How often do Master's programs accept applicants with online Bachelor's degrees?

Regarding question 2, the United States government does not track graduate admissions rates, but test preparation companies and academic communities may conduct surveys that give you a good sense. See the answer for Where to find grad school acceptance rates?  Some programs offering online undergraduate degrees might poll their students to learn the graduate admissions rates, but it might be hard to verify those numbers.

I would suggest that "students who have online degrees" is not the most helpful classification to use in determining your chances, because it is a large and varied group. The (U.S.) National Center for Education Statistics presents some data on how many students are taking online classes in American institutions. The takeaways are that online enrollment numbers are growing, that most students do not pursue 100% online programs, that different kinds of schools offer this (public, private non-profit, and private for-profit), and that the students who take online classes are more likely to be "non-traditional" (based on age and employment). Not all online programs are equal.

Instead, I would suggest you look carefully at the school offering the online degree. What is its reputation, is it accredited, how is it ranked in U.S. News & World Report (or international counterparts), what job/grad admissions resources does the college offer to its current students, and what does the school website say about where its students end up? Also find out whether the people teaching classes have advanced degrees, and take a skeptical look at how much contact you will have with professors during your online study. (Talking with classmates, instructors, and professors helps you learn, and it gives professors the chance to understand your goals and provide advice and potentially later a recommendation.)

Good luck with your studies and decisions!


Realizing no one at my school does quite what I want to do

Seek an external co-advisor who can give you the guidance you need.
A co-advising arrangement can be a win-win situation: your advisor would still have you as a graduated student under his belt, the co-advisor gets to be a co-author of the resulting papers, and you don't have to seek a new position and deal with the complexities of moving and changing your living circumstances halfway during your Ph.D.
Candidates for being a co-advisor are researchers that are enthusiastic about the research problem and possess the required expertise. Examples would be the "big name" researcher and some of the other people who gave you feedback.


Am I allowed to submit to a journal, a paper that was accepted to a conference but not presented yet?

If I understand your question correctly, you're planning to submit the journal paper after receiving the decision from the conference. In that case, if the journal is ok with considering an extended version of a conference paper, the conference organizers are probably not in a position to say anything against that. However, you have to follow the standard referencing rules when finalizing the journal paper:

The material that already appeared in the conference is not "new" for the journal paper, but has been published previously in the conference paper. Accordingly, the relevant section in the journal paper should be formulated as a review of existing results.
You must cite the conference paper from that section.


How to start an academic career after 5-6 years in industry, without an undergraduate degree?

As a current PhD student, my advice is to first ask yourself several questions before you decide that you want to apply to do a PhD.
First, why do you want to apply for a PhD program?
For some, the PhD is a stepping stone to a tenure-track job in academia.
For others, the PhD is seen as a mind-enriching experience, even though the student wants to work in industry.
For some industrial research jobs, having a PhD in a related field is a requirement before they will even consider hiring you for that job.
Second, what level of PhD program are you willing to accept?
There are also different levels of PhD programs.
If you want to get into a good PhD program (MIT, CMU, Stanford, etc),
you could take a look at current students of those programs and look at their CVs.
Usually, these students would have graduated from a top school with a good GPA,
and have had some undergrad research experience and maybe even a publication or two.
If you want to get a job in academia, you usually would have to graduate from a good PhD program.
If you only want to do a PhD to get a job in academia,
it may not be worth your while to get a PhD from a less reputable school.
However, this is a personal decision based on what is important to you.
Finally, are you both competent and interested in doing research in computer science?
The way that most people realize that they want to do research
is that they have some sort of undergraduate research experience,
or maybe even do a Master's.
Conclusion
If you think that you would want to get into a good PhD program in computer science,
you should first get a BSc in a good school,
and try to obtain some research experience while you are studying
in order to get a feel for what research is like and whether you are able to do it and whether you really like it.
I think that getting a BSc in a good school would probably be helpful in your career development
even if you decide not to get a PhD.
At the end of the day, you make your own decisions and deal with the consequences.
Good luck!
In response to OP's edits
A couple of thoughts:

You didn't mention in your original question that you had several published papers.
If you have some research experience and published papers, that definitely helps your PhD application.
I don't have personal experience being on an admission committee.
If you were able to meet someone on the admission committee of a university PhD program which you were interested in,
you could ask him/her how they would evaluate your application.
Since it is very rare for a PhD student not to have a BSc,
I don't know how open they would be to accepting you as a student.
Could you go back to the university which you dropped out of and finish of your degree in a year or two, by just completing missing requirements?
From what I understand, most master's degrees are based on course-work, and have no research component.
In that case, doing an MSc may not prepare you to do research as a PhD student.
On the other hand, if you were able to do a perhaps 2-year MSc which includes research with an adviser/supervisor,
this could be a great stepping stone into a good PhD program.


What do I do if a teacher fails me after they said I'd pass?

Contact your teacher (email) and start a paper trail where you outline the assignments in question: when they were due, when they were submitted, and if the teacher received them.
Given the break, schedule an appointment with the teacher after the break to sit down and discuss the issues at hand.
(As per aeismail's comment) I would agree to escalate to the department chair and inform your academic advisor before the dean.
At the same time as 5, should you choose to and if your institution has such a department, contact your ombudsperson office to create an informal avenue of conflict resolution outside of formal (and time consuming) solutions. They offer a means of conflict resolution that tries to arbitrate issues before you take formal action.
Depending on the results (no meet, meet but no success) escalate by appealing to your college Dean the issues and ensure that all paperwork is in order: an executive summary documenting the chronological order of events, all of your correspondence with the teacher indicating that you abided by the syllabus.
If and when you have a hearing, dress nice and present your case when you are called in for an appointment with the dean. Be factual and punctual. Don't demean or insinuate personal characteristics of the teacher in question, stick to the facts and what is the issue at hand.
At the end of the day, if all else fails, I would stand to believe that your college Dean answers to a higher 'officer' of the school. There should be a means to escalate your appeal to this final authority. There might be more, but for most if not all issues, this would be the highest authority to appeal to.


Could your supervisor decide what you post on social media?

First, it would help to know which country in Europe because there are big gaps in the way PhD programs work from country to country. There are untold agreements between supervisors and students depending on the country/university. How far into the program are you?

Second, what social media you are referring to. Is it LinkedIn or Facebook? It would help to know more background, because you can use their features to “trick” a post exposure.

Third, is he asking you politely, with arguments or he’s just pushing you to do that by imposing authority? If this is the case, there are legal aspects and PhD school directors or coordinators can help with this. Here is why it is important to know which country. In Scandinavia, for example, the system is well organized and you can go and talk to the PhD school director and ask for advice without any consequences. Moreover, the supervision there is not so abusive and if it is (like in your description) then you should consider going to another supervisor (this depends on funding, of course).

Is he imposing any consequences if you don’t do so? Did you try to talk to him about this? It always help to talk to them and see if you are on the same page.

Lastly, surely it is unethical and wrong to request something like this, but you should also try to understand why and if this makes sense. At the beginning of my PhD I thought that it would be unethical to add a supervisor/colleague in an article as a coauthor, but later I found out that it made sense after weighting the indirect contribution of that specific person.

These are the kind of things that you have to solve with a meeting and discuss with your supervisor about what’s bothering you. It’ll also help you to decide if it is worth continuing with this type of supervision. Moreover, if that’s the only thing he’s requiring and he does it politely, you might want to make a “sacrifice”. In the end, you are not sharing fake information or information about something that is not indirectly related to you. You can just share and then delete. Or share only with your group. There are always methods to make a small compromise if you feel like it is worth it from other perspective. If you are at the beginning, then brace yourself for more. You will be surprised how many compromises will need to make to have things running smooth and forward.


Pre-print servers: Authors using wrong parametrisation to avoid reproducibility before publishing?

I would not assume that this was intentionally done to mislead other researchers. If they wanted to keep their paper confidential, they would not upload it to ArXiv with incorrect parameters. As you have already shown, people are able to find a valid set of parameters by theirselves.

Please consider also the following possible reasons:

The wrong parameters were accidentally put into the paper. One may have forgotten to update the parameters in the paper and left in some placeholders.
You overlooked some important fact, e.g., scaling of parameters. So the error might also be on your side or the corresponding section of the paper is difficult to understand.
The parameters might only work under certain conditions, thus, the authors might be at error.

However, I would recommend to contact the authors using a short and friendly email. You should not assume an error on their side from the beginning as this might come across as rude. You may rather formulate this as a question, e.g., whether they have an idea why you are not able to reproduce the results.
You might either be able to see your own error or help the authors with improving their paper.


Should I add my business experience in my application of master program in math?

[Context: I am a CS lecturer in the target country] I really see no reason to hide an achievement of this nature, even if it is not tightly related to your application field. It shows that you are capable of committing to a long-term project with responsibilities. Perhaps it will not give you a significant edge over other candidates at this stade (application in master 1), but in the future, researchers interested in choosing you for an internship will certainly find this information useful.

It does not harm to mention this experience, and it might be useful now or later. Also, if you don't mention it and someone finds out, they will wonder why you wanted to conceal it. Really, I can't see a valid reason to do so (except maybe if what you founded was an escort agency or some other adult business, and you wanted to keep that for yourself).


How to refer to a method from a workshop in a conference paper?

I think you are mixing up a few different definitions of "count" here.

Workshop papers typically "count" very little on your CV. That is, having a few workshop papers will not make you graduate much sooner, and they are pretty much useless when you start looking for e.g., a tenure track position.
Workshop papers, but only those with no formal proceedings, don't "count" as publications. That is, you can hand in the same material again at a conference or journal without being accused of self-plagiarism. The workshop paper on the website of the workshop is basically a preprint. Hence, formally, the work is still unpublished and you can submit it wherever you want.
Workshop papers, no matter if they appeared in formal proceedings or not, can and should be cited. Clearly, if you use this citation to, e.g., support the validity of a statement, this carries less weight if the cited source is a workshop paper than if it is a well-known journal. However, if you want to apply method A, which you have already presented in a workshop, it seems correct to cite the workshop paper. Note that you will still need to describe the method, as you cannot assume the reader of your conference paper to go back and read the workshop paper first.


I'm looking for an application or workflow which integrates data values into the writing process

One possible workflow is using R for producing the results, LaTeX for writing the report, and Sweave to integrate both. With either TexStudio or LyX (or any text editor that supports track changes) as writing environments and Dropbox, you can set up some sort of "collaboration".


What should I do if my admission letter doesn't say anything about funding?

It is very common that an admission letter itself doesn't contain any information about funding. However, it is assumed (at least in the US) that information about funding will be made available to you well before you have to give an accept/decline decision. This often comes in a separate letter/email, sometimes within 1 day of the first letter, and sometimes more than a week after - all depends on the University processes and timelines.

Regardless, it is perfectly acceptable to contact (call or email) the University to inquire about funding offer timelines. Usually you would ask the graduate program administrator, and they can answer or direct you to who you should contact instead. It's fine to ask the professor, but they might not know and thus haven't answered (they may very well have seen your email and sent off an email of their own and are awaiting a proper answer). Funding in academia is often weirdly complicated, and often requires multiple calls and emails to multiple people to figure out all the exact details. Often this process is made invisible to the student.

If you've had silence from all channels for over a week - or if there is some very pressing deadline approaching for you - you should re-attempt contact and politely inform them of the deadline you are under, and your need to hear about funding prior to that time.

As to what to say to your professor, if you haven't contact them already, it's usually safe to confirm you received your offer of admission, say thanks and express that you were excited/glad/pleased to receive it, and note it didn't mention funding. Then just ask about the status of funding available for you - and that's pretty much it.

Congratulations on your offer of admission, and good luck!


Is there common policy in universities about departments or faculty/staff intervening in the case of misconduct related to Title IX?

I have encountered the belief that once this occurs, faculty/staff are prohibited from engaging on the matter further.

I am a former department chair at a large US university. I don’t know what you mean exactly by engaging further, but this belief sounds mostly false to me, or at best a distorted or misunderstood version of something that’s true but doesn’t quite mean what you think it means.

At my university, the department chair will typically remain involved and play an active role in coordinating the university’s response to the incident, usually in consultation with the Title IX officer or similar campus officials. The chair may be advised to not act independently of the title IX office or prior to consulting with them (and even more so to not act without keeping them informed), but it sounds inaccurate to describe this as a “prohibition”. And it’s not the case that the chair hands over the matter to some outside department and then steps away completely from the situation, as the belief you describe seems to be suggesting. (On the other hand, it’s possible that that is in fact the way things work at some US universities.)

  For example, can a department chair enact sanctions on a perpetrator?

Department chairs have a fair amount of independence to do things at the departmental level. So generally speaking, I’d say that yes, the chair can do such a thing, but whether it would be a good idea or recommended practice would depend on the specific details of the situation, and in the absence of more information I’d assume it wouldn’t be either of those things.

  Can faculty confront the perpetrator and demand their behavior cease?

Yes, similarly to the above: people can do all sorts of things, but if the matter is being handled by the Title IX office, most sensible people would recognize that letting the professionals (with the appropriate training, legal and psychological background etc) handle it is the best course of action.

  Can it even be discussed?

Not sure what you mean by this exactly. Information about sexual misconduct accusations would generally be regarded as confidential, but department chairs and certain other administrators would have a legitimate need to know and discuss such things, so yes, obviously they can discuss them. On the other hand, they would need to exercise discretion and not share details with random people who don’t have an official reason to be involved.


How to evaluate the research level of a paper before any publication?

While I think your "justice" metaphor is wrong, the answer in all cases is experience. You need experience in the field as a reviewer. You need to know what has been done and what is important yet to do. As an editor you need either that field experience or experience with your reviewers - who is trustworthy and who is not. As an author in the early career you don't have any experience other than some within the field, but it will grow.

For everyone here, the way you get experience is to make best effort attempts at whatever job you have and evaluate the response. As they say in engineering and computer science, "Good design comes from experience. Experience comes from bad design."

If you are looking for an algorithm, then I would say it doesn't exist. It might be possible in theory to construct one with an AI looking at tens of thousands of interactions, but it might show bias, as many such things have been shown to do.

But the system as a whole just depends on (nearly) everyone trying to do their best with what they have in front of them in world of imperfect information.

In theory, theory is the same as practice. But not in practice. - Fnord Bjørnberger


How widespread is the practice of delegating LoR writing to the applicant?

There's a spectrum of "writing your own LoR. " As a faculty member, for example, I might correspond with the student:

Asking for bullet points that the letter should hit
Asking for a few sentences or paragraphs of the highlights that the letter should address
Asking for an entire first draft that is then revised
A complete letter that is copy/pasted in its entirety

In principle, I write all of my LoRs myself. However, with students in large lecture courses or that I don't know that well (for example, those who have left for a couple of years, and suddenly need an LoR out of the blue), I might ask for a variation of #1 or #2. I always rewrite whatever they give me so that it is in my own words.

I especially ask for higlights for students who are going into industry since I've never been on the hiring side for industry (only academia) and don't know what should be accentuated .

From the student's perspective, though, when they get a #1 or #2 request - they might mistake it for a #3 request.

I've never asked for a #4 type letter and although there are rumors of faculty that do, I don't see how they serve either faculty or student purposes. Faculty who are lazy tend to also be risk adverse and signing your name to someone else's LoR is risky. It doesn't serve the student either as students don't know the genre of letter writing and are unlikely to be able to write a strong letter for themselves. So while I won't presume that in the entire universe of universities, such a case has existed, I would think the actually prevalence is quite low and the reality is #2 and #3 type requests that are misunderstood by the student to be #4s.


Is it possible/acceptable to publish the same article in 2 journals, if one is un-categorized?

It will most likely depend on the status of the "student journal". We had a "student journal" which was, officially, an archive of master theses in our program. As such, it is comparable to an archive of proceedings of a conference and does not prohibit submission to internationally recognized journals (or elsewhere) [in our field, "conference papers" do not exist - there are posters, but work presented on posters is usually later published in a journal paper without any issues].
Many of the papers published in this student journal ended up in high-ranked international journals without problems.


Where can I find samples of position papers?

How much evidence for the position is normally provided?

As much as possible, actually. In a position paper, you might want to develop an hypothesis that matches previously made findings. Or you might argue that past empirical research has got its results wrong in some way because of an unaccounted for measurement or protocol error. Or you might want to make a theoretical argument, or take multiple findings from existing papers and try to explain a connection between them. If you have an hypothesis which sounds plausible (as in consistent with correctly-made empirical observations and with at least one family of theories) and you find that you need some additional research before you can confirm or reject it, a position paper is a great way to expose it.

What kinds of questions are reasonable to leave unanswered?

The ones that need a costly / difficult proof. You want to expose an opinion or idea so you get feedback on it or potential collaborators.

How long are they?

It depends on your field. In computer science, they're usually short papers in conferences or full papers in workshops.

What level of counter-argument should be included?

I'm not sure I get this question. If you know about evidence that contradicts your hypothesis, include it, and explain why you think the evidence can be neglected.

Where to look for position papers?

Go to your favourite academic search engine and make a search on papers that contain "position paper" in their title. Also, look up all recent workshops in your specific field (those you'd submit your position paper to).


Is it common for advisers to have not understand a funded project?

(comment converted to answer)

No, this is not common in general. See if you can find out the secret of his success in getting the funding (grant money). Then write a grant proposal, with a different professor, whom you respect.


Does it matter where you go to medical school?

I disagree. There are very little differences between medical schools so long as you do well on your STEP I through STEP III exams. Basically what really matters is how you rank compared to the national average.
I have interviewed residency candidates from around the country-their alma mater means very little to me. Their STEP scores and extracurricular activities matter as well as their personal statements. Don't worry about medical school ranking-just worry about Step exam scores-that will really help you get into any residency program you want.


Where to Apply for International Relations?

International relations at the University of St Andrews are quite highly ranked. They definitely give you the option of eventually moving on to a PhD. I don't know much about their entry requirements though; I'd suggest that you contact them and ask.


How is grading by curve fair at all? Are there any arguments in favor of it?

My firm belief and policy is that a student's grade should depend on their own efforts and nothing else. In that case, curving the class is actually just wrong.
But my grading policy is pretty different from most. First, I use (used, actually, as I'm retired) cumulative grading. Every student task was assigned a point value and those added to, say, 1000. If you did a 100 point task, you might get 90 points based on assessments of quality. The breaks between grades were defined, say 900 to earn an A.
Second, I permitted rework if a student earned less than they expected to earn, but rework only got you back part of the lost marks. Therefore, I didn't get complaints about strict grading. "If you want more points on this, do a better job of it". This also allowed me to encourage students to do better work and rethink poor assumptions.
Third, I assumed that I wasn't perfect and that I occasionally was overly strict, so a student never missed a final grade by what I considered an infinitesimal amount. 899 points didn't mean a B.
When I came time to assign final grades, I'd look at the earned distribution and make a decision whether that represented what I thought they had actually learned and I might adjust all grades upwards (only upwards) a few points if I thought that, at that point I'd been too strict along the way.
I had the reputation of being very demanding, and I was, both in the quantity and difficult of work. But I was just a bit less strict than my reputation. Students after the last class were never disappointed when they saw their final grade. They were able to compute it along the way, and they might learn that they did a bit better than their expectations.

No student should suffer in a class simply because, just by chance, there are a number of genius level other students.
Curving, is, I think, an admission of failure of the admissions system itself, which tries to predict that admitted students will be successful. If the system is set up so that some are guaranteed to fail then something is extremely wrong.
Expecting that the distribution from one year to another should be the same in an individual course is also foolish. The students aren't randomly selected from a known distribution in large enough numbers (for a single class) that statistical assumptions have any validity. Some years the students just work harder than in others. Some years they have to deal with things (pandemics, say) that make their work much more difficult.
Grade individuals, based on their performance. Make it possible that the performance can be good or can improve. Don't assume that the students in your class don't really need to be there. Be a teacher, not a grader.

Also see this question and my answer there.

Note: To make rework possible and not overly burdensome on the grader, students turned in work on paper. For rework they also turned in (in a folder) all of the previous versions that had been commented by the grader. They also highlighted, in the new work, changes to the most recent version. It was easy and quick to see if additional points should be awarded and easy to mark up the latest document with suggestions, etc.
This may not scale beyond 30 students per grader, I realize. I know that at 40, scale starts to be an issue.


Are there specific organizational processes or tools (not necessarily software) that can help in developing and structuring research ideas?

May I recommend Org mode? It's free software, and it was created by Carsten Dominik, an academic himself. Its focus is to help you maintain hierarchical notes and to-do lists, but it has a lot of other features that are useful for juggling large amounts of information, such as tags, links, many kinds of summary reports, and capture (a way to quickly add a note in the right place before you forget it), as well as many features useful for scientists in particular, like tables, spreadsheets, mathematical notation, export (as papers, slideshows, or websites), and support for source code and reproducible research. Perhaps best of all, Org documents are text files, so you can munge them with standard Unix tools at whim. I've moved more and more of my workflow to Org since I started using it in 2010, and I regret nothing.

Org has a steep learning curve, which gets steeper if you aren't already a disciple of the Church of Emacs. But as I see it, getting used to Emacs is worth it even without Org mode, especially if you do a lot of programming. I was an Emacs zealot for years before I took up Org.


Submitting multiple papers to the same journal simultaneously

I don't see any downside to this as long as the ideas in the papers don't "compete" with each other. But if they are sufficiently different it should be acceptable.

That would not be the case for Special Issues, where the editors will be looking for a variety of authors/viewpoints/... but for ordinary issues it should be fine.

However, unless you are a recognized superstar in your field, don't expect more than one paper to appear in any given issue. It might be useful to you, if you are a bit new at this, to try out your best paper first and see what reception you get. If you get a good response you could try to be more bold in the future.


No.

The rules may allow rescinding an offer, but they will not do it.  The program needs to look after its reputation.  A student who got the occasional B is normal.  Rescinding an offer is not.


When I send a recommendation request, does each REU request a different "style" of rec letter?

Before you put their name down, email the professor again just to make sure they're still ok to write the letter.

Once they've agreed, don't worry about the different formats that may be required for different places. Professors are generally fully aware of what the letter writing process demands and would not (or at least, should not) commit to it unless they know they have time for it.

In your initial email, it may be a good idea to list the places you're applying to and their respective deadlines, so the professor has a rough idea of the time commitment.


Is it okay for a potential post doc to send an email to professor on the weekend?

Email is a form of asynchronous communication: it doesn't matter when mail is sent, it can be read whenever pleases the recipient.

High-ranking professionals should not sacrifice their operational efficiency to avoid the possibility of lower-ranking professionals feeling stressed, overwhelmed, etc. by out-of-hours emails. High-ranking professionals should make lower-ranking professionals aware of work-life balance. Managers and subordinates should discuss expectations.

Technology can help. Email should never raise notifications. (They're too numerous and interfere with flows.)  Messaging apps can be segregated: Some for work, others for home. (Signal at work, WhatsApp at home, for instance.) Work apps should only raise notifications during set hours.

Only individuals can establish their own, "best" work-life balance.


The Cambridge LLB was a Master's level qualification, which was renamed to LLM in the 1980s in order to avoid confusion with the more widely used meaning of LLB as an undergraduate degree.


Is there any way to do good research without people noticing or follow up on my work?

The prospect of getting "scooped" in extensions to your research project is rarely a big problem, because you always maintain a head-start on others through the period of time it takes for a paper to go from completion and submission to a journal to publication.  Even if your paper is extremely well-written in the first instance, there is usually at least a six month delay between initial submission and publication; if you require revisions to the paper then the period of delay is longer, and it can often take years until publication occurs.
Now, obviously you can start working on extensions to your work at any time you want.  If you do your work sequentially, and you start working on extensions as soon as you submit your previous work, you will still have a head-start of at least six months (if not a year or two) on those who later read your published work and then decide to extend it in like manner.  If that head-start is insufficient then you can always start working on your extensions before submitting the finished product of previous work.
Irrespective of this, I would encourage you to see interest from other researchers as a desirable outcome, and be flattered if there is a "flurry of papers" that follow your work.  (Oh, what I wouldn't give to have such a problem!)  This is desirable for the progression of science and other academic fields.  It is useful to have multiple researchers pursuing research in a field to progress it more broadly and rapidly, to give a heterogenous range of approaches on the subject, and to act as a check on erroneous work.  Most researchers have the opposite problem --- it is often difficult to get other people interested in your work, and many good papers end up with zero citations because they do not attract interest from others.


The credits refer to the quantity of studying. 60 ECTS credits makes up one year of study. To complete a degree, you need a fixed number of credits, ie you must pass a certain number of modules (or equivalent). The grade of the degree you are awarded is determined by how well you do in those courses.


A question in the future research section - is it considered appropriate to write a paper on it?

Just because an author puts forth a question doesn't mean that she or he owns that area of science.  You are free to pursue any question that was posed in or inspired by an article.  Even if the authors are actively pursuing the question, your research on the question will likely take a different form.  It is unlikely that you will have exactly the same methodology, so the results will be different.  And, even if the studies are exactly the same, the contribution you are making is important -- i.e., replication is essential to the advancement of science.

So, if you are inspired to pursue a given research question, full speed ahead!


Removing some citations between initial and final submission of paper

You are of course entitled to add or remove parts of your paper to adhere to length and content guidelines of a conference or journal. If such changes lead to a change in the references being cited, then that is reasonable. Of course, it is also reasonable for the journal or conference to determine if the changes that you've made affect the overall quality of the paper. So it cuts both ways.


How to leave graduate school without pain

Some thoughts:

Don't decide what you want to do with your life on the basis of not annoying your current supervisor. If you really want to stop at an MSc then do that, but if you really want to do a PhD with a different supervisor then see if you can do that. Or you might decide you prefer the freedom of a supervisor that doesn't much mind what you do.
Your supervisor is a professional. There's a chance they'll be really nasty, but it's more likely they will behave properly and sign the form, even if that isn't what they personally want.
Lying is not a good path in Canada (well, not for most people at least).


Is there a rule or style guide on use of gender-specific pronouns in academic papers?

The reason for using "her" more frequently nowadays is to correct an ongoing imbalance: in general, for a long time, "his" has been used, even where a more neutral pronoun ("one") should have been used instead.

Grammatically, however, any of the recipes you suggest would be appropriate: it is only the matter of the particular taste of the author. I would recommend, though, that when using both "he" and "she," that you use one consistently throughout a particular usage. Don't write "she/her" in one sentence, and then "he/his" in the one after. A few paragraphs later won't be a problem, though.

The reason "one" is not nearly as popular is that it is somewhat awkward-sounding; too many "one" and "one's" in the same sentence makes it feel too stiff and impersonal. (It's a bit of a catch-22, I know, but that's the way it is!)

One other option that you did not mention, though, may be the simplest route of all: simply use collective plural pronouns: use "they," "their," and "theirs." It gives you the benefit of including everybody, without having to contort your writing to do so.

(I would also comment that some books go out of their way to be gender-neutral, particularly through the use of "gender-neutral" names: Chris, Sam, Pat, Jean, and so on.)


Does publishing a paper on arXiv prevent me from submitting it to a non-open access journal?

You are generally allowed to publish even in a non-open access journal even if a pre-print is on the arXiv.  Most journal copyright agreements explicitly allow the authors to post the article online.  Here's an example of a fairly generous one:

  The ASL hereby grants to the Author the non-exclusive right to reproduce the Article, to create
  derivative works based upon the Article, and to distribute and display the Article and any such derivative
  work by any means and in any media, provided the provisions of clause (3) below are met. The Author may
  sub-license any publisher or other third party to exercise those rights.

and a less generous one which still allows the author to post a copy online:

  I understand that I retain or am hereby granted (without the need to obtain further permission) rights to use certain versions of the Article for certain
  scholarly purposes, as described and defined below (“Retained Rights”), and that no rights in patents, trademarks or other intellectual property rights
  are transferred to the journal.

  The Retained Rights include the right to use the Pre-print or  Accepted Authors Manuscript for Personal Use, Internal Institutional Use and for
  Scholarly Posting; and the Published Journal Article for Personal Use and Internal Institutional Use.

I've seen examples where the journal actually did some genuine copyediting beyond what the referee did where the author wasn't allowed to post the version that benefited from the copyediting, but could still post the earlier version.

So, for most journals, the answer is that you're allowed to post the article online because it's specifically allowed by the document they ask you to sign.  But it is possible that posting on the arxiv will rule out particular journals that have more restrictive policies.


People who have run an online conference, how much does it cost?

All four I know of have cost zero.  However, they have piggybacked off university licenses that the host institution already purchased for teaching classes and some small amount of university IT support, and various organizers may also have chipped in small amounts of personal funds for small items.


Will the Ph.D. stipend be enough to support my parents?

I estimate that I need to send about 400 USD a month to my parents. Will I be able to afford it?

I live on a graduate TAship that pays slightly more than 20K per year. I can put away about 200 USD every month. I live in a fairly expensive city, eat out once or twice a week, but don't have a car. Exactly how much you will be able to send home will depend on your lifestyle and where in the US you live. New York? You'll probably have very little left over. Middle of nowhere, out on the coutry? 400 USD is reasonable.

  Am I correct in assuming that the typical USA stipend would be about 20K a year?

Depends on your subject area and school. Some have more funding for grad students, others have less. Your advisor may also be able to supplement your salary from his grants if he's well-funded. (Bur yes, somewhere between 18 and 25K are the most common figures).

  Will I be violating any terms of employment of the university, if I take up part-time employment during my Ph.D.? What is the typical nature of part-time jobs one may find? Is it worth it?

Typically, you will have a TA-ship which will count as your part time job. Most schools require you to get special permission to have additional jobs, and these permits are very hard to obtain. In addition, a PhD is hard. You won't have time for much more work outside.

  Is one eligible to seek part-time employment under F1-visa (I am assuming that is the typical student visa)? If not, what are the other options? Are the other visas significantly harder to obtain?

You can only work for up to 20 hours a week during term-time on an F1-visa. These 20 hours have to be on campus, and typically your department will report your TA hours as your work hours. This effectively prevents you from working extra during the semesters. During holidays you can work for at most 40 hours a week, on or off campus. As a student, you need to be there as either an F1-student, or with permanent residence. Permanent residence is orders of magnitude harder to obtain (pretty much impossible).

  Are graduate school stipends taxable in the USA?

Depends on the state, and if all of it is payed out as a scholarship, or if some is payed out as a salary.


Efficient way to determine potentially good AI research groups in mainland Europe

This answer is coming very late, but just in case someone finds it useful:

http://csrankings.org/

This site ranks universities based on their research output in select top conferences in various fields, you could use this to narrow down your list.


How to get students to highlight academic text more effectively?

Don't.

Dunlosky, John, et al. "What works, what doesn't." Scientific American Mind 24.4 (2013): 46-53. -- What Doesn't Work:

  HIGHLIGHTING

  Students commonly report underlining, highlighting or otherwise
  marking material. It is simple and quick — but it does little to
  improve performance. In controlled studies, highlighting has failed to
  help U.S. Air Force basic trainees, children and remedial students, as
  well as typical undergraduates. Underlining was ineffective regardless
  of text length and topic, whether it was aerodynamics, ancient Greek
  schools or Tanzania.

  In fact, it may actually hurt performance on some higher-level tasks.
  One study of education majors found that underlining reduced their
  ability to draw inferences from a history textbook. It may be that
  underlining draws attention to individual items rather than to
  connections across items.

  WHAT YOU SHOULD DO INSTEAD:  Highlighting or underlining can be useful
  if it is the beginning of a journey — if the marked information is
  then turned into flash cards or self-tests. Given that students are
  very likely to continue to use this popular technique, future research
  should be aimed at teaching students how to highlight more
  effectively—which likely means doing it more judiciously (most
  undergraduates overmark texts) and putting that information to work
  with a more useful learning technique.


Changing Citation after acceptance of an article

You certainly should update the citation if it is still possible, so readers can follow up on your references without wasting time searching for an inexistent patent.

Contact the editor. Typically such minor changes can be done in the proof editing stage, but publishers are usually happiest to hear of such changes as soon as possible.

And congratulations on the acceptance of your paper!


What should someone who has been rejected from all PhD programs do to improve their application for later admissions cycles?

It's difficult to really answer your question without actually seeing your application, but here's some general advice.

Remember that the admissions process is random. — There is nothing you can do to absolutely guarantee admission anywhere.  The most you can do is maximize your expected return.
Calibrate your expectations. — Are you really a good candidate for a top-5 department?  (Hint: Do you have a STOC/FOCS/SODA paper?)  For a top-10 department?  For a top-25 department?  Really?  Be respectful but brutally honest with yourself.  Ask your letter-writers or other faculty mentors to be brutally honest with you as well.  Listen to them.
Identify potential advisors. — Every department you apply to should have at least two faculty, preferably more, whose specific research interests closely match yours.  Your research statement should not only name those faculty but explain why you think they'd be a good match.  Ask your references (or other mentors) for feedback and advice.  Listen to them.
Spread your applications. — The rule of thumb I heard when I was applying was apply for four schools where you have a reasonable chance of being admitted, one or two backup schools, and one dream school.  Do not let the backup schools know that they are backup schools!
Get good letters. — Your letters must address your potential for research in personal, specific, and credible terms.  A letter that only describes your performance in class is worthless.  Your letters must come from research faculty — not PhD students, not postdocs, not lecturers, not managers.  If possible, your references should have direct experience with strong PhD students (either as a reference or as an advisor) to make direct comparisons.  If possible, your references should be well-known active researchers, but this is actually less important than experience with students.  Since you've taken half a dozen graduate classes, you should be in good shape here.
Write a good statement. — Your research statement (or "statement of purpose" as everyone bizarrely insists on calling it) must address your potential for research in specific and credible terms.  Do not start with an inspiring quotation.  Do not write about how computers are changing the world.  Do not write about how you've been programming since you were in the womb; nobody cares.  Write about your research.  Describe your experience.  Describe your specific interests (not just "theoretical computer science").  Describe a problem that you might want to work on, with enough background and technical language to convince the reader you know what you're talking about and that you actually care.  Bonus points if you correctly cite one of your potential advisor's recent papers, but don't force it.
Get feedback. — Send the final version of your research statement to your letter-writers (or other faculty mentors) and ask for their brutally honest feedback.  Give them plenty of time.  Expect to get your statement back soaked in red ink.  Expect different people to give you conflicting advice.  Listen to all of them.  Lather, revise, repeat.
But this is all about the form of the application.  The best way to improve the content of your application is DO RESEARCH.  Get paid to do research if you can, but do research anyway if you can't.  Find a mentor (at your undergrad institution?) if you can, but do research anyway if you can't.  Post technical questions and answers to cstheory.stackexchange.  Follow CS theory blogs and read the papers that they write about.  Keep a copy of the most recent STOC or SODA proceedings nearby to read while you're compiling, or waiting for the laundry, or riding the bus, or whatever.  Talk regularly with your letter-writers about your progress.  Write, write, write.


Do contemporary publications cite more sources? Why?

jakebeal has pointed at the more technical reasons for the increase of references. We should, however, not forget some of the more subtle, but perhaps also, more fundamental changes that has happened.

First, there is a gradual change in how science is communicated. Scientific papers have developed from letters that were read aloud in front of scientific societies and also published as personal letters. The scientific debate was more closely akin to debates between persons making observations. Obviously this was possible for the reason that there were very few involved in any one research question. So, in part the development seen is due to a development of publishing driven by changes in the form and volume of debate.

Second, research questions have become more complicated involving larger and larger groups of scientists with varying expertise. This increase in complexity also means references are no longer required to cover just a specific question but also information from adjacent or supporting fields.

Third, science is disseminated in smaller parts today that what was the case back in time. This is partly out of necessity related to the second point above. Additionally, and this is perhaps not the greatest aspect of developments, there is the pressure to publish due, mostly, to the fact that academic careers are measured in terms of number of publications and number of citations. The number of publications has thus increased for several reasons and hence also the number of somewhat relevant papers to cite. I will not get into bad behaviour such as self-citations here but it is clear that any system will have flaws and some people will make use of such flaws to benefit themselves.

So at least some of the change in number of publications is due to developments in the way we perform and communicate science and also changing pressure from the academic world on researchers to publish and be cited.


Is it appropriate to "shop" through high-impact journals before sending the paper to more specialized journals?

Judging the value of work is subjective, and can differ significantly between different researchers.

There is not harm in trying high-impact journals if some experienced people (like your mentor) consider it worth-while. But if you tried three different journals and get more or less immediate rejections, you should probably aim lower. Otherwise you just waste time in waiting for another five rejections (and you also waste the time of the editors/reviewers).

Maybe, after three rejections, you can discuss this topic with your mentor again, mentioning that you don't want to wait another three years for your paper to be published.


Professor charging class cash for magazine

This is a bit subtle in general, but the specific case seems benign unless the professor requires you to buy if from him/her specifically. If you can show that you already have access to it (possibly destructive access, depending on the use - cutting it up) but still must again purchase it then it would be questionable.

However, note that many professors assign required textbooks that you must purchase. Sometimes, believing that the best book for the course is the one they wrote themselves, you are actually contributing a few dollars to their pocket when you buy it. Noting that a $US100 textbook gives the author(s) around $5 back money probably isn't an important element of their decision. There are some professors who will return there royalties to students in some cases when the student buys a new copy.

I once wrote a supplementary set of notes for one of my advanced classes. They were required (and referred to daily in class), and cost the students the amount required to duplicate them. I didn't gain from the transaction, nor was I specifically paid to create them.

It is acceptable, in my view, for a professor to require such a resource. It is less acceptable to require purchase from a specific source from which the professor profits.


How to handle peer evaluations in two person team assignments?

Is this evaluation fair for small teams (2 or 3 people)?

With peer-evaluation schemes like this, the fewer students there are in the group, the more vulnerable students are to gamesmanship and unfairly false ratings.   Even if they're not actually unfair to each other, their feelings of vulnerability to one another's unfairness is deadly for your student ratings.  They will blame you for putting them in this vulnerable position.  Plus, if there isn't exactly the same number of students in each group, it's difficult for students to feel that the scoring is fair.  More broadly, I have found that students hate "allocate points" schemes.  Perhaps it seems like I'm too pandering to students with regard to their student ratings, but I believe there are good reasons to take a hit on ratings (e.g., a rigorous course) and unwise reasons to take a hit on ratings (e.g., using a peer evaluation technique that they think is unfair).

My approach to this problem has been to ...

(1) promise that peer ratings will stay completely anonymous -- which can even be accomplished in two-person teams by combining the peer rating with another scored element (e.g., class participation) when reporting their scores.

(2) gather peer ratings as responses to some 1-10 rating questions (e.g., "Attended all group meetings, 1 = Disagree Completely, 10 = Agree Completely") rather than an allocate points scheme, and

(3) delay the grief of doing peer evaluations until the end of the semester.

I realize that what I do doesn't fit with your current plan, but maybe it's something to think about.


Should I report this infraction on Masters applications?

No, you don't need to report it, and in the US it won't be reported either due to privacy laws. The school handled it and it is done.
Move on.
I worry about the professor, actually. If you cited the original it isn't plagiarism in fact. But if you quote it (rather than paraphrasing)with citation then it should be clearly "quoted" using some sort of writing convention, such as quote marks. Paraphrasing "incorrectly" doesn't make sense to me unless you somehow misunderstood and changed the meaning. That isn't academic misconduct of the same sort.
This shouldn't be a future issue in any case.


Is it ethical to use previous data from work in academic research?

In your current academic organization, there should be an Ethical Approval Committee and they can help with legal obligations on using any data. In my opinion, the first step will be talking to the committee.


Trying to switch fields from PhD in computational biology to postdoc in machine learning/stats, how to increase likelihood of success?

My answer is based more on experience from computational biology, but I think it is relevant for other fields:

Changing fields is very common in academia, especially at the PhD/postdoc transition. In many cases it is actually considered an advantage, since you can import your skills, expertise and a certain thought-process into a field in which many people do not have those skills. For example, many physicists, computer scientists and mathematicians have migrated to biology and have made significant contributions. In fact, there are even postdoctoral fellowships that specifically fund this type of field-change.
Regarding your "will they take me seriously" questions: Since you are aiming mostly at applied ML/stats, I don't think you should be too concerned if the ML/stats theoretical community take you seriously. Many theorists tend to look down on applied science - don't worry about it, you can still have a significant impact without advancing any theory. It sounds like in the future you will either belong to the department in which you want to apply the techniques (e.g. a biology department) or will work very closely with people in those departments. In this case, you will usually be considered the ML/stats expert.
Having said all that, of course it is your job to become an expert. Teaching yourself the theory is important, but if you are going for applied science, especially applied ML/stats, it would be a big advantage to get actual experience in using them. There is a huge difference between learning about these methods and actually implementing and using them. You will see that during your PhD you can often expand your research in directions you are more interested in. It shouldn't be too difficult to use some ML/stats creatively in some sub-projects (which could later be expanded).


The importance of the title "Mathematical Physics" vs. "Physics" on one's degree for grad school/jobs

Switch to Math Phys. It won't hurt your job prospects at all, since you don't want to be an experimentalist or phenomenologist. Math Phys covers any decent theoretical physics ground anyway. You'll be doing yourself a big favor and it will even help you focus more on one area of research, and put you into a healthier social environment.


How to overcome changing undergrad course/university due to failure

Difficult times occur. This is normal. Unless you did something foolish that caused your failure (and nothing indicates you did), there is no reason to feel regret.

You cannot control everything in your life. Whoever does not attempt anything, does not fail; people of action fail regularly. Failure is a central part of life, and there is no reason to regret attempting to study physics and then finding out it's not for you at this phase of your life. In fact, I actually recommend testing ones limits early, and knowing where they are makes one a more mature personality. Your current success is point-in-case.

And, keep in mind: limits may be expanded, albeit slowly. Therefore, my recommendation depends on whether your regret refers to ceasing to do physics itself (the topic!), or it is rather the failure to complete (the studies!) that you regret.

If you feel that you would have liked to do physics (the topic!) after all, perhaps you can consider reactivating your studies (or add a Master's degree as suggested elsewhere). But if it is only the missed opportunity, then I recommend to notch your physics studies up as valuable experience and move on the path where you have made progress and which clearly suits you well.


Keeping track of all you have to do in academia

Another nice todo list system is Trello which lets you do things like add mini-check lists to items, make separate lists for each thing, add notes to items, add pictures to items, and add other people to items.  The ability to add sub-items helps a lot in that it makes it feel like I'm getting somewhere on large projects that take a lot of time and hang around in my to-do list for weeks.

Trello is also really nice for sharing/collaborating/delegating work.  In our lab, we have a Trello board for any projects where multiple people are collaborating so everyone is able to keep track of who's responsible for what.

Last, it lets you move your items around so that you can prioritize them.  Stuff that you need to get done sooner goes on the top while less critical stuff is on the bottom.  I also have a bit of a garbage cleaning policy where if it's been sitting in the low priority for a while and I still haven't gotten around to it, it goes into a theoretical "someday when I have free time" list.


How to phrase potential contributions in thesis proposal?

"If the proposed research is successful, there will be three main
  contributions.  First,....  Second, ... Third,..."

What you need to fill in is the specific nature of your contributions.  It's not enough to say that your algorithms will be "better" or "interesting" or even "useful".  You might use these questions to form a list of specific contributions:

Will you be discovering something new about the problem of data
classification and prediction that no one knew before, or only
understood poorly?
Will you be combining two or more methods that had never been combined before?
Will you be simplifying the problem in some non-trivial way?  Or expanding it? Generalizing it?  Making it more specific or concrete?
Will you be formalizing the analysis in ways that have not before?  What will your formal analysis be proving?
Are you applying an algorithm or formalism from another domain, that has never been done before in this one?
Are you demonstrating through experiments or other empirical research the viability of theoretical methods that have little empirical support?

Finally, imagine that you have completed your dissertation, and maybe you have published articles based on it.  Now imagine what other researchers might need to use your work and build on it, and therefore to cite it.  Why would future researchers need to use your work or build on it?


How much feedback should you get from a Supervisor?

I meet with my supervisor nearly every week

This sounds like a good level of engagement. Some people may prefer more frequent contact, some may prefer less (and it may vary by stage of a project), but I'd say "nearly every week" is a pretty solid middle ground.

Whenever I ask the supervisor on things I don’t understand they never have an answer and say they don’t know

It's reasonable to expect students to do their own work towards finding answers, and when you get into "research-level" investigation rather than "coursework-level", experts in the field do not have full knowledge of everything. There's too much "stuff" out there, it's not possible for even experts to be on top of everything except their very narrow world. Even most things they may have read may not come to memory on cue. This can even include details of ones own past work! Knowledge at the research level mostly involves being able to find the information you want efficiently and to understand it - sometimes this involves just knowing the general area enough to know search terms to use, sometimes it involves knowing particular individuals who may have written on the topic, sometimes it involves realizing you've read something similar before and finding the paper in some way you've organized papers (perhaps in a literal file cabinet, or in these digital days perhaps a PDF on your file system).
It's also quite common that there is no answer, or the answer depends on so many different factors that the answer is ultimately up to informed opinion, and different people will come to different conclusions.
Without knowing what sorts of things you are asking about, it's hard to know if your supervisor is just nudging you to do more background work on your own, or if they're pushing you off to save their own time investment, or if they're entirely clueless.

“I didn’t read it in detail but I thought it was good”

This response would be frustrating to me, too, but without knowing your advisor it's tough to judge. Perhaps they really do think your work is just fine. That's great, and nothing you need to do about it! Perhaps they think your work is good enough for a masters thesis. That's great, though unfortunate if you're trying to polish some skills, but should get you through the proximate goal of graduation.

Also I asked them about a key idea in the project that was central to one of the papers and they just said “I don’t understand it either”.

It's not entirely clear but I assume you mean this is a paper that is part of a project you're working on, with your advisor as one of the authors? It's unfortunate, then, if they are an author on a paper they don't entirely understand, but sometimes that's what happens when you collaborate. Hopefully they at least understood at the time of publication, but in this situation I might ask that they direct you to someone who does understand better. Sometimes experts rely on other experts with differing expertise: this is a much more efficient way to work in interdisciplinary areas than attempting to become an expert in everything (which is futile).

I submitted my most recent draft and after cancelling our meeting they said they would give me an email of written feedback and it never arrived.

This is rude, though it's reasonable for you to give them another nudge and ask when you can expert feedback. Hopefully they respond productively.

I don’t know if I’m expecting too much from a supervisor or if this one is the norm. I thought they were meant to be experts in the field.

Nothing in the story you tell sounds to me like it conflicts with your supervisor being an expert in the field. It sounds like there are some orthogonal issues: maybe they're too busy (which is a bad excuse, but not particularly uncommon), maybe they see your project as not particularly important, maybe they have more expectations of independence from the students they advise. What you describe sounds "normal" to me, but "normal" doesn't mean "acceptable". My own research advisors were always more helpful than what you describe. From the selection of questions we get on this site, others are much worse.

If you were earlier in the process, I'd suggest finding a different supervisor that aligns better with the guidance you're looking for. Being just a month from your due date, though, I'd keep a shorter view and look to just your immediate next goals. Ask very specific questions of your advisor about your next goals, not vague requests for feedback. Questions like: "is this work sufficient for a masters thesis so that I can graduate/get good marks/publish in a peer reviewed journal?" And, if not, what specifically do you need to do to fix that.


I train graduate students to lead biology discussion sections, but the philosophy should transfer...

I think your instincts are excellent - students do not need more lectures. What they often need help with is figuring out what they do not understand, and learning how to overcome being "stuck." That, and practice with feedback. Some suggestions, particularly since summer courses are so fast. I'm going to assume they have homework, and that the homework can be worked on in a discussion environment (you will not be "doing their homework for them").

Instruct students to bring their homework problem set. Look over the problems yourself the night before, and determine the easy ones from the hard ones, and make notes to yourself where students are likely to get stuck.
When students arrive, tell them to start work on a difficult problem. Plan on giving them 5-10 minutes -- whatever they need until many of them slow down. Walk around as they work and just see how they choose to work.
After several are stuck (it may take you practice to figure out what question to use to get this level of difficulty), have them get into groups of three and compare their techniques and what they found difficult. Walk around again and ask questions like, "Tell me how far you are. Can you show me a part that is difficult? Can you get out your lecture notes and find the section relevant to this problem?"
Usually at this point you will see a sticky point that more than one student is wrestling with. Now is a great time to pull everyone's attention back to the front of the room and you can work through that problem (or one similar) and answer questions for 5-10 minutes.
Have students return to the problem and complete it. Have them go back and do a simpler problem on their own to reinforce.
Rinse and repeat.

Using discussion time like this makes students happy because they are getting their homework done. Smarter students help slower students, which keeps them engaged. You as an instructor learn a lot about what students don't understand, which is often a complete surprise. Plus, it's active and not boring and doesn't require a huge amount of prep.

If this gets really dull, you can have small-group competitions where students have a single sheet of scratch paper and have to respond to a prompt you flash on the screen. I like to split the room into the right half (five groups of 3 students) and left half (five groups of 3 students) and have competitions like this for "basics" material. The half of the room with the groups with the most right answers gets a point for each round of competition. Everyone participates, but the answer is the group's and so shame for wrong answers is reduced.


Can I post on the Internet a page which summarizes the essential technical contributions of a paywalled article?

As long as you write the summary yourself, rather than copying the important sentences, there is no problem. It would be the same as an open newspaper article reporting about some research study.

Don't forget to provide proper citations, but as far as I understand, you are already doing that.


Put a half-baked paper in arXiv for the purpose of documentation

ArXiv.org is a preprint server.  It is not intended for your purposes.

Even though people do upload all kinds of documents (half baked ideas, their PhD thesis, lecture notes, ...), I personally think it inappropriate.

You might consider putting it on your website, or even emailing it to people who are likely to be interested.  Or, make time to finish it!


Is a paper with no citations likely to contribute to citation metrics in a way which reduces my job prospects?

No, this is not a problem. Everyone has papers on their CV which have few citations, including older papers. If this were true for all your papers, in particular even all of those which are several years old, this could be an issue - but this does not seem to be a problem at all in your case.  (Note that the distribution of citations vs. papers is somewhat similar for everyone, reflected e.g. in the fact that there is a clear relation between the number of publications and the h-index.)
Moreover, if you really feel later on that a given paper does not represent you well, you can always omit it from your publication record - you are not obliged to list everything you ever published there, in particular if you feel it is not relevant.
So I would go with being a coauthor of the paper, if the others offer coauthorship to you, and you feel it is deserved.

Edit: To follow up on your updated title, a paper with a low number of citations will not have a negative effect on citation metrics: Typical metrics are either the total number of papers, the total number of citations, or (most importantly) the h-index, none of which gets worse if you add little-cited papers.  The only indicator which would be affected is the number of citations per paper, but this is rarely used - and even then, a single little-cited paper will not have a big effect.


How do you promote your papers in Mendeley?

Mendeley has two types of groups- Public and Private According to their website

  Create and join Public Groups to share knowledge and discuss new
  research with others with similar interests. You can also create
  Private Groups that are only visible to invited members, letting you
  share information securely.

When discussing setting up a profile it promotes the idea of you been able to publize your publications through mendeley.

  Publications - Adding your publications to your profile allows you to
  publicize your work to a global audience. You can add your
  publications to the My Publications folder in Mendeley Desktop or Web
  Library, or upload them directly via your profile. You can also add
  the entire contents of your Scopus Author Profile in one batch

On another page it states that you can promote your work publicly

  By connecting your Mendeley profile to your Scopus Author Profile, you
  are able to claim your work as identified by Scopus. This allows you
  to publicly promote your authored work, and access a wealth of data
  provided by Scopus - as well as several other Elsevier services - in
  the form of Stats.

For your publications to be seen publicly you probably would have to edit your privacy settings and select for you publications to be seen by everyone. Picture source


What is the difference between the promoter and the advisor?

As far as I understand, in the Netherlands, only full professors may be appointed "promoter", i.e. the official advisor, the super-boss if you will. Other faculty members must apparently get authorization from the university (see comment).

So if you are going to be supervised by someone who is not full professor (e.g. associate/assistant professor), that person will be appointed as "(co)advisor", while a full professor will be acting as an official advisor/promoter and will chair the doctoral examination committee.


Can instructors fail honest students when tests are too hard because most students are cheating?

I agree that the policy seems to be that using previous years' tests to study is allowed. However, if this is the case, the faculty should say something and make sure that all students have equal access to previous tests. The fact that some students are unaware that using previous tests to study is permitted is a problem, as is the unequal distribution of tests. I could easily see a student who was marginalized from the group for some reason (sex, race, nationality, etc) not getting these unofficial emails, and then it would be an issue of discrimination.

I would recommend the faculty post the previous year's tests to the website to make sure everyone has equal access and is aware that these are permitted study aids.

As a student, I would push for a clear statement in class on whether or not these aids were permitted. If faculty refuse to make a statement or take any action I would recommend speaking to your academic advisor about the issue.


What should I do if my advisor is forcing me to vote on a specific candidate in IEEE elections?

Allow me to hypothesize a different tack from most of the other answers: Simply don't engage in this issue at all. As my mentor said once, "You constantly get institutional demands for some action, in some cases it's best to ignore them, and you'll find that many just go away."

This request is so incredibly unethical, and also so completely orthogonal to your responsibilities as a graduate student, that it's hard for me to imagine your advisor spending time on tracking you down and taking revenge over it. If you think you might receive more pressure later on (e.g., I've sadly cracked under such circumstances), go ahead and cast the online vote in the privacy of your own home, and then later on say, "Oh sorry, I got a notification and cast the vote immediately."

The request is so inflammatory that I don't see any use to "politely having an open discussion with your advisor". I think that only opens the door for defensiveness and retaliation. As wildly unacceptable as it is, I don't see it as being a good use of your time tracking down where to lodge a complaint over this matter (which your advisor seems canny enough to avoid documenting except verbally, so it would be just your word against his, according to comments above).

At least consider the null action as a possibility.


Ethics of using public and illegally obtained databases for academic purposes

Relating to just the AshleyMaddison data, there is a plethora of articles on your exact question. I will summarize the main talking points and provide links at the end.

1. Can I download it?

The data is probably public-domain, but it depends on where you live. In some countries like the US, the data itself is publicly accessible and part of a wider conversation about personal rights to privacy, whilst in others like Canada, is has been explicitly decided that AshleyMaddison still holds the copyright and downloading the data is akin to acquiring stolen property (note, AM is owned by AvidLifeMedia, a Canadian company, and people have said that this decision was to offer some degree of protection to ALM, as hacked users cannot use the data dump as evidence in court). Other countries say that fundamentally nothing that can be downloaded can be stolen, so this doesn't even apply.

2. Can I share portions of the data with others?

If you are in a jurisdiction that allows you to download it, you can by default share it - and many (perfectly legal) sites exist for just that. You type your name or e-mail address in to see if you are part of the hack (or your spouse was). For better or for worse, there is no crime for making public-domain data easier to access.

3. Can I process the data and share summary statistics?

Oddly, unlike the above 2 issues, this is legal in every country which offers protection for journalists and researchers - including Canada. Many researchers, particularly those researching infidelity, have asked lawyers this question, and they all say the same thing - yes it's legal. In fact, top US lawyers have gone as far as to say that journalists are probably in the clear if they publish a list of names of celebrities who appear in the hack, for whatever little public good/interest there might be there.

Many articles also point out that there is a big difference between the legality of this, and the ethics of this. Both the law of the land and what is considered ethical behaviour changes over time, and they don't always have to be in sync. Some say that in using the data you are condoning and even encouraging the hack - which may lead to more hacking/data dumps in the future. Other's say that your research may be the only grain of good to come out of the whole debacle.

I will summarize by saying what I would personally do, which is use the data, get the outcomes, then way up the pros and cons of those outcomes with the example you will be setting for others in using this data. Legality is really not the issue here at all, because even if it is illegal, you are incredibly unlikely to find yourself going to court from either Ashley Madison or hacked users, as both parties would have a very poor case. Those aren't my words, those are the words of Jennifer Granick, a law professor at the Stanford Center for Internet and Society.

So if the real question here is the ethics, then this is something that is ultimately up to you to decide on. There may be all manner of real repercussions from your department - particularly if someone in the department turns up in the database... - but that's a very different question.

http://www.huffingtonpost.com/entry/ashley-madison-hack-creates-ethical-conundrum-for-researchers_us_55e4ac43e4b0b7a96339dfe9

http://www.al.com/news/index.ssf/2015/08/is_it_illegal_to_download_the.html

https://onlinejournalismblog.com/2015/07/20/ashley-madison-ethics-journalism-hacked-documents/

http://fortune.com/2015/08/19/ashley-madison-media/

Finally, there are many stories that people have posted online detailing their experience at the hands of the hack. Some say it wasn't really them, some say it was. Some are outraged, some are just numb. I would suggest reading one or two of the longer blog posts to really get a sense of what this data means to some people. It's more than just a resource. People have committed suicide due to the shame or discrimination they faced as a result - most notably people from the LGBT community - so it's really important to not shy away from that when deciding to proceed, or not, with your research.


As someone who is doing my PhD in Natural Language Understanding I first of all recommend you are careful what you wish for. Undertaking a teaching post while doing a PhD is very time consuming and I have found that it has got in the way of my research. So much so in fact that I limit myself to no more than 6 hours of teaching a week.

  In my imaginary world, I would teach courses in Computer Science that
  overlap with Computational Linguistics (e.g. Structure of Programming
  Languages, Artificial Intelligence, etc.), as well as French and
  Japanese.

I'm sure it's different depending on the university, but whatever department is paying your PhD stipend most definitely has first call on where and what you teach. Although I'm a mathematical linguist, I spend all of my time teaching programming and artificial intelligence. Another reason for this is because my background is mathematics and computer science.

  Granted this is pretty specific to my case, so how about I generalize:
  how plausible is it to teach multiple subjects that are
  inter-departmental at the university level?

Taking on a PhD project is about becoming a specialist, not a generalist. Everyone is arguably a generalist. If you are a Computational Linguist, just take on modules such as Intelligent Systems, Computational Linguistics, Mathematical Linguistics, Logic Programming, Math for Computer Science, etc.

  If it is indeed plausible and is something that I can specifically
  work toward, what steps are necessary to be able to do so?

I think it is possible. However, you would need to get explicit permission from your project advisors which I imagine would be difficult. You would then have to discuss how you can help with the other departments such as Linguistics. However, be prepared for rejection if you are not classically trained in the subject and hold some sort of academic merit.

When you start your PhD you will not become a lecturer most likely. You will be encouraged to take on a teaching assistant or demonstrator role, aiding a lecturer. This is still good as it's the next best thing and sometimes you can get loads of marking. It will also give you loads of time to reflect and decide what you want to teach.


I can't figure out why my professor hates me

My answer to your question is, I believe, pretty good advice to follow in general: you should act professionally.

At the end of the day it doesn't matter whether or not your professor likes or dislikes you. If you handle yourself professionally (show up to class on time and prepared, complete your homework assignments to the best of your ability, ask for help when it is needed and interact respectfully with your professors) then you should expect that you will be treated fairly and equitably and should complain if you aren't.

(I've taught at the college level for more than ten years and have never disliked a student. The worst that happens is that occasionally I'll have a student that I find exasperating -- perhaps they talk over other students in class or consistently show up to class 5-10 minutes late -- but these sort of students pop up so regularly that I can't imagine actively disliking any of them. I have a similarly difficult time imagining a professor actively disliking one of their students barring some sort of (extraordinarily rare) extenuating circumstances.)


How much do I have to know about a group's research before I email the PI about openings?

For me, it really depends on the stage of interaction with our group.

For the first contact, I would expect that you have at least visited our website and know what we work on, in general. Browsing the website and some paper titles should be fine for this. If none of the paper titles make sense or sound interesting to you, then why are you applying to work with us in the first place?
If we end up chatting more detailedly (e.g., if you have a phone interview with members of my lab) I would expect that you looked at all the recent papers involving the people interviewing you, and have read at least a subset of those. I don't care whether you understand the work line-by-line, and I am fully aware that some of our work can be technical and academic. However, if you can't be bothered to at least skim some of our papers and try to grasp the core ideas, it does not reflect very well on your commitment to our line of research.


A good question!

There is not much you can do now. You cannot prove anything and can not even name the cheating person. If you think that explaining the situation can help the invilgator to make cheating less likely the next time, you should write them an anonymous email.

I've heard that there are some universities with so-called "honor codes" that tell you to report this - if this is the case for you, do absolutely report it (anonymously).


Boxplot whiskers for a journal publication using APA style guide

Major statistical software such as Stata, SPSS, SAS, and R all use John Tukey's definition (hyperlinks are to the related technical documents), with various degrees of customizability. Some of them also cite William Cleveland's scheme, which is the same as Tukey's.

  one standard deviation above and below the mean of the data

This does not make sense as box plot is largely a device to display the central tendency of data using the more robust percentile statistics and I have a hard time pairing it with standard deviations (and its related statistics standard error and 95% CI), which based on the actual value of the data rather than their rank. If showing mean and SD (or SE) is the motive, there are error bar plots for this purpose.

  the minimum and maximum of all of the data

While min and max also indicate spread, they are also sensitive to extreme values, and hence a less robust indicator of dispersion. So also not making much sense.

  the 9th percentile and the 91st percentile & the 2nd percentile and
  the 98th percentile

I have less opposition against these schemes, the only reason I'd opt for not using them is just we don't need any more schemes.

So, my bet is on Tukey's. And if you're uncertain if readers may be confused, by all means in the footnote state that the scheme is based on Tukey's box plot.


There are basically two ways to leave an academic program permanently: withdrawal and termination.

Withdrawal is a voluntary process, which can occur for any of a number of reasons: academic dissatisfaction, financial, psychological, medical, or family are usually the most common of these. The key factor here is that withdrawal is normally initiated by the student. It is "neutral" in the sense that normally the student hasn't done anything wrong, and could have continued in the program had she so chosen.
Termination is an involuntary process initiated by the supervisor or department. Usually, under such cases, the reason is inadequate performance or violating departmental policies. For instance, one might fail a qualifying examination, fail to pass required courses, committed "academic dishonesty," or violated some other regulation. This is the sort of "black mark" that you are referring to. Depending on the situation, this can have catastrophic effects on the student's ability to apply and be accepted elsewhere. It all depends on the nature of the situation, and what the student's role in the situation was.

On the other hand, suspension or probation are serious issues that require disciplinary action but are not so serious as to require termination. Probation may or may not need to be reported, but an action which leads to a suspension—or temporary removal from the graduate program—probably would need to be reported, if asked about it.

It is not necessarily a given if you will be asked about this in a graduate application—it depends very much on the particular program or school to which one applies.


Stylistically is it acceptable to include equations and formulae in a literature review?

If the equation is important and not trivial knowledge (this can be debatable based on readership, especially in interdisciplinary work) there is nothing wrong with including it in a literature review (properly cited).
When in doubt, cite more than needed in the draft, as cutting down later will be easier than finding the reference again later.

The same goes for important illustrations/figures - for example of a reaction mechanism in chemistry.

Some people actively like to have equations or figures in the review as it provides a visual break in the text which can make reading easier.
Having said that, attitudes will differ based on subject field, country and just whoever reads it.


Returning to academia after long break with new research topics

I have been in a very similar situation for quite some time. Sadly, I don't think there is a way out, or rather 'back in' - without the right connections. Unlike me, you seem to have at least one connection, the professor you mention.

You have not given any details of that possible project (and how it would be financed). You should be able to talk to that professor and evaluate the chances for a (later) postdoc position from there. Again, this critically depends on his connections.

If you are really passionate for this research topic, I think you should take a shot.
If you are OK with not being a researcher, an ordinary job would of course be the safer route.


Harvard Multiple authors- Alphabetical or not?

Always use the order of authors as given in the book or article, regardless of the reference style (Harvard or otherwise).

The order of authors has some significance in many disciplines (for example, in my field the first author is the one who did the most work). So, no referencing system asks you to change the order of authors.


Is it ethical to upload an automatically generated paper to a non peer-reviewed site as part of a larger research?

"Shall I poison a well to see how many drink out of it?"

Frankly, the idea of debunking review processes is not that new, and the latest wave started with the Sokal hoax. There were a couple of follow-ups, with computer-generated papers.

The result was a scandal, a journalistic anecdote. It created attention. Been there, done that. It's no longer an original idea. We got it. You can fool badly screened journals and predatory conferences.

But ok, now, you talk about actual "research" with fake paper dissemination. That may or may not be a legitimate research question, but the fact that you talk about "poisoning" arXiv, which is a serious and expressly not peer-reviewed site makes it already very questionable what you are trying to achieve.

It is one thing to embarrass badly screened journals or conferences (possibly even suspected predatory ones - namely the conferences in question) which Sokal and the SciGen people did, but quite another to abuse a perfectly legitimate repository for non-peer-reviewed papers. In other words, it relies on good will and honesty of the submitters trying to submit good quality work. There are minor safeguards in place to avoid obvious scientific spam, but not against antagonistic submitters.

I do not know (and I do not want to know) what you are trying to achieve with this experiment, but the damage that you are likely to do with this can be so substantial in terms of loss of trust of arXiv and preprint services etc, that you would seriously need to pass it through an ethics committee who can evaluate what legitimate experimental parameters for such a large scale social experiment would be.

Without such a permission and clear delineation of your duties and limitations (which your institution's ethical committee has to evaluate), this research will be unpublishable in a serious journal. And frankly, your academic reputation will be finished. Damaging one of the most valuable resources of openly accessibly publications will make you persona non grata in academia.

Let me add one more thing. There are other preprint servers which have a less strong reputation. There, your experiment may do less damage, though also be less expressive. However, even there, I should believe that they rely on good will and that wilful tainting of wells for scientific knowledge is simply maximally antagonistic to the endeavour of science.

TL;DR: I believe the experiment is highly unethical and extremely damaging. However, you may want to see whether your institution's ethics committee can identify conditions under which such a social experiment might be feasible.


Conference held in year X, proceedings published in X+2 - which to use?

When I cite an article submitted to [a conference held in year X and published in year X+2] - how do I indicate the correct year?

The citation should include the publication year, not the year the conference was held. But, the conference year is useful, so it is worth including too. Perhaps:

Author (X+2) Title. In proceedings of Conf'X...

The Chicago Manual of Style supports this style.


How common is it to inadvertently "reinvent the wheel" in academia?

How common is it to inadvertently publish a finding that was already discovered?

Far more common than anyone realizes or wants to admit.

Stigler's Law of Eponymy states that No scientific discovery is named after its original discoverer.  (Stigler's law was proposed in this precise form in 1980 by Stephen Stigler, who self-referentially attributed it to Richard Merton, but of course similar statements were made earlier by many others, including Stigler's own father.)  I wouldn't go as far as claiming that every scientific discovery is misattributed, but there are hundreds of examples.  Off the top of my head: Fibonacci numbers, Pascal's triangle, Gaussian elimination, Euler's formula (both of them!), Voronoi diagrams, Markov's inequality, Chebyshev’s inequality, Dijkstra's algorithm for shortest paths, Prim's algorithm for minimum spanning trees, the Cooley-Tukey FFT algorithm, the Gale-Shapley stable matching algorithm (for which Shapley recently won the Nobel Prize in economics), ...

  What do you when you happen to find yourself in this situation?

Be brutally honest, both with yourself and with the scientific community.

If your work has already been published, post a reference to the prior art in your web page listing your publications.  (You do have a web page listing your publications, don't you?)  If possible, publish an addendum to your paper.  Email anyone who has cited your paper already, giving them the earlier reference.  When asked to review papers that cite your paper, include the earlier reference in your report.  Become a walking advertisement for the earlier work.

If your work hasn't already been published, try to figure out which parts of your work have actually been done before.  Some of your results will appear verbatim in the earlier work, so you can't take credit for them.  Some of your results will be easy corollaries of the earlier work, so you still can't take credit for them.  But perhaps some of your results will take the old work in a new nontrivial direction.  Build on that.

Also, if your results were previously known in a different field, there may be some value in bringing those results to the attention of your research community.

  Should you just scrap your work if your methods are too similar to someone else's?

Of course not!  Now you have evidence that your methods actually work!  Push them further!


Is academic collaboration overrated? Should one seek it or avoid it?

In many fields collaboration is not only advisable but necessary because the expertise of a single individual is not enough to complete the work necessary. The days when one scientist can do everything themselves is long gone. People have specific areas of expertise and the work required to become a competent expert in every domain needed for a particular effort is too great.

For instance, I do modeling in a number of materials applications. There is literally no way I could do the experiments necessary to support all of the work in my research, so I need to rely on collaborators who have the necessary experience who can perform and guide the complementary experiments, as well as provide the experimental equipment!


Why is it acceptable to cite unpublished works?

You seem to be interpreting citations as a way of proving something by appeal to authority.  That is not what citations are.  A citation is a way of giving appropriate credit to the originator of an idea and pointing the reader to the explanation of that idea.  Not giving credit to the person who gave you an important original idea is unethical, whether that idea has been published or not.

Citing a "personal communication" related to a mathematical fact (for instance) does not eliminate the need to prove that fact.  Appropriate usage would be to write something like "the following was communicated to me by X. Y. [personal communication]", followed by (for instance) a theorem statement and its proof.

Note that if something is in a technical report or on arXiv, it is not unpublished.  People publish blog posts, novels, and Youtube videos.  Published and peer-reviewed are completely different things and it's wrong to conflate them.


How to avoid competition while giving a talk or presenting a poster?

Firstly, I think you overestimate the risk of someone stealing your ideas at a conference talk and publishing them ahead of you. Really, at the point when you're presenting your ideas at a conference, you are so much closer to a successful publication than most people:

you have studied a lot in a chosen narrow field and understand the background of your problem really well
you have a nice idea which you understand better than others
you have a working code or set of experiments or other solid evidence of success
you have made at least some literature review
you have at least a draft of your paper in mind (and some plots already on your slides)

It is really unlikely some freshman in the area will understand your methods and results and publish them ahead of you. Also, bear in mind that most conference talks only hint the idea anyway, as 95% of details are impossible to fit and explain during the conference. And of course, the fact that you present something at conference is remembered by your colleagues, who might then be involved in the revision process. So my strategy is - the more publicity the better (but I am not prepared to make my git repository public yet, so don't ask).

However, if you really want to protect your contribution - only present what is published. Many people still do this, and they're mostly as successful as others.


As an undergraduate, should I have done research on all of my research interests listed in my resume?

Yes, include potential research interests that you are interested in and not just those you have participated in. Graduate schools like to know your goals and where you want to go with your graduate degree, so including what research would be interesting helps them know if they have faculty that can guide you in that direction.