing some classes while you're in the postdoc.

  Am I completely as doomed as I think I could be?

There are some interdisciplinary fields, such as mathematical ecology, that are new enough that many of the people in those fields originally trained in something else.

Final comment: the tail end of a PhD can be a desolate time, and a stressful time.  So please take this growing ennui with a grain of salt.


How to establish a relationship with a department head as an undergraduate?

It's possible that you are misunderstanding what the signature of a department head implies or requires. In general, signatures are used to ensure that policies and procedures have been appropriately followed. Save for unfortunate cases where resources are solely allocated due to rather extreme corruption (beyond anything I've personally encountered), you don't have to have some sort of deep personal history or relationship just to take part in an existing publicly advertised academic program.

The most common way this comes up is a form that requires two signatures - one from your advisor (or other faculty member relevant to the request), and one from the head of the department. The advisor/faculty member is usually the one responsible for making sure you meet all the program requirements, and believes you should have the request indicated by the form authorized. Then the signature from the head of the department is generally just a bureaucratic formality, and the department head's job (often delegated to an assistant) is to ensure you qualify, etc (making sure the faculty member did their job correctly), maybe ask a few questions or require supporting paper work if applicable (if it's routine they won't even do that), and then sign. And off you go!

To see what is truly required to get into your school's program, you'll need to look up further information about it on the website - if one exists (it may not have useful info), and talk with whoever administers the program. You might also just go to your department office and ask the assistant for more information about the program. You can just say, "I read about the program where you can work towards a masters while you are an undergrad - how can I find out more about this program?"

You can then find out if the program is a competitive application process, are there certain qualifications you need before applying to the program (such as completing a certain number of courses, having a certain GPA, meeting with a graduate advisor, etc), and all the other details you might want to know about to decide if the program is right for you and how you can join. It could be as simple as ask to join, give your transcript to the assistant and they will have the chair sign, and you are in (so long as you pay the bills, which might increase to be a part of that program). But you won't know until you talk directly to the appropriate staff members - no need for scheming just yet!


What options do rejected applicants have if mistakenly told they were admitted to a program?

I've been putting off answering this because it's really a legal question, not an academic question, and I'm a computer scientist.  In my one business law course, I learned that the essence of a contract is an offer and an acceptance.  We have those.

If I were in this boat, I'd probably suck it up and apply elsewhere.  If I really-really wanted to go to the school that first accepted, then rejected me, I'd consider paying a lawyer a few hundred dollars to call the counsel for the university.  My lawyer would say something like, "My client is damaged blah-blah and has cause of action blah-blah.  However, we do not want to be unreasonable.  All we want you to do is honor the offer you made in writing and later confirmed verbally.  Um, and keep these circumstances confidential from anyone who could assign a grade to or otherwise evaluate my client."

There is a huge down side to doing that.  It is that the circumstances are quite likely to leak out.  Then one is facing professors who know how one was admitted.


Should I get a letter of recommendation from my mother, who is a famous researcher in my field?

I would say no, this is a very very bad idea. Your mother going on about how likely you are to succeed will probably not carry much weight. What else would your mother say? If you were unlikely to be successful, would she say that? (even if she would, the perception of the people reading the letter will be that she would not)


When to write response document in context of complex major revisions and collaboration?

I have had to this on a number of occasions (as I am sure many have), and have, with the help of my collaborators. At the moment, my colleagues and I are doing exactly this for a paper.

In answer to your questions:

  When preparing a response to a complex set of revisions, when should you write the response document: (a) while you are writing the response to each point, or (b) at the end, once all the points are made, or (c) rough draft initially that is reviewed at the end?

I tend to do (a) and (c). Details in answer to the 3rd question. But, I find that it is always good practice to take the time and critically review everything I do in academia.

Alongside the manuscript, the response to review is an important document in terms of the publication of your paper. As such, it needs to be completed methodically and reviewed before submission.

  Relatedly, how important is it to have a clear strategy about how all the revisions will be handled before starting to make any revisions?

I believe that it is always crucial to have clear strategies.  Making (and refining) a 'plan of action' is a good way to increasing the efficiency and the effectiveness of how the revisions are handled.

An important part of this is to decide who will address the reviewer comments first, and who would review the corrections and responses (we have the first author do this, as an example).

  More generally, are there workflow tricks for dealing with the issue of ensuring that the response document stays consistent with the manuscript changes?

What I have done for complex revisions on collaborative papers (and found to work rather well):

First make a printed 'working desk copy' of the reviewers' comments and have the manuscript on the screen.

for convenience, we put the comments in a table, with a column for our notes in response to the reviewers' comments. Additionally, we put another, thinner column for where the change occurs in the paper (page/line number etc).  But, this is up to personal preference - the point is to have a printed copy that you can write over.
As I have often found that reviewer comments are in the order that they appear in the paper, we use the same order when we go through the comments. if the comments are not in order, it is helpful to put them in order.
One suggestion I have seen for this stage is to put all the comments in the order that they appear in the paper. But, we prefer to have a separate page for each reviewer's comments, and have the desk copies side by side (as a response to a suggestion from one reviewer may affect an earlier suggestion from another reviewer).
Take the time to consider each suggestion individually, writing in the revisions as you make them to the manuscript (highlighting any changes if you wish, for this stage).
Once you have completed the review desk copy, type the responses into the response to review digital version - as you do, double check that everything is included accurately.
Send the revised document and the response to the collaborators to check and review that all comments are addressed and that the responses are accurate.

Then of course, the final step is to prepare both documents for submission (re-submission) to the journal in accordance to their guidelines.


Can you submit to journals after presenting cases as eposter in conferences?

Very few medical journals consider a poster presentation a publication. So vanishingly few that I have never encountered one in my career. Indeed, the primary expectation of the posters I've encountered is "This'll someday be a paper, but these are the preliminary results."

As long as it hasn't been worked into a full paper as part of the conference, there's no reason to worry.

If you're concerned about it, you can include a sentence in your cover letter to the journal something like the following:

"This manuscript is not under consideration at any other journal, however the preliminary results have been presented as an ePoster at the Conference of Big Deal Science."


Is it possible to submit a paper to a scholarly, peer-reviewed journal without PhD and get it accepted?

Submitting an academic paper for publication (and potentially getting it accepted) does not require any qualifications whatsoever.  You don't need a PhD; you don't even need to have gone to college.  There are no educational, employment, or membership requirements at all.

That's not to say it's easy to get a paper accepted with no formal training in the field.  Learning how to write a compelling paper is much easier if you have a mentor to offer guidance.  However, if you can figure out how to do it without a PhD, then your lack of a PhD will not be held against you.


Citing an article under a double-blind review process

Considering the following extreme case can help to clarify: what will you do if article B is accepted before article A finishes peer review?  This could easily happen, given the high variability in time in review cycle and number of reviews.

At that point you've got basically two options:

Drop the references.  Can your paper survive without them?  If so, it's not a big deal.
Put your blind review article into a pre-print archive, in order for it to be available.  This might "spoil" the blind review process, but only if the reviewers go looking for it and only if it significantly changes their opinion.

In the mean time, I would recommend citing it as "[omitted due to ongoing blind review; available on request]", and letting the reviewers request through the editor if they feel reading your pre-print article is important.


External collaboration without doctoral supervisor - is it a fair request to pursue this?

Your advisor doesn't own you, so yes, in general you can pursue other research collaborations.

However, there are situations in which the answer would be otherwise. If you are in a lab science (or similar) in which you are depended on and this would interfere with the work of others, then you have to cover your obligations.

Since you mention funding as a tag, it may be that you have a grant that requires full time attention to the work of that grant. That might make it more complicated.

The personality of the advisor might make it inadvisable to do this prior to finishing your degree. It wouldn't be right to forbid you to do this, but it could happen.


Best margins for master thesis written in LaTeX

Your question may not be completely appropriate for academia.sx but probably not for TeX.sx either.

Anyway. rather than focussing on the width of margins you can consider the width of the text area. Research (I do not have references at hand at the moment) has shown that around 65 (within the range 45-75) characters per line is optimal. This means that if you switch type face or size, the number of characters will change. Hence the same text area may not be optimal for 10, 11 and 12 pt or conversely your text optimal area will change with type face and size. To some extent, this is built into LaTeX which is at least partly why the margins may seem less than optimal.

So to approach the question of margins, try to select the type face and the type size you want to use and then check the resulting text area size for line lengths between 45 and 75 focussing around 65 characters.

The question of right and left page margins is a matter of simplicity. If you centre the text area on the page the areas will appear the same on all pages. When viewed as a pdf the text will not move around from page to page which can be slightly annoying, particularly if inside and outside margins have widely different widths. So will your text be read frequently in digital format use simple margins, if the print is important differing in- and outside margins may be preferable. Just make sure any printer does not screw up the margins by removing or missing printing blank pages that will result in a shift of left and right hand pages.


Changing my information in a published paper

If the paper has already been published, you can't. It's too late. Even if the print versions have not been printed, the electronic version will have been distributed, and it's not possible to issue a recall.
If the issue is severe enough you could publish a corrigendum/erratum, for which you'd have to ask the journal.


Should I scold the act of cheating before an exam?

Treat ethics seriously. Students should be aware that their actions do have consequences, and should be held responsible for their deeds and misdeeds. Jokes are inappropriate, and references about "cleaning your soles" with cheating-tainted diplomas are probably a little too hyperbolic.

That said, you can certainly give a warning to your students not to cheat on the exam. In some places, you must give such a warning as part of the exam instructions!


How to deal with inconsistencies in my last name spelling on official documents?

I think this problem is widespread enough that it shouldn't be a problem, provided that you make people aware of it. You suggest a note in your CV and that should be fine. It could appear elsewhere also.
If you are questioned on it or someone makes a mistake in thinking you are acting improperly, just inform them of the issues. I think people will, in general, try to be reasonable, though I can't predict for everyone.
I know one person who immigrated to the US from China. His brother did also a bit later. They have "different" family names when written in Roman letters because of this issue. Most English speakers even pronounce the names a bit differently now. My own family name is spelled in at least three different ways in the US because my ancestors coming from Ireland were illiterate on arrival and people wrote down a spelling for them when they arrived based on pronunciation.