Why is it acceptable that publishers sell papers they didn’t pay for?

History.

In the dark ages (i.e., before the internet), publishers provided a valuable service. If an author has a great idea, they want the whole world to read about it and the best way to do that is to get someone to publish their work. The publisher arranges for reviews, copyedits your work, and, most importantly, prints thousands of copies and sends them to libraries and archives around the world. (Note that, legally, they need to have the rights to distribute the work, and they claim ownership of the copyediting work.) Doing all this printing, mailing, and copyediting costs a lot money and thus publishers have to charge for their services. They also make a small profit from all of this.

Fast forward to the 21st century and the picture has changed considerably. Since the arrival of personal computers and software like LaTeX and Microsoft Word, copyediting is now mostly done by authors. (Reviewers and editors are rarely paid.) And, due to the internet, it is very easy to distribute papers using websites like arXiv. Going to the library to find a print journal is now a thing of the past, as journals these days just have websites.
Of course, publishers are still doing something, but it's a fraction of what it used to be.

Publishers made a lot of sense 50 years ago, but these days their model doesn't make a lot of sense; they still collect a lot of money, even though the services could be provided much more cheaply. So why does this model persist? Firstly, publishers still own the copyrights to lots of old work that is still relevant. More importantly, publishers own the "prestige" of their journals, which means academics keep sending them their work.


Ethicality of continuing my Ph.D. with intentions of leaving

How unethical is it to continue this year and finish up without
  mentioning any of my intentions to leave the program for another?

It is not at all unethical to continue until you know for certain. I see this as a situation where you are considering your options. You would LIKE to leave, but you are also considering staying if you have no funding at the second program. I certainly don't think you have any obligation to mention your decision until you hear about funding. In February, your current program will still have the opportunity to give away your funding to a new student/another student, so you are not harming anyone by waiting to speak up.

  If I do withdraw from the lab rotation, should I mention why I am
  doing so or just mention that I was not expecting the course work to
  be so intense (which is true due to my teaching taking up so much
  time, I am behind).

I don't think you should withdraw. If you stay, this would be your advisor. And if you don't get funding, you may stay. So you should make sure you have a good backup plan with this advisor at your current school.

  How unethical is it to use my 6 credit tuition waiver to take courses
  in the spring that would hopefully transfer to my other program?

You will likely need to decide on spring courses before you decide if you should stay. If possible, choose courses that would prepare you for either path. If not possible, I don't see a problem with using the waiver you have earned through your teaching in a way that would be of most use to you.


Searching for open source literature management software

I have been in your shoes before and am currently looking for some form of pdf organization.

Here are a few alternatives : http://alternativeto.net/software/mendeley/

What I use, is dropbox.  I even dropped Mendeley because it didn't sync well with android for annotations.  I can favorite papers I need to have on my phone/tablet at all times and always have access to them.  My fellow cohort feels the same way about the lack of pdf organization as we generally just print out what we need.  I've been searching for years and the only thing I can come up with is paper.

Sorry this is isn't more useful, but from my experience, paper is really the way to go.


How honest should I be in disclosing not-so-exciting results?

In research, you don't set out to prove that something is true. You set out to discover whether or not it is true. This would be knowledge. The other is just propaganda.

Negative results are not a failure. They give you evidence just as do positive results. If you ignore, or obscure, results you are lying to yourself and others. If you design an "experiment" so that it is guaranteed a priori to produce positive results, it isn't research.

Hoping that something is true isn't evidence. Many researchers start out with that idea. I think this is true. I really want it to be true. But if it is false, it is just as valuable (possibly more so) to know that and to be able to investigate why.

Report all your results. Try to explain why different aspects lead you in different directions. Only then can your learning begin.


Unattributed work in academia is generally considered unethical. In my own experience, however, I believe that I've come across very few instances of actual ghostwriting where the real author was unnamed. Normally, at least some acknowledgment is called for, either in an editor's note or introduction.

Now, to answer Mankoff's comeent below, by "unattributed work," it can be okay for authors to choose to remain anonymous, if they feel it is in their best interests to do so. However, to take someone else's work and to pass it off as their own is clearly unethical behavior. However, from an ethics standpoint, even if the ghost author is asked about attribution and declines, the "named" author should not attempt to claim sole credit for the work. Instead, the author should make some sort of reference to those who assisted in the preparation of the manuscript. Otherwise, they're passing off someone else's work as their own.


I've seen such grading used for true-false and multiple-choice questions in an exam, where a right answer gained you points and a wrong answer cost you points, but I've never heard of a problem worth "nothing" that cost you points if you got it wrong.

Personally, I dislike such systems—I'd rather give credit than subtract for mistakes—but instructors often have broad latitude in the design and scoring of exams. Some schools do have rules with regards to specific situations (if I remember, there were some weird regulations regarding all multiple-choice exams at my old institution), but in the absence of those, professors are free to set grading criteria as they choose, so long as they are applied consistently.


There is no universal process for writing papers.

Some faculty members don't touch a manuscript until the student has written a draft. Others are intensively involved in the planning process before the paper writing process starts. Still others largely write most of the paper themselves. It really is a function of the individual advisor's tendencies.

However, I think the optimal use of everyone's time and expertise—and to improve the student's development, since the student will ultimately have to write her own papers someday, is to follow a strategy of "taking the training wheels off" over time. For a first paper, the advisor should be very intensely involved throughout the process of organizing and writing. As the student gains experience and learns to work more independently, less and less direct involvement and input from the advisor occurs—although some involvement at the planning and writing stages is best. For the last papers the student writes, she should be the primary driver of the process.


Some professors a my institution are asking for "common" spaces in which post-docs are not allowed. Is this ok?

You ask if this is common in academia. In all universities I've been in (only Europe), I've never seen something like this. Common rooms where usually for every employee of the respective department (administrative staff included).

Solar Mike mentions in the comments "Professors have a need to discuss "privileged" information such as grades which postdocs may not have the right to, so separate spaces are a reasonable necessity - and not a social slur...". That professors need to discuss privileged information is true -- but I usually saw a simple solution for that: People were allowed to book rooms for meetings and then only invited people were allowed to enter. This also takes care of the fact that sometimes privileged information needs to be discussed only by some professors (not every professor who drops in), sometimes between professors and postdocs (or between postdocs or phd students). If  your professors' argument is also that they need to discuss privileged information, you might want to suggest this possibility.

However, I suggest you to choose your battles wisely. Academia is a very hierarchical world -- it can be dangerous to start a battle about minor issues (as long as you are not a tenured professors).  Especially if your faculty wants to have a faculty only room (i.e. they themselves are no advocates of "flat hierarchies"), it may be dangerous to suggest too many revolutionary battles. If equality is really so important for you, try to find a professor who advocates for you.

(Depending on how your institution is, you might also want to fight for a "non-professor only" room.)


What to say to a student who has failed?

I think that you explained the situation very clearly and sensitively in your third paragraph, and that you should send a message to the student along the same lines. All you'd really have to say is that while you of course sympathize with the student, her performance on the final exam makes clear that she did not gain sufficient mastery of the course material to pass the class.

I'll add that I think your message to the student should be clear and concise. The longer your response to the student the more likely it is that you'll wind up in a long, drawn out exchange that stresses both of you out while benefiting no one.


How to find ranking of textbooks by popularity used in a course?

This question is interesting, unfortunately the question is also too broad.  (Course of an specific school or just the subject? By country or which country? At university, MBA or Doctorate level?, etc). But the way to find a possible ranking would be to see best selling books per topic. For example:

Cambridge:https://www.cambridge.org/ar/academic/collections/classical-studies-btu
Amazon's'Best Sellers in Academic & Commercial Writing Reference':
https://www.amazon.com/Best-Sellers-Books-Academic-Commercial-Writing-Reference/zgbs/books/12017
ALIBRI: https://www.alibris.com/search/books/subject/Academic

There you can add filters per subject, which do can do also with many other bookselling sites. This however will give you best sellers per subject/topic in wide.

But you could also search for the program's syllabus and the books are listed there. If it's for your current school and the school sells books, just go ask for their most sold books for your research.

However consider that:

A textbook used is not necessarily the one suggested to be bought.
Rather than textbooks, students can use online materials instead.
In some countries, teachers force students to buy certain books
and certain editions (which they receive some revenue from).
Popular for teachers is not necessarily popular for students.
Piracy always adds a level of error int he estimations.


Good approaches to integrate research and teaching?

An experience that worked out well in my past: in grad school as a TA, I helped to create an "intensive" section of the main introductory artificial intelligence course.  Students who opted into the intensive section did two projects and got 25% more units of course credit.

For each project, the students had two options, an "applied" option and a "research" option, each on something highly topical.  The research options were always restricted-scope versions of academic research problems that the professor and/or TAs were actually involved in.  This was a nice motivator for students, since they could see how what they were doing related to a real scientific problem.
The applied option was similarly relevant to industrial R&D. For example, the machine learning project's applied option was typically to build a spam filter against whatever turned up in that year's "wild-harvested" corpus.  Students met with their TAs multiple times got guidance while working on the project, and were coached on how to produce a good technical report at the end.

These projects also gave a nice path to getting talented and interested students involved in research as undergraduates.  We made a point of reaching out to students whose projects were particularly good and offering to help get them connected with undergraduate research opportunities.  Many ended up working joining the professor's research group, and many others joined research groups of other professors where we helped make introductions.  A large fraction of those went on to grad school, and at least some to faculty positions (though I don't think anybody ever did a proper quantitative assessment). In effect, doing a "trial run" of working on research-style projects in class both helped students discover interest in research that they might not have realized, and also helped reduce the risk for professors to take them on afterwards.

The main challenges in doing this were:

selecting appropriately scoped projects, complex and interesting enough to give the students a taste of research, but not requiring deep background or more than a few dozen hours of work, and
making sure TAs were sufficiently advanced as grad students to be able to coach the students well.


When writing a peer review is it better protocol to quote parts of the orginal work or paraphrase?

For a review it doesn't matter that much, but it's safer to quote, so that there's no chance of misinterpretation.


What are acceptable “relationships with referees”?

Assuming that you mean "references", they should be people who know your academic work well. Basically anyone is acceptable as long as they can be expected to give a fair and accurate statement about what you have done and about your probable likelihood of success in the academic program.

Professors, advisors, employers, Lab PIs. etc. are all fine. They need not be supervisors, but can be. Your mom, and uncles, however, aren't the best, nor is a spouse or child. Anyone with whom you have had a professional/academic relationship and has some stature is a good choice.

As for the description, just say it like it is.


How do I voice my opinion that the teaching of students is being neglected?

The fact is that institutional norms and expectations regarding teaching vs research for faculty vary widely. At my current institution, teaching is very important. At my previous institution, no one really cared. Basically, I would not voice this opinion in any strong way unless you want to make your life difficult. It would only work if the faculty member you are working for is disliked and the person you complain to is firmly on your side.
I did have a similar situation as this in my PhD institution and "voiced my concerns" in a very tactful way. I argued that the course was extra challenging because it was a new advanced level course and had not been given enough resources. (Note that I was careful to say nothing about the effort or quality of the instructor.) The department was able to pay me extra as a TA to take over some of the instructor’s responsibilities. But the instructor was someone who got on the other faculty’s nerves, and my advisor was the associate dean for academics.


Will a masters degree from Japan be seen as less valuable?

I think your decision should be based on future aspirations. Specifically, you need to decide if you are heading into industry or academia when you complete your studies. If you are going into industry, companies want people who know their stuff and can actually do something. It is the application of theory through making it tangible and not necessarily the knowledge of theory that is most valued. Studying in Japan should not injury you in this regard. Having overseas experience is yet another benefit to many companies seeking employees, especially in a country that is a leader in this field.

If you decide to go into academia the advice of your professor is probably wisest to abide by. Exceptions to this would be if you choose to stay in Japan, which would not hurt with a Japanese degree or if you complete a PhD somewhere, which would help to overcome a master degree that some may see as "second rate."Explaining your reason for going to Japan in the admission process should mollify many PhD admission committees


What is the basic difference between a researcher in a corporation, and a university?

As a researcher in a company, I need to take issue with the current answers as reflecting a very narrow view of corporate research. This view is common in academia and reflects the typically limited experience of university researchers with the diversity of the non-academic research ecosystem.
A large amount of research in corporations is, indeed, focused on the near-term needs of products. Companies whose business model is based on widget sales will tend to put their money into better widgets, after all. There are a lot of business models, however, that are not about widget sales.  Some examples:

Some corporations have government funded R&D as a long-term component of their business model. There are important aspects of the research space (even basic research!) that universities are often ill-suited to execute, including:

Research with high team complexity or high integration complexity (professors are not typically professional program managers)
Research that requires a high degree of quality control (grad students are often unreliable!)
Research involving classified or otherwise controlled information
Research at intermediate levels of maturity (where papers are scarce, but the relationship to widget sales is still hazy)

Some corporations have long-term strategic interests that they support by means of R&D investments, including university-like basic R&D. This was the old Bell Labs model (which is still going strong!) and it's still in play in many large corporations, such as IBM, Microsoft Research, etc.
Some corporations, especially non-profits, have missions that explicitly include research goals.
Some corporations are education-focused (just with different educational models), and carry out research as part of advancing their educational mission.
The boundaries between universities and companies can often become blurry, particularly around university "advanced ventures" organizations and in the medical space, where there's a near-fractal complexity in the academic/corporate relationships in many university medical complexes.

The life that you will lead as a researcher in these different sorts of organizations is very heterogeneous. Even within a single organization, such as the one that I work at, the goals and incentives are very different for researchers on the primary investigator track, the program manager track, and the implementer track. Even tenure can be less different than you might think, given the existence of fellows programs and the like.
So what is the basic difference?

All universities are primarily focused on student education, and all professor positions fall into one of a small number of career models.
Every other research organization is much less constrained in form, and you cannot make any assumptions until you understand their business model.


Is it possible to add a new citation after a paper is published?

No.

You cannot change a paper in any way after it is published.

The only thing you can do, is publish an erratum.  But that is intended for serious errors that affect the main conclusions, not for a "I have another related paper".

Note that many people use not only references but also citations to look for related papers.  So if the new citation is your own, newer paper, and cites your old paper, people will find the new paper from the old paper anyway if they use standard scientific databases.


Is this plagiarism or something similar in a master's project?

Passing off others' work as your own is plagiarism, acknowledge the help you were given, there's no shame, on the contrary, you'll be praised for initiative.

You needn't necessarily* provide references to individual posts or your account, which will avoid privacy issues.

You can provide the names of those that helped. If that poses a privacy concern (e.g., you can be identified, because the group that helped you didn't help any other individual), then you could omit some names (e.g., names with lower reputation) and mention that you've done so for anonymity.

You could offer to privately reveal direct references to your examiners, as long as those references are kept confidential.

* Case-by-case decisions should be made on whether an individual post merits referencing directly.


Research after the bachelor's degree has ended but before applying to Master's program

Contact the professor and ask (politely!).

Nobody ever explained to me how you applied for a doctorate until after I found out my undergrad results and people started suggesting I should think about it, so I approached a few of the departmental lecturers whose work I liked, explained that I was interested in working with them and asked if there was any way I could get experience in their group. One of them turned out to have some short-term funding and paid for me to work with the group for a year as long as I did two days a week of general group jobs. During the year I was able to get to know the group, contribute to papers and apply for doctoral funding (which was successful).

So, from personal experience of being in a similar situation, it's worth asking. This took place in the UK about (ahem) 20 years ago, but unpaid or self-funded 'placements' are common in other countries too. Since you have a clear aim (a specific project or area that you want to strengthen your CV in, for a defined period) and it doesn't sound like there is a specific structure in place to facilitate this, then I'd give it a go.


Reference manager that sorts by number of citations

Zotero has a plug-in that will allow you to add a field called 'extra' that contains the number of citations. Keep in mind that the number of citations are taken from google scholar and not from WoS or scopus. But it's a starting point.


I would recommend sticking with what you started using, since there is no real advantage not to. That said, if you really want to change I don't think a change in first name will affect you much. Depending on the citation style, the name change won't even be visible. I don't think this particular change is anywhere near a change of last name in terms of impact on your popularity.

With regards to Google Scholar: you can always add your new publications manually to your profile in the unlikely case that scholar borks, so that's not an issue.


No reply after almost two months since the first interview

Yes, you can ask about the status. And you can ask again for an estimate of the time to resolution of any problems, though it may not be possible to give you an adequate answer.
I also hope that you are continuing to follow up with any other options you have. And if there aren't other options at the moment, all you can do is be patient - and try to develop other options.


How do I handle a colleague's gender change when citing their paper?

Is it an option to ask M Smith if she would be ok if the first citation were to read as the following?

  Smith, M. (published G.) 2014, recent advances in foo, international journal of foo sciences 12:56, 427-865

This would eliminate the only reason I can think of for misgendering the person, namely that readers might be unsure whether they are looking up the correct source. This would be a weak reason, though, since we have DOIs (Digital Object Identifiers) now.

Edited on second thought: What is the worst thing that could happen if you use the new name? Someone might find it more difficult to look up the paper; that's a minor inconvenience. Compare this to the frustration, if not anger and distress, that it would cause M. Smith to be referred to in cold print by a name that doesn't reflect her identity and that she is struggling to leave behind.


How to address the issue of the widespread use of protected material in informal publications?

From an ethical point of view, I think most people can still sleep well despite taking the first fish from Google from time to time.

From a legal perspective, it depends on your jurisdiction and the license of the image. As Jeff points out, it's often fine in many places.

You should define your goals (ethics vs. legal), and act accordingly (which is my case would be do nothing).


This answer comes late, but I hope it is still relevant to you, or maybe to others in a similar situation.

You don't need degrees to do research. Anyone can do it and anyone can publish their research, provided it is acceptable to reviewers and editors.

The difficult part, however, is to get feedback on what you are doing so that you get some assurance of both its correctness and its value. That is easier for graduate students and faculty members at universities and institutes. But it isn't impossible for an independent researcher.

The key is to build a circle of people (or even a single person) with similar interests, who is willing to read your work and give you feedback. One way to do this is to contact some professors at a local university and ask for assistance. Some will be willing to help, even to collaborate, but others won't want to make the effort. So it may take a search.

One of the most important mathematicians of the 20th century, Srinivasa Ramanujan working in India and with little formal education, made contact with G. H. Hardy in England, and it was that association that brought his work to the fore.


Is it plagiarism to reuse your own full-text material from a previous conference in a new conference?

Yeah, copying 25% of a prior paper without attribution is definitely self-plagiarism.  Report it to the program chairs of the conference, and let them sort out how to manage the problem from there.

Additional information, for any coming from different publication cultures: electrical engineering / computer science conferences are serious publications that take originality very seriously, and IEEE policy on the matter is quite explicit.


How free are graduate students to choose research topics given their department?

This will vary based on your adviser, your level of study (i.e. what degree you're going for), your committee and your department.  In almost all cases for computer science, you will be required to demonstrate mastery of the subject.  Incorporating outside knowledge from another subject area, say, cell biology, where you re-implemented or improved a gene matching algorithm, for example, would probably be allowed.

Simply doing an experiment from cell-biology with no tie-in to CS would almost certainly not be approved--but, this is where your adviser, et. al. come in.  If you've got a smashing idea, a good adviser/committee will help you try and find a way to tie it into your degree and PhD students are typically given more leeway here than Masters students.

Though, be prepared, in some cases, an adviser will play a big role in determining what your thesis will be.  Also, if you are being funded by a particular grant under a PI (principal investigator--typically a research professor), it is traditional (at least at my University) to pursue research related to what the PI is doing.  Though it's definitely easy just to ask to be exempt from this tradition.

So, basically, the answer to your question is it depends.  Almost certainly you will be required to do something Computer Science-y for a CS degree, but there can be a lot of leeway in determining what Computer Science-y means.


By googling your title, I found this style valid for online videos, webinars, etc.:

  Author/Speaker (Year) Title of communication [Medium]. Available at: URL (Accessed:
  date).

The source I used was London Metropolitan University Library Services' Harvard Referencing Guide, but their stance seems to be corroborated by other referencing guides.

Adapted reference list example:

  Stepp, K. (2013) HR & the workplace of the future [Webinar]. Available at:
  http://www.slideshare.net/thetalentproject/hr-the-workplace-of-the-future (Accessed: 18
  December 2013).

Note that there actually is no definitive Harvard referencing guide, so the journal you submit to (or university for a thesis) could have slightly different requirements. Nevertheless, the above citation is clear enough, and should be acceptable in most places.


If your professor did their graduate degree in the particular program you're applying to, this could help. The reason is that their letter can be more specific about the reasons you will succeed in that program: "She will be prepared to pass the quals in subjects X and Y immediately, based on her performance at Undergrad U., and will have no trouble passing the qual in Z at the end of the first year. Compared with the students who entered the Ph.D. program with me in 1992, she would have been in the top 25%." (This benefit can also apply when a recommender was previously on the faculty in the department you're applying to.) I do not think it matters so much whether current faculty remember your recommender personally. However, if the reputation or structure of the program has changed significantly since your recommender was there, their impression will be less relevant.

If your professor did only their undergraduate degree at this school, or a graduate degree in another department, then this will not matter or be noticed at all.


Is it advisable to publish a paper with the same name as your thesis?

I agree with Buffy that this is a bit tricky. One could argue that using two different titles (or even two different texts sharing the same thoughts) for two documents with practically the same content is an effort to give the impression that you want two "publications" for one. For this aspect, the title or the text themselves are not so important, but the ideas are. In this sense, all thesises with results published in a paper share the problem with you. But I do not recall that this was ever discussed as problematic, so I see no fundamental problem here. But the discussion here already shows that there are different opinions.

In my experience, it is extremely rare that an MSc thesis is good enough for me to publish as it is. I usually have to improve the discussion a lot to be completely happy. So you can be proud of yourself if your advisors will pass your text including the exact same title to peer-review. Have they said that they will do so without major editing?

Self plagiarism might be an issue, if your university has a policy on that, but I have not yet really understood why this term exists at all. However, you should check the copyright situation in general with the journal you select. Many journals allow to use the contents of the paper for thesises and the like, but you might have to ask for permission. Or you could go for open access.

By the way: I know many people who change titles for instance when they present the same results at different conferences, just to make it look better on the publication list. I would not call this good practice. Buffy hits a point when encouraging you to make things transparent.


Are contributions to a open source project helpful for graduate admissions?

Does open source code contribution matter for graduate admissions?

Yes.

Admission to graduate school is based primarily on your potential for research.  Independent, creative, intellectual work of any kind strongly correlates with potential for research, especially if that work is directly related to the interests described in your research statement.  Contributing to open-source software projects is independent, creative, intellectual work.

Of course, your contribution would matter more if it were merged into the main branch of the project, but something is better than nothing.


"Garbage in, garbage out" - Is it rude to call others' works as 'garbage' compared to ours?

Yes, it's rude to describe somebody else's work as garbage, and unnecessarily so.  You've already said it much better yourself:

  if we used less valid models we should expect less accurate results

There's no reason to confuse this simple factual statement with a value judgement.  Just because something works poorly doesn't mean it's garbage---it may also simply be earlier and less well engineered.  Would you call a Model T "garbage" just because it gives inferior performance compared to a current car?


There is no generic rule that PhD students can't patent their work. When they do, usually, the university or research institution has rules about who owns the IP of what's being done in their labs. My alma mater had a 3-thirds rule where the student, the supervisor and the institution all held a third of the IP.

I don't find it particularly surprising that only few students end up patenting their work. Patents are much less useful than good scientific publications when applying for academic positions or grants. It seems normal that the focus is set on the later.

Also relevant: patenting costs money to file and money to maintain. It only makes sense to secure future sales. Students rarely have the funds for this and institutions usually prefer to spend on other things more closely related to their mission. Most of the time the decision not to patent is motivated by the low potential gain vs. costs ratio.

Universities are usually a bit generous in what they accept to file, but then eventually drop the payments later on if it's evident that the work does not bring any profit.


Why do educators use curve to adjust the performance?

Instructors often use some kind of curve to adjust for the varying difficulty of exams from one year to the next.

The general idea is that if (for example) the class average on an exam is lower than it has been for the same course in previous years but the quality of the students' work is the same, then the exam given this year might have been more difficult than the exam in previous years. It would be unfair to students (and also reduces the signaling power of grades) if their grade is strongly dependent on the year in which they happened to take the course. An instructor might choose to adjust the students' grades to account for this.

It's generally unwise to assign grades in a way that is strictly norm-referenced, without taking into account the students' demonstrated mastery of the course material, for reasons described in this answer. For example, if the class average on an exam is lower than it has been in previous years, but the average quality of work submitted by students is also worse than usual, then the average grade of the class should be lower (to preserve "fairness" and also the signaling power of grades.)

Some instructors might use a curve for other reasons, e.g. if their department has a policy about the maximum number of "A" grades an instructor can give out. (Like this example.)


Is it common for prestigious universities to contact you after you dropped out to see whether you wish to enroll again?

The answer may depend on why you had to drop out, but many universities simply consider you to still be their student even if your studentship is disrupted by events beyond your control, and will assume you are likely to wish to continue your education there.

You do not say why you had to drop out, but common reasons for somebody to withdraw or fail include: mental health issues, financial crisis, physical illness, death or serious illness of a close family member, visa problems, etc.  None of these indicate anything negative about your potential as a student even if they caused you to fail all of your classes.  I have known people who dropped out for a wide variety of such reasons, many of whom then returned to finish at the same prestigious institution after their life circumstances had improved.

Many universities thus make it easy for a student who left for such circumstances to return and complete their studies, and that is likely what is going on with your university as well.


Ideally you should report them both. Online forms might not let you do that, however. If you can only report one, I'd suggest that you list your CS GPA but put a note somewhere detailing the other. You want to give the most complete information so that no one can suggest you have been dishonest.

You will probably have to explain, somewhere, why you abandoned biology for now and simply saying it was because you didn't do so well would, IMO, be a mistake.

However, your university might, independently, give your GPA, in which case you should know how it will be reported by them. If they combine them, then you probably need to do so also, but explain in your application materials the history of it.


Designing the "user experience" for labs without giving too much away

As @MassimoOrtolano mentioned in a comment (and I think this extends to all lab courses, not just EE), "the main factor is the time constraint." Clearly your suggestion to make the preparatory/emphasized steps "cookie cutter" and the learning objectives more open-ended is a way to approach this time constraint with balance.

It sounds like your main concern is in determining which of these steps should be cookie cutter and which should not. You give two approaches: start from the beginning and work forwards, or start from the end and work backwards.

However, that assumes you are going into this with no information. That might be a principled approach in some cases, but if I can be a Bayesian for a moment, you are missing a crucial piece of prior information: you should have some idea of what your learning objectives are before you even start.

The approach I would take is to first identify learning goals, then sketch out the procedure and identify which steps are relevant to the learning goals and which are not. Cookie cutter those that aren't, leave open-ended those that are. Surely, this won't produce a perfect lab course on first pass, and it might take some tweaking over time, but it seems like you expect this and it is a better approach than either extreme.

Second, involve your students in your goals. I think it's best to think of students as if they are quite capable and smart. Let them know: "I designed these labs so that I give you a step-by-step through some of the things that aren't relevant to the learning goals of the day. At the start of each lab, I will provide you with a list of the intended learning goals. I am looking for feedback if you either a) feel like you are spending too much time on something that isn't a learning goal, or b) feel like the answers are being handed to you for the things that are."

When in doubt, it seems like it makes some sense to bias towards cookie-cutter towards the beginning of the course and towards more freedom in the end, but that depends on how well the different pieces fit together and how complex the problems get by the end.


In my field, it is not common to use first singular personal pronoun even when the paper has only one author. Using 'we' and 'our' in this case means that the author refers to the reader and him/herself.


How to address in-group bullying without compromising PhD/career?

I have spoken to … but have not wished to pursue any formal complaints procedures out of fear my supervisor will compromise my PhD … and ruin my ability to work in research …

Okay, so I am going to be the bad-guy here.  What you say you fear will happen here has already happened.  What you describe ---if accurate--- is already massively compromising your PhD and your ability to research.  The university has formal mechanisms in place to deal with this kind of issue.  If you are not willing to avail yourself of the mechanisms in place to deal with these problems then there is nothing that anyone can do.  (And frankly, it is quite difficult to muster sympathy for complainants who refuse to make a proper complaint when avenues are available for this.)  You should have complained formally or got out years ago, but since you are still there you have a choice: use the mechanisms available to you for complaints of this kind, or not.  Do not become a victim of the sunk cost fallacy.

If you decide to avail yourself of the complaint mechanisms at your university, the main thing you should do is this: document, document, document.  Document everything well, and collect and keep all relevant evidence of treatment that is unfair to you.  Make a chronological list of incidents, since the start of your candidature, detailing dates (or rough dates if you can't remember exact dates), what happened in each incident, and any documentation (emails, etc.) that constitutes evidence of the incident.  Write this in a neutral factual way, but make sure you briefly explain how each incident negatively affected your candidature.  Seek written statements from other sympathetic students that can back up your assertions.  You have said that the university has breached its policies when dealing with you.  Make sure you document instances of this as well.  If that is correct, then the university will be in a weak position in respect to the conflict, and you have a greater prospect of extracting some reasonable concessions in a complaint process.


Changing advisors within the same department

I'd say try to be up-front about what you're contemplating with both professors, beginning with the current advisor. Unless your current advisor is new to the position, he'll be well aware that sometimes people just don't "click" as you might expect. If you can do some work with the second professor, you should be able to get a better feel for how you two mesh. Definitely be respectful in communications and make an effort to finish anything your current advisor expects you to finish before transitioning. I'd probably also ask up-front about your concerns of funding to make sure you've got the information to make an informed decision.


I found a huge error in my master's thesis which I defended a year ago

Correct the mistake for any peer-reviewed publications (journal, conference, etc). Don't worry about the thesis published at your institution.

Reason being, your committee signed off in the work as a whole as fulfilling the merits of the degree. Yes, it's unfortunate, but theses often aren't indexed by journal searches, and even when they are, they are generally interpreted with less weight.

On the bright side, you recognized an error others might not have. Apply this lesson moving forward. In any other case, you'd have to retract.

PS - I did the same thing during my masters thesis. Didn't sleep for a week.


How to cite an old poem which appears in a new collection/anthology put together by a different editor? (Chicago)

If the publisher gives you the option of using BibTeX, here are the BibTeX database entries I've used in an equivalent situation:

@INCOLLECTION{Newton:1726:PNP, crossref="Motte:1846:NPM",
author="Isaac Newton", title="Philosophiae Naturalis Principia
Mathematica", pages="73--507", edition="Third", year=1726,
note="Translated into {E}nglish by {A}ndrew {M}otte; first edition
published 1687",
url="https://archive.org/details/newtonspmathema00newtrich" }
@BOOK{Motte:1846:NPM, editor="Andrew Motte", title="{N}EWTON'S
PRINCIPIA: THE MATHEMATICAL PRINCIPLES OF NATURAL PHILOSOPHY",
booktitle="{N}EWTON'S PRINCIPIA: THE MATHEMATICAL PRINCIPLES OF
NATURAL PHILOSOPHY", publisher="Daniel Adee", year=1846,
edition="FIRST {A}MERICAN", address="New York",
url="https://archive.org/details/newtonspmathema00newtrich" }

Then you can let the publisher's BibTeX style file sort out the CMS formatting.


Will it hurt my grad school chances if I don't mention/contact a particular proffessor-potential guide?

If it's a PhD program, very probably yes.
Most PhDs are earned by working closely with one professor.  In experimental physics, you work in their lab space.  If there is not a professor you can work with during your PhD, then you will not be successful.  Admissions committees want to see that you have identified a small number of faculty who would be suitable for you to work with.
Also, some professors may have funding.  If they want to use the funding to pay you, you will probably be admitted.
We cannot tell you who to approach.


I got the same referee report from two different journals

As a reviewer, when I get asked to review a paper the second time I will see whether my comments from the initial review were addressed. If not, then I will submit the same review. Why should I update my review if the paper has not been updated?

Getting the same reviewer is a very common occurrence. Perhaps in your situation the reviewer is misguided. However, when re-submitting a paper you should make every effort to address previous reviews.  And, in any case, legitimate issues raised by the reviewer should be addressed. Even if you think the reviewer is confused, you should seek to clarify the confusing points. They may be confusing to others too.

In your position there is probably not much you can do other than write to the editor explaining the situation. The best argument you can put forth is to explain that all of the points in the review have already been addressed in the submission. That makes it look like the reviewer didn't read it, which means the editor may side with you.


Not citing a secondary source for a reason

You are mixing up to different things. It sounds like you are copying the sentence structure of the secondary source. If this is the case, that is plagiarism. It doesn't matter if you cite the secondary source or not, as no one will know that the citation is referring to the sentence structure. The second issue is the facts. For these, you should be citing the primary source. You do not need to cite every source that has cited the primary source. It is generally much better to cite primary sources than secondary sources, because as you have discovered, things can get messy the further away from the primary source you go.


Should I choose the schools that I apply to, or should I ask my advisors to do that for me?

Fortunately, this isn't an either-or proposition!  I agree with your assessment that you shouldn't come to your advisors empty-handed and ask for some schools to apply to.  However, it would be perfectly reasonable for you come to them with a couple schools you like - probably spread out by competitiveness and such - and maybe some guidelines for what you want to focus on and where you would be willing to move to.
Ask their opinions on the schools you picked, and ask them if they have some others they would recommend, based on what they know about you.


I have different last names on passport and local official identity, which one should I use for publication?

From a practical perspective: you might also want to consider to check a major publication database of your field and see, if one of the two possibilities / names has not been used by another researcher. This might become useful once people look for your publications.


What is the difference between open access and open archive?

As Elsevier uses these terms, "open access" means an article is free to access as soon as it is published. "Open archive" means an article is published in a journal that makes articles available for free after some embargo period (not immediately when it is published).

More on Open Archive:

  Elsevier enables subscribers and the general public to have free access to archived material in 98 Elsevier journals... Articles featured in the archives are free for everyone to read and download and are made available after an embargo period.


is workshop a relevant experience to be considered for a graduate school admission?

Most workshops would likely have little if any effect, other than to show your interest in the field.

There could be exceptions, of course. Long workshops (months), perhaps. Workshops in which you build something significant, perhaps. Workshops that result in letters of recommendation that highlight something especially interesting, perhaps.

You can mention such things in your CV, but don't expect a lot of bang.


How to properly cite a domain-specific result of a generic concept from a paper?

To be pedantic, you can say something like "The following equation (eq-A) is from [paper-A], in [paper-B] the special case (eq-B) is derived from the above."

Season to taste.


Path to a good grad school in math during undergrad?

Here are my suggestions, having just finished a year of graduate school in math. It's therefore mostly anecdotal and should be taken lightly!

REUs: Try to do as many as you can! You get to meet other people who like math, learn new stuff, practice struggling with research, travel a bit, and get some cash to boot. They also, of course, look good on applications.

Publications: I don't personally have any publications. I wrote a few papers during my REUs and projects, but they were only published on the REU websites. So they're not necessary to get in. However, I did have a great deal of trouble getting acceptances. Maybe a publication would have helped, but I think it's very rare for an undergraduate to actually publish a paper.

Graduate Courses: I took several of these as an undergraduate. I enjoyed them, but realize now that I should have taken them a little more seriously! I've forgotten a great deal of what I saw in them. However, I have noticed that I'm quite strong in the area I took graduate courses in compared to my peers. So they definitely give you an edge! However, don't become too obsessed with loading up with graduate courses. Three of them is quite a lot of work, if you give them justice. Since most graduate courses are graded very lightly, you can make high marks in them without putting forth as much effort as you would in an undergraduate course! (At least, this was how it worked at my undergraduate institution.)

That said, keep in mind that some of your time in college should be spent having fun, too. Don't become a math robot just yet! You have time for that in grad school. :)

Reading Textbooks: The fact you're already reading the "core" undergraduate books before even entering the university puts you far, far ahead of the curve. Many people won't learn those things until sophomore or junior year. I certainly didn't. Make sure you're doing the bulk of the exercises in those books, especially Rudin. Try to prove statements you come across without looking at their proofs. I feel that this is where most of the learning happens. You can easily read things and not understand them, so just watch out! Other than that, finish those books and then you should be set to take the advanced undergraduate/first year graduate courses at your institution.

The Math Subject GRE: I hate this thing and did very poorly on it. You'll blow the math portion of the general GRE out of the water. It's easy stuff for any math major. However, if you don't spend a little time reviewing, you can really mess up the subject test, since it's timed and covers things you might not have thought about for several years. The topics are almost completely disjoint from what a student taking graduate courses has been doing. Look at a few practice tests, identify what sorts of questions are asked, and train yourself to quickly answer such questions. Speed is key. You don't want the subject GRE to be a weak point on your application, especially since it's an easily prevented weak point.

So, do REUs, take graduate courses, don't sweat not having publications (but if you can get some do), and study for the subject GRE!


software to organize (1) research questions (2) secondary literature (3) own notes

Try using Microsoft's One Note. It recently became free to use and is a very good application to store your content, no matter how lengthy it may be.


Is it possible to get IRB approval after the fact?

The human research ethics committee is in place to ensure that human research is undertaken in a way that safeguards the dignity, rights, health, safety and privacy of those involved. This assessment is difficult to make by the investigator because he or she has a vested interest in proceeding. Thus, an independent body is required.

In the institutions in which I've been involved, conducting human research without ethical review is, quite simply, research misconduct and subject to investigations and disciplinary actions. A priori ethical review is required. Regulations are in place that specifically disallow approval of research that has already been conducted.

I've been a member of institutional review boards and have chaired three -- one based in a hospital and two in research-intensive universities. I've been involved in these investigations in the past. As the original poster implies, most are found at the point in which the journal requires evidence from the IRB and the author quickly shoot an email to the office requesting one. In these investigations, it is often the case that there is a lack of training in the expectations and regulations of human research and offenders usually fall in three categories:

inexperienced researchers, including students (often poorly supervised) or practitioners with no research training
researchers trained "elsewhere", including those from countries with little to no requirements for ethical review
researchers from fields that don't usually involve human subjects

My worst case was a person from an electrical engineering background who collected data on body image for an app he was developing. During these sessions, the person gave advice that drove one participant to self harm. During the investigation, the offender did not think that ethical review was necessary because the questions were "innocuous (his term)".

As I said, in most cases the consequences are far less severe than this. For example, a common scenario is a young doctor who collects information from patient files, performs a few statistical tests and write up the results of this audit and sends the publication to a journal that then requests evidence of IRB approval. In cases like this, IRB approval is not provided and the doctor is placed under supervision.


I apologize if this is something trivial, but I struggle to find some reliable explanation regarding this issue. Understanding the nuances in the journal naming system would help me better categorize and search journals that suit me.

There is no reliable way to use the name to conclude about the eminence of a journal. There are some heuristics, though:

IEEE Transactions are typically supposed to be the flagship journals for a broader field. Quality between different transactions varies, but from the top of my head I cannot think of an IEEE transactions journal that is really bad.

IEEE magazines (IEEE Software, IEEE Internet Computing, IEEE Computer, etc.) are also mostly very well-respected, but their scope is entirely different. They publish short papers written for a broad audience. They are heavily copy-edited (for instance, the copy editor will typically re-draw all figures in a common style across all papers in an issue), and they tend to have a large impact (because these magazines are circulated very widely). However, due to limited size, they are often scientifically more shallow than transactions papers.

Other journals, that fall into neither category, vary in quality and esteem (though they are typically weaker than the relevant transactions in the field). Their scope is typically more narrow than transactions, but the opposite can also be true.


Is it bad practice to use examples from textbooks in your in-class teaching?

Personally, I think that the source of an example doesn't matter half so much as the quality of the example.  If you've got a really good example that came from a textbook, then that's just as OK as having a really good example that came from another professor or one that you made up yourself.

The question, to me, is whether you've made the example your own.  If you've taken the time and effort to really understand the example, then when you present it, you will not present it exactly the same way that it was presented in the textbook.  Your own understanding of the material and personal style will color the presentation, marking it with commentary, pacing, and choices of emphasis, all of this together giving your own "voice" to the presentation.  I think that students recognize when somebody is presenting material in this way, even if they don't know how to name it as that.  They may or may not like your style, but they certainly will not think you are merely following steps from the textbook.

Likewise, I think that there is no reason to hide where you've gotten an example, particularly if you give your reasons, e.g., "this example we're going to work is one from the textbook that gives a very nice illustration of the consequences of Kirchhoff's Law." In fact, giving credit to your sources is a good way to inculcate more of the culture of academic honest in students by example, as well as an aid to students who might want to go over the example again with the textbook.


Advisor wants me to send manuscript to a potentially shady journal

Why not? A quick look at the controversy indicates that the disagreements were entirely around the editor-in-chief publishing his own papers in the journal, papers which were lightly reviewed + indulged in a lot of self-citation. This means:

It's only the editor-in-chief's papers that are affected; none of the papers by other authors published in the journal are;
Once the editor-in-chief changed, it's no longer a problem.

So even if the editor-in-chief was in the wrong (which is not certain), it should be fine for you to publish there.

If it still concerns you, note that Clarivate Analytics / Web of science still has the journal indexed, i.e. they think the journal still meets their standards, and it has an impact factor of (as of time of writing) 3.064 which is good for the field.


My student's family won't let her study what she wants

Some thoughts:

Suggest counseling.  They are much more likely to be able to help support her in expressing her goals to her parents, understanding their position, and perhaps in negotiating some sort of compromise with them.  Family relationship issues are likely to be a pretty common concern for college students, and a university counseling service will have had lots of experience with them.
Suggest talking to the financial aid office. They may be able to explore other options for funding if she decides to go on without her parents' financial support, though admittedly there may not be a lot of options for international students.
Talk to your contacts at the other university. See if you can connect her with someone who may be sympathetic to her situation, and who might be able to help her with some of the other things mentioned here.
Help her explore degree and course options. Is there some other degree offered by the institution that might represent a compromise between what she wants and what her parents are willing to pay for?  Are there ways for her to take more classes that she's interested in?
She needs to be able to succeed at things even when they don't interest her.  You write "She couldn't care less about her other courses and her grades".  Regardless of the degree she pursues, this is a recipe for disaster in US academia, where breadth is considered essential and degree requirements are designed accordingly, and overall GPA is widely used as a metric of success,  e.g. for graduate schools and jobs.

(I am guessing from your terminology that you are in the US.  If not, please correct me.)

She doesn't have to like all her courses, but she does have to be able to push through and do her best work even in those she dislikes.  That's a necessary academic and life skill, and as a faculty member you may be able to help her develop that skill.  Counseling services may also help with this, if she has some emotional resistance to get past.
She might find these courses more interesting if she gives them a chance. Even pure mathematicians can benefit greatly from knowledge about other fields, and you or other faculty members might be able to help her see connections with things that interest her more.


Changing the thesis topic and supervisor

By all means you may go for your current research interest. Switching research area isn't uncommon. It will give you a refreshing start with new challenges (it did for me when I switched from data security to machine learning).

Interest and determination is the prime factor in research that's worth more than knowledge in the field. I've noticed quite a few grad students (both PhD and masters) who have put themselves in random fields without interest and regretted their experience dearly.

As for your promise, it is advisable to state your reasons as in your question to your previous supervisor. But the decision remains yours.


How to ask a professor via email about possible postdoc positions?

Generally such positions are advertised and often must be. Adverts are placed in such places as professional journals/newsletters and in newsgroups related to the field in question. Given this practice, blind letters may not even be answered and you can assume that there are no positions available.

Alternatively, if your relationship to your advisor is good enough s/he can ask around among acquaintances about the possible availability or future availability of such jobs. The advisor probably won't be ignored.

A third possibility is to attend a suitable conference or other meeting and get to know people and explore the possibilities in person, making yourself known, but also trying to build a network of future collaborators.

Your letter is probably fine, but it will probably be trashed. There are too many blind appeals for people to spend any time on them. In the old days of departmental secretaries it was different, but no more.


How to get the word out about an academic competition?

If you are aiming to reach out to members of a specific field, then I'd suggest reaching out to the department chairs of universities that offer it. For example, if you are looking into something designed for communications majors, professors, etc., then perhaps look up colleges with communications programs. Then find the contact information for the department chair and send them an email. You can repeat this for as many schools as necessary.

If you are going for something a bit broader, you may want to call the administrative offices for the schools, or see if they have an email address that you can contact them through.

This way, if the message comes across more like spam, then hopefully you've irked as few people as possible. If it's useful and the recipient is interested, then they will have the ability to disperse the information throughout their department or university. It's a lot of work, but sometimes that is what is necessary.


How to change the idea that supervsiors got about you?

The same way you would change anyone's perception of you for any other reason: Prove them wrong.

If you started out lazy, then kick yourself into high gear: Get tasks done ahead of time; predict future work, and get it done before it's asked for. Turn out quality work at a high pace. This sounds hard because it is. Unfortunately, you may have burned good-will at this point, and you need to rebuild it.

If you found things hard, or found that the supervisors expectations of velocity were unreasonable, discuss it with your supervisor. Discuss what background she may not know you have missed, discuss how you spent your time, and why things didn't get done fast enough.

Key here is the relationship. Your relationship sounds like it's on rocky ground, and if you're in it for another 3-5 years, then don't underestimate how much effort you're going to need to making sure that relationship doesn't break down.


Research article inspired by a question on MSE?

Assuming that you weren't the original source of the question, then it is entirely proper that you mention and cite it.
Interesting mathematical questions can come from anywhere and from anyone. But if you are inspired by the thoughts of another person, then hey should get credit for that.
Ideally a citation should point to a real person, though anonymity on SO may make that impossible.


It is normally enough to cite it once. If it is clear to the reader there should be no issue. The caption is complete, with the citation. The text itself can read more naturally.

But this is just a style suggestion. Correctness and clarity are the goals.

Caveat: Some journal may have their own style guide, but you will be told of that as part of the review process. For a dissertation it is fine to say it once unless your advisor objects.


The position I applied for was advertised as Associate Professor with Tenure, but now they’re saying it’s tenure-track Associate Professor

Based on what you've said,

  In my view, there is a flaw in their advertising. The position description clearly stated "the University of X invites applications for a tenure-track Assistant Professor or Tenured Associate Professor in...."

Well...yes, you're exactly right.  It sounds like the department and the dean were not on the same page when the position announcement was posted.

  While I understand that each university has its own interest in mind, this seems like a very bad start of a relationship. If I accepted this demotion, I would probably do so with some resentment. The University in question is academically equal to the one I first received tenure from.

Again, I agree completely.  You've had two different tenured positions, including one at a US institution of (you say, and I'm going with it) comparable academic quality to the one you're applying for.  You applied to this position and interviewed for it -- presumably taking some trouble doing so, since you now live in Europe and have family there -- based on the information you received in writing that it would come with tenure.  Only at the end of the process have you been informed otherwise.  Well...yes, that's a seriously alarming bait and switch.

In my opinion there is really only one thing to do.  You should respond by calling attention to precisely the facts you mentioned to us, especially that (i) the position was advertised as with tenure and that's why you applied for it and (ii) your last two academic jobs have had tenure, including at US institution X (you don't need to explicitly say that it's of comparable academic quality; I would leave them to claim otherwise if they want to), that you are very excited and interested in the job, but only under the original terms: you are not contemplating making an international move from a permanent academic job to a possibly temporary one.

In other words, I think the issue is serious enough to prevent you from taking the academic job...again, for exactly the reasons you say.  The type of employer who will not be held to what they told you before is exactly the type of employer to cause you N years of deep worry that they might not give you tenure, and nothing in your question suggests that you should subject yourself to that.

I really hope that they respond well to your holding your ground. Good luck!


Applying to grad school for mathematics with low GPA, but reluctant to bring up the health issues that caused it

You certainly have no obligation to mention your depression when applying.  You can say nothing about the subject and let your recently improved work stand for itself, or you can allude to personal issues and reassure the committee that they are no longer troubling you.  If you do well in your last two years of college, then difficulties in your first two will matter far less.

On the other hand, I think it could be worth mentioning.  In mathematics there's less stigma surrounding depression than you might expect (at least in the U.S.).  Compared with the rest of society, the mathematical community is unusually tolerant of various forms of psychological variation, provided that you can do good mathematics.  A number of famous mathematicians have suffered from depression, so it would be foolish to dismiss an applicant for that reason, and many mathematicians know colleagues who have been depressed.  The key question is whether you have found treatment that keeps it under control.  If you leave your situation vague, then you leave open the possibility that whatever was causing the bad grades might return.  If you explain that you sought treatment for depression and found it successful, then that will reassure the committee that your recent improvements are likely to be long lasting.

If you do mention this issue, I'd keep it brief.  A single sentence in your personal statement would be enough (the committee doesn't need or want any details about your health or treatment).  And, as I said above, there's no need to say anything at all if you aren't comfortable with it.  However, I don't believe doing so could hurt your application, and it might help explain your grades.


Do I mention that a paper in mathematics is a "Short Communication" or "Note" or "Research Article" when citing it?

No, you should NOT include this information. These designations are journal-specific and would provide little information to someone not familiar with each of the journal's classification schemes. For example, a short communication in one journal might represent a more impressive paper (because for some journals a very short paper might be, on average, more impressive than that journal's average quality paper [1]) than in another journal where the bulk of the papers might be short papers, often being "announcement of results" type papers. Also, many journals have no such classification, and thus the reader of your bibliography may wonder whether the paper was not classified in this way by the journal or whether you simply forgot to include the journal's classification.
[1] "Shorter Notes was established to publish very short papers of unusually elegant and polished character ..."


In the United States, is associate professor a subset of professor, or a distinct category?

In the US, Assistant and Associate Professors are also titled Prof. X when being referred to formally. This is unlike in Europe and parts of Asia, where "Professor" is a title that can be used only if they're a full professor. Others are simply referred to as Dr. X (or Mr. or Ms. X, if they don't hold a doctorate).


Checklist for cited references, including nasty details

The best strategy for dealing with a reference database (be that a citation manager or just a .bib file), is to clean everything when you initially add it. Otherwise going through these things later, when you need put together a reference list, is a major pain and prone to error. Establishing a standard set of formatting rules/procedures up front is always your best bet.


How much does participation in online predictive challenges (DREAM, Kaggle, Innocentive) improve your resume?

At the very least, it shows you are actively interested in the subject.  Participation can be enough to show you are more enthusiastic about the subject than other applicants.  It is also helpful for entry level data scientist positions where experience isn't necessarily expected, but appreciated. If you have won any competitions, or if you are at the 'Master' Kaggle level, definitely include it.


Publishing a work; not sure what should I do

First, you should ask someone famliliar with the field whether it is

really unpublished
a good idea.

Sometimes ideas are very old and might be published in books which are not available online, and therefor harder to find. Or you might have used the wrong terms for your search.

If after that you still think it is a unique and useful idea, you should try to publish it. The "useful" is important here, sometimes people are publishing new stuff which noone applied to the problem before just because it makes little sense with regards to the big picture of the discipline.

If your instructor did contribute to the paper and the research, then it should be on the paper unless he declares it is not necessary. I would ask my student to come with a paper outline first (so you could approach your instructor with a clear plan of the publication), we improve the sketch and then the studet writes the first draft which I as a supervisor try to bring it in a form which suits the standards of the respective conference or journal. Usually, this involves some feedback rounds and includes additional scientific discussion etc. .

From your OP I got the impression your instructor might not be willing to put much effort in it, but sometimes people when they see someone is willing to go an extra mile.

If you are on your own, try to read some books about scientific writing, there are lots of formal errors which can be easily avoided.

I definitely encourage you to try to publish, it is a good experience and, if successful, is great for your CV.


Is hastily writing down the professor's lecture a good way of learning?

Prior to electronic media generally and after the start of mass, rather than individual instruction, this was the primary way of teaching a lot of things. It can be a good start to learning, actually. However, it isn't enough, and never was. Learning is an active sport, not a spectator sport.
We learn by actively engaging the brain. Copying down notes is somewhat active. Certainly more active than taking a phone picture of the board once it is full, or downloading a lecture. It is even more engaging than (just) reading a lecture.
However, if you really want to learn, or teach someone how to learn, I suggest a few additional steps.
One is to review the notes after a day or so.
A more extreme version is to take the notes by hand (pencil and paper) and then transcribe them and add annotations that are needed, perhaps preparing questions for the instructor or yourself to answer.
One is to extract and write down the most important message in a lecture. Or maybe a couple of them. This can be done at the immediate end of the lecture.
One is to ask questions during the lecture if a step in a proof isn't clear to you. (Yes, instructors make mistakes).
One is to review the most important points of the previous lecture just before the next one.
But the most important aspect is to do some kind of exercises based on the lecture. Perhaps these will be assigned. Perhaps they are available in a text book. Try to get some sort of feedback on your solutions.
Another is to start a discussion group with a few students to review the lecture material and update the notes.
But the real key to this is that you learn by actually rewiring the synapses in your brain and that takes repetition and reinforcement. To assure that you are reinforcing the correct ideas, you need feedback.
Note that watching lectures (say on the internet) without active participation is almost completely ineffective for most people. Especially for long term retention and the ability to put the knowledge to use.

For some of the biology behind learning that suggests reinforcement and feedback see: The Art of Changing the Brain by James E Zull

Note also that, as a professor, I've had to explicitly teach this to students and force some of the activities. For those that learn easily they may not seem to be needed, but eventually things will get hard and having good practice can save you.
For example, I'd end a lecture a couple of minutes early and ask for "the most important lesson of the day", expecting that the students would have note cards with a few ideas.


How to mitigate bad grade in research on PhD application?

If this project is your only experience doing research, you are right that any admissions committee is going to look at it. My advice would be to put a couple of sentences about it in your cover letter. Briefly state what the project was about, and finish with something like "I learned a lot about doing research even though the final result was a bit disappointing." That will show them that you did put actual time and thought into the project, and in the end the grade given to you by one unnamed project supervisor will count for a lot less than a good reference letter from your Masters thesis advisor.


You give a number of reasons why you don't want a PhD and one reason why you might want it: A chance of a higher income after graduation. Is there anything else? If not, I would rather look for other ways to earn more money. A PhD is not the sure-fire way to make money. And lacking intrinsic motivation, you will most likely struggle more than others, have a higher chance of dropping out than others, and perhaps need more time to graduate.
That said, your PhD program is starting only in a few years. Preferences and motivations change and that change is hard to predict. Why not enroll in a research-based course in your undergrad studies, and take stock after the BA to reflect back on what you enjoyed about it and what you struggled with.


Is it ok to record a conversation with a professor without their knowledge and can it be used as evidence?

First, the legality varies. Legal in some places, but not in others. A lawyer can give legal advice.
Second, a recording might be ruled inadmissible in any proceedings. The "chain of possession" is an important consideration for evidence in legal proceedings in many places.
Third, and, perhaps more important, recording someone without permission might be perceived by them as a threat, resulting in a dangerous situation. So, I don't recommend this as a course of action.
If you have actually been harassed then report it. If you think you might be harassed, then find a way to avoid the situation in which it might occur or take some action to protect yourself. For example, not meeting the potential harasser privately, especially behind a closed door, for example.


My supervisor is too involved, what should I do?

The first part (rewriting your text) is quite frequent. Believe it or not, most PhD students are terrible writers and though a good adviser would patiently go over the paper with a student pointing out the presentation flaws and asking the student to fix them himself (take my word for it, you do not want to get that list from the reviewer after the paper has been submitted), I know many people who lost their patience in that respect eons ago and other people who give up after 6 months of modifications and still do the job themselves.

So, the first question to ask is "How well was your paper written in the first place?". If not too well, there is a chance that you should be merely grateful for the revision and stop at there.

The second point is "throwing his ideas at you". Here the question is "How fast are you coming with workable ideas of your own?" Giving a PhD student the solution together with the problem is a terrible idea, insisting that the student do things your way and your way only is even more terrible, but giving him no suggestions after 6 months of no progress is also not good.

The third question is whether the supervisor should be a co-author. Unfortunately, your post is somewhat self-contradictory on this point: compare

  My supervisor made some suggestions here and there, but nothing substantial.

with

  he throws methodology and research design at me, before I have a chance to think about the topic myself and come to my own conclusions, and then encourages me to do it his way and not explore my way.

So was that particular paper done his way or your way? In the first case, IMHO, it is his choice whether he should become a co-author or not though you may still drop a hint that "the job market is tough and having a single author paper is a nearly must to land at the place you want to go to", in the second case it should be yours even if he rewrote the whole thing and you have all moral rights to insist on a single authorship if it is important to you. How exactly to do it without offending him I don't know (different people need different approaches), but judging from the tone of your post, you have had arguments with your adviser before, so you should know better than I what upsets him and what makes him cooperative.

So, alas, the only things I can tell you are the usual "Look into the mirror and try to figure out what exactly you see there before making final judgements" and "Hold your ground but use your common sense and pay attention to the reaction to your words when insisting on something". I should confess that I often fail on both accounts myself, but I'm in a different position than you. Let's see if other people can come up with some better advice :-).


Am I beholden to a professor that helped my application - would it reflect poorly on me if I don't join that professor's group?

Assuming you've been accepted by the university and the department (and have it in writing, i.e. an acceptance letter) -- the short answer is no, you aren't beholden to them.

The longer answer is that while you aren't beholden to them, it sounds like they already expect that you'll be joining them. How to approach this depends more on the faculty member than anything else. Some faculty members, when told that you "want to shop around and see what the university has to offer", will gladly nod and tell you that makes perfect sense, and they're hoping you'll still join them. Others may consider this a "rejection" of their help, or even a betrayal, and thus your bridge with that faculty member is burned forever.

Here's the trick: you want to avoid the latter category of advisors anyway. So tell this potential advisor the truth, see how they react, and best of luck at your new university!


I did my PhD in my fifties, after a computer science industry career. I am also a permanent resident alien. I can see two problems you are going to have that I avoided:

I didn't start my PhD until after I had my retirement fund saved up, so my standard of living did not change.
I continued in computer science, so my industry experience helped. I could read current computer science papers without too much difficulty.

One approach to the standard of living issue is to rehearse by trying to live for a year at a graduate student spending rate. That will let you find out if you can do it, and build up your investments with the money you are not spending.

The biggest problem I see is the transition to Mathematics. You could perhaps use the Mathematics GRE subject test to evaluate where you are relative to what you will be expected to know. You might do better doing a computer science PhD but specializing in theory. There are some fine open problems, including the great P=NP question.


Am I obliged to share my most promising data?

What does your supervisor say about this?

I've seen situations where someone not sharing data not only prevented papers being written, but completely obliterated the collaboration.

One possibility is handing the data over, but helping with its analysis and the subsequent writing of the paper (with co-authorship). You could offer the same to the other candidate.

In any case, as you have only just started, I wouldn't worry about the negative impact. There's plenty of time to build.


What are the masters options available for getting into computer vision and image processing research from an electronics background?

There are Masters of Science programs in Computer Visions and even Computer Science that you can definitely look into. I'm not sure if your preference is to attend school online or on campus. I'm not sure of your location or budget either, so this answer will sound quite generic. However, I have included Georiga Tech's program. The Georgia Tech link is just a course in Computer Visions that's part of their Master of Science in Computer Science program. I believe their program is $7,000 (if it hadn't increased) and it's fully online. I've included their online Masters site link.

Georgia Tech
Georiga Tech Online Masters


Is submitting two papers with identical introduction and methods considered plagiarism?

If we were to submit this to two different journals, is it plagiarism?

Reusing text from another paper (even a closely related paper) without explicitly saying so would generally be considered self-plagiarism.  Unless they have exceptionally permissive publishing agreements, you would be in violation of your agreements with both publishers if you didn't get explicit permission to do this.  Even if the journals have the same publisher, they would probably still be unhappy, because this is a violation of scholarly norms.

If you feel your particular case is reasonable and would be considered acceptable in your field, then all you need to do is to be clear about it.  Include a sentence like "For the convenience of the reader, Section 2.1 is copied verbatim from [citation to part 1]" and explain the situation to both publishers when you submit the papers.  If they are OK with it (and you are honest with the reader), then everything's fine, but you certainly shouldn't submit the papers in this state without comment.

For this to work, you'll need permission from both publishers.  In mathematics that would be an unusual request, and I doubt you would receive permission, but things may work differently in your field.  In any case, you may come across as naive or eccentric if it doesn't work the way you expect, but at least nobody will be able to accuse you of being dishonest or manipulative.


Should we include tool usability evaluation based only on the research team opinions in the paper?

We decided to describe the tool in a paper and attempt to publish it.

Why do you want to publish the description? Do you expect that other people will want to use this exact tool? Then you may need somebody outside the original team to evaluate it. Do you expect that nobody will use this exact tool, but the ideas and concepts might be useful to others in developing their own tools?  Then the usability aspect is probably irrelevant.


Should I include proof of my extenuating circumstances when applying for a PhD?

You might mention extenuating circumstances if:

They significantly decreased your past performance.
You explain why your performance will not be reduced in the future for the same reason.

Do not include any evidence unless it is requested, or perhaps if the circumstances were something very unlikely.  Having been imprisoned for a crime and later exonerated might be an example where evidence would be a good idea.


I have a MSc degree, want to apply for PhD degree. Should I submit my BSc transcript during admission?

Go ahead and submit your undergraduate transcript.  The admissions committee will be expecting to see one and your application might be screened out before consideration simply because this transcript is missing.

The fact that you've had good grades in your master's program may help you to overcome the bad impression left by your poor undergraduate GPA.  Having good letters of recommendation and one or more publications (of high quality) will help a lot more.


Seeking Feedback on Research Topic Outside Department/University

I too had a topic which was outside of the expertise of my committee. If you are set on your topic, this seems like a good approach. After talking to your current committee and getting their buy-in on the plan, you could also approach other faculty at your current institution to tap their networks.

Another way of doing some networking to get feedback is to attend local or subject area conferences. The big AEA conference is pretty difficult to use for networking, but you could make contacts at these other conferences which could be helpful. Especially once you get your work to a poster stage.

I would also like to advocate a second idea, which is to change topics to something more similar to your committee's area of expertise. While this is not what I did, I definitely saw the merits of it as my friends who took this approach were able to coauthor with their committee, have more useful RA experiences, and come out with more lines on their CV for the job market.


How can I prove my publication list is mine?

When it comes to hiring a faculty member, you can expect that members of the search committee will look at a candidate's papers.  Since the published paper typically shows the affiliation of the author and the past affiliations of a candidate will appear on the CV, it would generally be obvious if a paper was authored by someone other than the candidate with the same or similar name.

Of course, a candidate could lie about his/her past affiliations, but we have letters of recommendation and reference phone calls to ensure that doesn't happen.


Should I worry that a graduate student somewhere gave a talk using my abstract?

I think there are basically two cases here:

The student is presenting or leading discussion on your work as part of a "journal club" sort of series, and the abstract is your abstract because they're talking about your paper.
The student is baldly and ridiculously plagiarizing.

I think a good way to approach this is to assume case #1, and make contact with the student.  You might email the student (paper trail), cc'ing both their advisor and yours, with something like:

  I noticed online that you gave a presentation on my paper [preprint link].  I'm interested to know how it was received, and if there was any interesting feedback.  Would you mind sharing your notes?

Now, if it's case #1, you've made positive contact with a possible fan and collaborator, and something really nice might come out of it.  If it's case #2, though, you've established a paper trail and made certain that the relevant supervisors on both sides are aware of it, so that if any incident happens in the future, your position is exceedingly clear and strong.


Who decides which, if any, solutions are publicized to students?

I would be surprised if any publisher required a particular outcome or, especially, overrode an author's decision. It would make for an awkward relationship with the author.
They might, however, make suggestions, since the commercial value of a book might be affected by the decision. But the commercial value and the educational value might be at odds. I've never had a discussion with an editor about this subject and have published with several.
I do know of one case where a grad student was paid to produce solutions. I believe the funding came from the publisher, but it has been too long ago to remember details. But this is something an author could request of the editor. However, such payments usually come out of future royalties to the author, I'd expect.


Is it common for supervisors to approach their student and ask to work on publishing the student's masters thesis?

There are in all likelihood differences between fields of study. In mine, it is uncommon, but if it happend it would be a good sign: You have produced something that is worth publishing, which is rare for a Master thesis in my field. Turning that research in an article that can be published is an art, which I would not expect a master student to master. So having the supervisor help you in that would be necessary in my field. It is right, that your supervisor immediately cleared who would be first author, and also right that you are the first author. That to me is a sign, that (s)he has the best intentions.

When I make such offers, I consider this as offering those students an opportunity to get an advantage very early in their (potential) academic career, or at least to get some inside experience of what working in academia is really like.


Is it worth self-funding a PhD to attend a top 10 university?

Unless you're independently wealthy I think it is always unwise to do an unfunded Ph.D. program.  With the current academic market the way that it is, there's just no guarantee that you will get a good job with the Ph.D. that will allow you to quickly pay off your debt.  There's also no guarantee that you'll get a Ph.D. at all.  We're talking about over a hundred thousand euros!  There are some advantages to a top ranked department (as ff524 says, university ranking is irrelevant), but it's not 100K euros worth of advantage (especially since often a lot of the advantage of a top dept. is that they're better funded and so students can concentrate more on research).


How to network with people in virtual conferences?

There are no methods that actually work.

You can present your work, including your contact information.  But you were doing this anyway, since it is the same as in-person conferences.

You can try asking questions during the conference.  Most of the time, most of the questions are not answered, and most people do not know who asked them.

You can network using non-conference methods based on what you learned from the conference.  For example, send emails to other participants.


There shouldn't be a problem with this provided that all of the following are true.

Are you working at the intersection of the two fields? Do you intend to add something significant to both fields?
Are the two potential supervisors compatible with each other? This means mostly in non-technical qualities.
Are you comfortable with each of the supervisors and their work separately?
Is the institution ok with it?

If any of the above are false, however, it might be a bad idea. For example, if you are working primarily in telecom but only need some help in the database area it would probably be better to have one supervisor and seek the additional help less formally.

You don't want two supervisors with different ideas about your progress or about what is important or about when you are done.

Caveat: There may be a few more considerations that you should consider but I can't think of.


When does it no longer matter whether you got a PhD or MSc

A PhD is just vocational training for researchers, so if a company is not looking for a researcher then the PhD should be a disadvantage; you are not going to hire a carpenter if you want a plumber.

In practice, it is a bit more complicated because the PhD has the undeserved stigma as "highest" level of education. So a PhD could still get an advantage even in situations where (s)he shouldn't. How fast this undeserved advantage decreases depends on many factors, e.g. country, industry. So there can be no single answer to your question.


How to talk to an intimidating professor?

This is coming from someone who worked and still works with the most intimidating professor in our lab. This professor was my teacher when I was a bachelor student and he was also my supervisor project for my Master degree (And that's when I developed my fear). Now he is one of my co-supervisors for my PhD. I never approached him until this year (5 years to overcome my fear). So all this just to tell you that "I know :)".

The year I approached him, I discovered the following information (and the mistakes I made):

The professor was just professional: strict when it comes to deadlines and assignments, meetings were heavy and only work-oriented (a lot of information, a lot of tasks to do). This was stressful to a lot of students.
The professor is seriously passionate, so he takes everything to the next level. You really should arrive to class punctually, no small talks, stay focused. You break the rules, you leave.
I kept hearing past stories, or bad experiences, from other students and let those experiences affect our professor-student relationship.
And mostly, I missed many opportunities by not taking the first step in the past.
I made the mistake of mixing "How he does his job" with "Who he is".

So here is the only answer I have to your question: Just do it, I am sure that this intimidation is just in your head. I even noticed that I can easily start these off-class relations with other professors, but never with him. So here is something I would do:

I will schedule a meeting by sending an email (my professor was the Head Of our Lab, he is always busy). I will say that I need a recommendation letter for example.
During the meeting, introduce yourself and why you need the recommendation letter and try to start a conversation from there. Tell him your future plans, and ask for his opinion. He is your professor after all, his job is to guide you :).
During class, be active and always be interested. You can not earn his respect if he does not see how passionate you are.
Always take the first step. And if doesn't go your way, it's okay. As Buffy said, take it easy, you have a lot of time and "several opportunities to reinforce any interest"

Good luck.


Should phd candidates spend time on extra-curricular?

Whether or not you get a tenure-track job is going to be driven by your research credentials, and not by extra-curricular activities. However...

Interviews and job applications often ask about your service contributions; how you would go about managing people, budgets, and competing demands; etc. Extra-curricular activities such as student leadership may give you some concrete examples to draw on in addressing such questions. This is likely to result in a more compelling answer, which may help your overall application.
Your circumstances or preferences may evolve over the next few years, and you may not be able to find the right academic position when you graduate from your PhD. Participation in extra-curricular activities may help your CV when applying for non-academic jobs.
Networking is always helpful. You never know where you'll meet someone interesting or useful, even if it's just a fellow PhD student from a different department whose research connects to your own.
Variety is important. In my experience, it's good to have a reason to step away from your research regularly and think about something completely different. Often inspiration for difficult problems strikes when you're not actively thinking about them.


Does going to a graduate school with less prestige than your undergraduate school hurt you?

Edited heavily based on further information provided by OP
If you are going into industry, or pursuing a Master's, it may hurt you in the short term
A Master's degree is mostly course work. It's too short for you to create a body of work that stands on its own. The quality of the courses largely determines, consequently, the quality of the Master's. Prospective employers may use an institution's reputation as a heuristic/proxy for the quality teaching.
Attending a less prestigious institution will make it more difficult to get interviews. Not being able to attend the bigger names also means you miss out on their alumni networks.
Create a compensatory professional network that overcomes these limitations. Most Master's in CS programs have a semester-long project. Make an impressive project and shop it around. This is a good way to build rapport with potential employers.