I think I may have violated academic integrity last year - what should I do?

The past is the past and cannot be undone. Whether you are ashamed or not, you need to move on. But you don't need to invite external punishment for past misdeeds that haven't harmed others.

It is best if you do your own work, of course, since that maximizes your learning. It is worst if you copy since you haven't really learned anything. In between is getting hints about things, with various graduations of that. The best hints come from your instructor, since s/he can give you a minimal hint to get you past a block so that you can advance. Getting hints from others is worse since those others may not be taking your educational development in to account.

So, for the past, let it go. For the future think about the goals of the exercise, not just the end point. Seek appropriate assistance that won't hinder  your learning rather than inappropriate assistance that might.

Probably you transgressed norms since you describe it yourself as copying. But treat it as a learning experience and move on.


Can I cite an unpublished Master Thesis?

Just because it's not published doesn't preclude being able to cite it. You can't not cite the thesis if you're taking information from it!

The degree-granting institution should perpetually retain copies in its library, and most universities these days store PDF copies as well. A copy may be harder to track down, but a determined reader should have no enormous difficulty in getting a copy of the thesis.

  Example:

  Smith B. (2013), General Relativity, MSc thesis, University of
  Cambridge, UK.


I envy you the fact that it is only a word count that counts. I am in a system where everything has to fit a certain number of pages with 12pt Times-Roman and 2.5 cm margins.

With the word limit as your main limitation you have the possibility to illustrate your application more freely. If suitable, I strongly suggest you try to come up with conceptual graphics to strengthen the text and make difficult concepts  easier to grasp. This can be a huge advantage. Since your are not limited to pages you can afford complex and larger illustrations than otherwise possible.

As for typesetting, you use LaTeX (as do I) which produces excellent text. Trust the LaTeX settings for text width, line-spacing etc. to get a readable text. Too long or too short lines makes the text difficult to read. See the geometry package for details if you are not already using it. EDIT: I do not think two-column format is good for proposals. It is a way to put as much text into a small area and also involves using smalller type sizes, typically around 9 in order to get enough characters into a line to make it readable. Since the number of pages is not a limit, I would aim for something which is as easily read as possible, typically 11-12 pt single columns. the margin widths can be determined so as to get reasonable line lengths. I do not think wide or narrow margins make a difference but wider margins make the page more attractive than narrow (basically a typographical design issue).

EDIT: With one-column format you can add figures at full width and with the no-page-limit do not have to worry about the size of the graphics (in the sense of having to make it as small as possible so to not use up space. I think a straight-forward simple formatting is best. There is no need to be overly creative. What conveys the message without resistance is the best.

One of the more useful concepts in grant writing I have come across is given in the book Writing Successful Science Proposals by Andrew J. Friedland and Carol L. Folt which outlines a two-paragraph summary, akin to an abstract whith which you introduce your proposal. The point of this is to quickly and concisely convey the key points of the proposal to the reader. This involves starting from the big picture metion key gaps in knowledge, how to tackle them (methods), preliminary results (if existent) and expected results. I obviously cannot copy the book content here but the point is to make the reader of the proposal completely clear over what to expect in the proposal and so all details given is just putting substance to the known structure. I believe this is what you aim for in what you call an overview section.

EDIT: After having started your text with a brief introduction, you simply follow up by the usual type of structure:

background (to focus on the gap of knowledge to be targeted)
objectives
project outline
time table (milestones; can be a gantt plot)
if applicable: research group/resources
references
For references I would go for footnote type references since the harvard-style citations uses up many characters. It is also possible to abbreviate the reference list by omitting the paper title, similar to what is done in Nature and Science.


Do citations of an edited volume of which I wrote one chapter count towards my own bibliometric indicators?

Let's split this into two different questions: 1) should citations of a "collection" book count as citations of an individual chapter in said book, and 2) will these citations count in any particular database.

Considering the first question, I can see an argument for and an argument against whether such citations should count.  In favor of counting, your work clearly is part of the collection, and if the collection has "citable quality" then your work is likely to contribute to that in some way.  Opposing this is the fact that "collection" books where each group writes a chapter independently are generally completely lacking in unity as a scientific work.  From what I have seen, citing such a book is tantamount to saying, "a bunch of people are working in this area."  I thus view a citation of the book as essentially equivalent to citing the ubiquitous "introductory review" chapter where the editors explain their vision of the field, then try to map that onto the collection of chapters they ended up with.  In short, I think it typically should not count as a citation of individual chapters.

For the second question: will citation databases agree with me, or will they count a citation of the book as a citation of you?  Well, that depends on just what sort of secretive sausage-making happens to be going on inside a particular database at a particular time.  From my personal experiences, though, I've seen chapters being treated separately, and the book as a whole being treated as a separate creation by the editors.  Take heart, though, that often means the editor's introduction will count as a citation for you!


For how many years does a university keep the thesis?

As far as I am aware, most universities keep a record of PhD thesis awards (title and recipient) in perpetuity. It is also the responsibility of the university library to archive the thesis; which is usually done on a permanent basis.

The reason for this is that future researchers, when doing their literature search should be reading these thesis to understand prior knowledge, as each PhD should be an original contribution to the sum of knowledge. Technology has enabled most universities to eliminate some of the burden associated with the perpetual storage of the thesis documents by allowing the microfilming of the thesis, which has now become the scanning and electronic storage of the work. There are consortia of university libraries that are working to ensure the problem of permanent storage of electronic texts is addressed in an era where we have non archival quality of electronic media.

The answer for the storage of PhD thesis and records would be "forever". For a Master's thesis or dissertation the answer is less clear. In many universities I am familiar with, often only the awarding department archives the Masters, and they are less reliable. I have seen with my own eyes archives of older Masters works being "tidied up". To me it was a travesty, but to others it was modernity.

A degree is not usually revoked on the discover of a "mistake" in a thesis. A degree might be revoked if it was discovered that nothing in a thesis was the original work of the student who submitted it; otherwise known as plagiarism, theft or deceit. It would depend on the statutes and regulations on the awarding institution on whether or how this might happen. One can consult the news archives to find many reported incidents of this happening. The revocation can even happen posthumously!


PhD Application - if/where to explain reasons for poor GPA 10 years ago

Explain poor grades in your statement of purpose/essay, which is where evaluators are going to look for it. These statements can be up to a couple of pages long, so you can (and should) spare a paragraph (or two, if necessary) to the topic. The explanation must be detailed enough to give a reader a picture of what happened, and the confidence that the underlying problems have since been addressed.


As a graduate student, is it better to use a Gmail address or name@mywebsite.com?

I don't know how people view things in the humanities, but in mathematics having your own domain named after you sounds a little presumptuous, at least to me.  Some people do, and I find this normal for people like  writers or some programmers, but not most types of academics.  In addition, sometimes these go defunct because people stop renewing them, so something like gmail is a more "stable" solution.  If you dislike gmail and don't want to use your institutional address, check out some other email providers (yahoo, zoho, mail.com).

Note: to me, instituional addresses still seem more "professional" than something like gmail, but sufficiently many people use gmail for professional reasons that it doesn't look strange to use it.  In fact, something like gmail is often a better choice for young people who haven't settled down and may change their institutional address several times.


Underrating and overrating of student in recommendation letter for post-doc: Balancing approach

In most of the cases, we overrate or underrate the performance and if it is the latter, we are sometimes held accountable that we have jeopardized their opportunities.

Personally, I think that a good approach here is not to write a recommendation letter unless you are comfortable showing it to the student.  Unless there is some strict restriction to the contrary on the process, you can show the student the letter you have written and then let them decide whether they still want to use you as a reference.  This gives you the freedom to openly disclose negative aspects of the student's abilities, and leave it up to the student whether they still wish to use you as a reference.  This also has the secondary advantage that your student is able to see your assessment of their abilities, and if you have a negative view of some aspect of their skills/abilities/attitude, this is not a secret to them.  All you can reasonably be expected to do is to  make an assessment of the quality of the student to the best of your abilities; it is up to the student to decide whether you are a good person from whom to solicit a recommendation.  Blaming you for jeopardising their opportunities is shooting the messenger.

This idea relates to a selection problem that comes from the fact that some academics refuse to write a letter if they would say anything negative about the student.  Several of the comments to your question recommend this approach, and as a result, it is sometimes expected that all letters of recommendation will be unambiguously positive.  That is, it is expected that a good student will be able to find a given number of referees that can be unambiguously positive about their abilities.  Whatever you think of that filtering mechanism, in my view it is generally a good idea if the student knows what their professors think of them, and this is best accomplished simply by showing them the letter you have written.  For my part, in cases where I have asked my professors for recommendations for an academic program or job, most of my professors have sent me a copy of their recommendation without me asking them to do so.  (Often they have written a recommendation by email, and BCCed me into the email, even if the process says that applicants do not get to see the recommendations.)

Another related problem here is when academics (erroneously) think it is their duty to over-rate their students in order to be generous in their recommendation letters.  If enough academics do this then it becomes "normal" and other academics feel the need to follow suit so that their own unbiased ratings do not disadvantage their students relative to the prevailing norm.  So, the first rule for recommendation letters should be to give the most objective assessment of the student you can, and don't intentionally over-rate or under-rate the student.  In particular, don't feel the need to be generous to the student in order to assist them with getting a place in graduate school.  The second rule is that nothing you write in your letter should come as a surprise to the student; either you have showed them the letter, or they are otherwise aware of your views on their strengths and weaknesses.

  Is there a way out to have a balanced approach while writing recommendations?

As to the substance of how to avoid over-rating or under-rating the student, I would recommend that you start by setting out basic factual information about the marks the student got in your courses, and how that compared to the cohort.  This will lead you naturally to the ability to say that the student was "in the top X% of students taking my such-and-such course" (best to compare over several years if possible), which gives some basic quantification of accomplishment in your courses.  By placing the student's mark in the context of other outcomes in their cohort, you go beyond reiterating information that is already in their transcript, and this also gives you a "jumping off" point for further discussion of the strengths and weaknesses of the student.

To progress from this point, it is usual to give some information on the existing skills of the student, the speed at which they are able to learn new skills, their ability to take a task from initiation to completion, and how much guidance and encouragement they require to do this.  It is common to also comment on what it is like to work with the student; i.e., their general attitude, and whether there are any difficulties in dealing with them.  For students of sufficient quality to be applying for grad-school or post-doc positions, they are usually good on all fronts, but if there is a weakness you should feel free to disclose this.  If you want to try to be balanced to an individual student, imagine that you have to write and submit letters for all your students, and the relative quality of each student will emerge by comparison of all these letters.  Thus, if you over-rate one student, then ceteris paribus, that detracts from the recommendations to the other students.  Try to be fair to all of your students by making sure you are objective in your assessment of each individual.

Finally, one important thing to ensure that you do not over-rate or under-rate the student is to avoid commenting on things where you do not have enough information.  Thus, if a student was just one person in a sea of faces in a large lecture course, you might not have any idea of their abilities beyond their performance in the course.  In these cases you should stick to what you know, and don't speculate on what you don't know.

  As a typical example, if the student is an extremely good experimentalist but is not so good, probably poor, in visualization of data, then what should be our approach if we have to address this attribute without being too harsh or too mild.

I would recommend you frame your assessment of the student in terms of your view on their potential for research in the program/position to which they are applying.  For any given skill, you can give an assessment of the present ability of the student, and also an assessment of whether the student has shown the required qualities to develop this skill to a higher level.  So if the student is poor in visualization of data, you would need to make an assessment of whether the student will be able to improve this.  Assuming your assessment is positive, you could then say something to the effect that the student has highly-developed skills as an experimentalist, but they need to develop their data visualization skills further (and you think they can do this).

This is another reason why it is generally a good idea to allow the student to read your letter.  If you inform the student of this drawback in their skills, you can also let them know that if they are able to develop that skill further, then you will be able to write them a more positive letter in the future.  This might spur the student to take an additional course on data visualization, or do some extra practice, and then come and show you that they can now do it really well.  For any identified areas of weakness, the student can see this as an opportunity to "plug the gap" and then come back to you for an even better reference at a future point.


Telling my supervisor about my medical condition

Contact the disability center first.
You haven't listed a location, but most developed nations have laws prohibiting discrimination against individuals with disabilities, and mandating reasonable accommodations for their disabilities. The university disability office will likely have a better understanding of the university's policies and procedures as well as what reasonable accommodations you're entitled to than a random professor will (unless that's their research area or something). Additionally, helping you is literally their job, so you might as well take advantage of their services; it's not going to cost you or your lab/work group anything to do so, after all, and they should keep the contents of your communications with them private.


Student comments from meetings frequently overreacted to by senior 'management'

[Converting a comment to an answer at the invitation of @hueblue...]

I feel you are focussing on the wrong part of the issue here. It does not make sense to encourage 'management' to ignore the student representative's views; inevitably this will just create problems and bad feeling in the future, when students get the impression that their input is ignored.

The real issue is that (at least in your perception) the student representatives are not doing their job properly: they are using their position as a platform for their personal views, rather than those of the student body at large. It seems to me that this is what you should aim to address. Some things to consider:

How well do the student body understand the role played by their representative(s)?
How are elections handled? Are they treated as important, or an annoyance to be dispatched as quickly as possible in the first lecture of the year?
Is the student body aware of the issues that are being discussed in meetings attended by their representative(s)? Do they know when meetings are due to take place?
Are students reminded to send comments to their representative(s) in advance of relevant meetings?
Is there a clear, well-advertised, equitable opportunity for the student body to get together and discuss any issues and concerns they have with the representative(s)?
Do students have any way of knowing what their representative(s) said in meetings? Are minutes or summaries circulated to the student body at large?

I suspect that at present, the answer to most of the above questions is 'No' - certainly that was the case when I was a student. If you can change some of them to 'Yes', you will probably see a marked improvement in the quality of representation.


What makes good research questions good?

Do you want to know the answer?  Really?
Do you realistically have a good shot at finding the answer, in a reasonable amount of time?  Really?
Will lots of other people be happy to learn the answer (even if the question had never occurred to them before)?  Really?
Are you sure nobody already knows the answer?  Really?

If you can answer yes to all eight questions, it's a good research question.

(Unfortunately, some of these points may depend on what the actual answer is, which of course you don't know.)


Does working for a prestigious company help in a PhD application?

The short answer is "probably." The long answer is "it depends."

Admission to a graduate program is almost solely dependent on how well you impress that department's graduate admissions committee (assuming you meet any minimum admissions standards: grades, GRE, etc). If they attach value to your work in industry, it'll help you out immensely. If they don't, it probably won't hurt you.

This Kaplan page outlines the general process.


How to make my master thesis defending smooth with good english speech?

Use short, simple sentences.
Write a draft script to go with your slides.
Find a friend or an editor for hire to check your draft script.
Make sure you understand each of the corrections this person provides.
Create a target listener.  Ideally, this person will be well aligned with your committee members' profiles.  Reduce the background information part of your talk as much as possible.  Include only the background information your target listener really needs to hear.
Give practice talks to friends.
Videotape one of your practice talks.  Many people gesture too much with their laser pointer or ruler, so watch out for that.
After your talk, during the Question period, make sure to repeat each and every question that is posed before you start to answer it.  This will (1) ensure you have understood the question, (2) ensure everyone in the room has heard the question, and (3) buy you thinking time.  Practice doing this.


How do I deal with feelings of guilt and shame related to how long my PhD has taken?

Talk to a counselor about your feelings. They can help.
But you aren't alone in taking a long time. Your disabilities are part of it, but success in research can't really be scheduled. Depending on the research questions you've been asking your extra three years (say) can be perfectly normal. Insight comes when it comes. And, I suspect you've had necessary timeouts for medical reasons.
But you are probably feeling a bit of both burn out and possibly imposter syndrome. Both are common at the end of a doctoral program, even if it doesn't take longer than (whatever it means to be) normal.
Congratulations on finishing. Thank everyone who has supported you.


What should I do if the first author wants me to write the whole paper?

First of all: Good call to talk about authorship issues at the beginning, rather than only once troubles started! Now authorship issues do occasionally have to be re-negotiated depending on the course the project takes.

There do seem to be potentially two separate aspects in your question:

A. What to do if I have contributed as much as I am willing as a secondary author, yet the first author keeps asking for more?
- Point out that you have done X, Y and Z, and that you are only willing to do significantly more if you are the first author (fundamental reading + commenting remain unaffected of course).

B. I started a side-project, and I no longer want to work on this AT ALL.
- Make clear to your co-author that you have no intention to work on this project anymore, and that this pertains to the future, too. Either give them free rein to continue the project without you (either with you on the author list or not, depending on your preferences); OR make sure you are still available for basic reading/commenting, but simply nothing more extensive.

In both cases, if the coauthor shows a significantly stronger reaction than "medium annoyance", then maintaining a positive relationship to them is futile anyway.


Recently published paper deliberately not citing our very relevant work -- anything to do?

You have no real recourse. Authors can cite what they like and snub others for no reason. Plus, you can't cite everything so someone's going to get left out. But if it seems purposeful it very well may be. I would send your paper(s) to the snubbing PI and say something like 'looks like these slipped past you'.

It's in their best interest because of your work truly is that related, you'll probably review their papers eventually.


What to do when a journal publishes a paper plagiarizing one's work but doesn't care about it?

Document everything.
If you can't get a reply from the editors of the journal, write to the publisher. Or if it's the journal of a learned society, contact them.
You probably can't act alone, but you may get more powerful allies (deeper pockets) on your side. There are others around you who have a vested interest in your work.

In particular, the journal where you published your work… given that you transferred them the copyright, I suppose they might act in their own name against the plagiarist. Even if it does not escalate all the way to a legal action, the publisher of the plagiarized work might respond (or respond faster) to a well-known publisher.

Your employer may also have an interest in helping you enforcing your copyright. They may also have a legal department who can advise you on this matter.


What visa for a short term course in the USA?

I am not a lawyer and this is not legal advice, but my understanding is that B1 visas are typically the right visa for academic conferences and similar events.  See this document from the US government, particularly the entries on “Conference, meeting, trade show, or business event attendee” and “training.”


Is it possible for non-debating person to survive in research?

You don’t need to debate as a researcher, but you do need to be able to defend your ideas to someone who’s going to want to know the details. This will apply not only to your advisor, but attendees at conferences and seminars, and people who read your work and respond to it.


Describing Middle School in european grant application

Describe it like you did here: 8th grade, and then in parenthesis put (ages 12-13) to remove any ambiguity. That will only cost you a couple of words, and no one can misunderstand.

To expand on @ORMapper commented, in Sweden middle school would be "mellanstadiet" which is grades 3-5, and the students are aged 9-11. So specify both what the gade was "called" and the age, and avoid descritors like "middle school"that can vary a lot by country.


Is it possible to hire a phd student or postdoc by hours?

would it be possible to hire a phd or postdoc by working hours for the projects ?

Yes, but, can you afford one? You've highlighted the cost of a part-time postdoc [at] around 50k annually and noted [you] do not have much money.

  does anyone have rough idea about the price range/hour?

Compute the hourly postdoc rate (from the above salary) and multiply it by some factor (probably greater than two). (The hourly rate is non-trivial to compute, given that many postdocs work more than their contractual hours.)


Will my accepted paper appear in conference proceeding without presentation?

The IEEE policy on non-presented papers is as follows:

  Authors are expected to attend the conference in person to present their papers and share their ideas.

  To encourage attendance, IEEE recommends that conferences exclude or limit the distribution of any paper that was not presented at the conference. This policy is not mandatory and only applies to conference proceedings where IEEE is the copyright holder.

  If authors are unable to attend the conference and present their papers, they should contact the program chair as soon as possible so that substitute arrangements can be made.

That is, it is at the conference organizer's discretion. Some IEEE conferences do pull a paper from the published proceedings if it isn't presented at the conference: for example, the IEEE Signal Processing Society has the policy that papers not presented will not be distributed on IEEEXplore.

The only way to be sure your paper will appear in the conference proceedings is to confirm with the conference organizer.


Dealing with poor management, lack of supervision, and the desire to move into a different field

It almost goes without saying but still: it's really hard for internet strangers to correctly judge exactly how difficult this situation is for you. I'm answering just based on what you wrote and it's entirely possible I am missing the mark here. In that case, feel free to disregard my answer.

I'd be a bit wary to apply to a different school for a PhD now. It will indeed look bad on your application, you will need to get letters of recommendation from other people than your current supervisor, and you will essentially lose all the time you put into your PhD until now.

Your supervisor's absence and lack of local leadership is really demotivating. And it is easy to lose interest in your own research in such circumstances. Then again, research can at times be very demotivating and future research employers will want to see a certain tenacity in you dealing with demotivation. Giving up three years of research to go somewhere else does not show that tenacity.

Are there other options to explore? Can you move overseas with your supervisor? Can you start collaborating with a local professor, or find local trustworthy people to help you regain direction and interest? Is there any way you can involve your current supervisor more in your project?


What are some good books to read in order to improve my academic writing?

Different books work well for different people, depending on your natural writing style, how you think, and your writing process (long writing sessions or short bursts, frequent iterative revision to 'perfect' each sentence as you go, or drafting the whole thing and revising from start to end later, etc.).

I recommend first googling "thesis writing tips" and reading reviews of the books that pop up in the results (on Amazon, etc.)

Also you might find some ready-made lists of resources helpful, such as this one from UIUC:
http://www.library.illinois.edu/learn/research/writing_tips.html

In addition, there are some fundamental classics on general writing strategies that can dramatically improve your academic writing. One such classic is Zinsser's "On Writing Well" (http://amzn.com/0060891548).

You might also appreciate some one-off resources that offer advice about specific sections of a thesis, such as the literature review, methodology, analysis, results, and conclusions. Google "tips for writing [fill in section here]" and see what comes up.

For instance, doing this for "literature review" brings up resources such as this handout, from the University of Toronto:
https://ctl.utsc.utoronto.ca/twc/sites/default/files/LitReview.pdf

or this presentation from faculty at UCSD:
http://www.jacobsschool.ucsd.edu/student/student_grad/docs/How_to_Write_an_Effective_Literature_Review.pdf

or this page from the UNC Writing Center:
http://writingcenter.unc.edu/handouts/literature-reviews/

In general, university writing centers exist for the very purpose of assisting students with writing needs. I highly recommend spending an hour at your university's center perusing their resources and learning about the types of support they provide. Try a consulting session with one or two of their writing assistants and see if it helps. Often a 1-hr consultation can help to correct some persistent trouble spots. They can provide actionable advice on everything from the right 'attitude' (ways to motivate yourself to write and to structure your time accordingly) to thesis organization, to grammar and style issues.

With regard to technical aspects, a helpful resource would be the APA Publication Manual, now in its sixth edition. Proper formatting seems a trivial after-thought, but appearances do matter in the academe. How you cite authors in a citation, or what part of the citation you italicize, can jump out at your reviewers (professors or journal peer reviewers, should you choose to submit the thesis for publication - which I recommend) and either enhance or hurt the overall impression about the quality of your written work. Good luck!


Copyright issue of recorded video game when publishing research paper about it?

Don't worry about it.
After all, you might be using copyrighted data during your research, but when you're writing your paper, it's not going to include the music or gameplay recordings itself, right? It'll probably be a pdf file written in LaTeX, which wouldn't include encodings for rich media formats; at most, you'd just include screenshots of the process used to produce the data, or individual still images from the gameplay. Neither are likely to infringe copyright, being fairly clear Fair Use.
Of course, using copyrighted material in your datasets might prevent you from distributing the raw datasets, but that wouldn't stop you from writing papers about the analyses performed on the data, or the conclusions drawn from those analyses.


How serious is plagiarism in a master’s thesis?

Edit based on subsequent info by the OP...

This has to be raised with the relevant department / committee / Dean so that it can be addressed in a manner they see fit.

They could demand changes, or they could leave all alone.

If you don't report this, then if the Master's thesis gets published first YOU will be accused of plagiarism...

So you have to report this, but how you do that is going to be a difficult choice.

you could see your advisor first and get the master's student to change those chapters.
If that is not successful, then you have to go further, as the possible consequences of leaving it could be serious for you.


How would you decide to publish (or not) in F1000Research or other journals with alternative peer-review methods?

How would I decide?

Funding, Readership and Tenure.

Does the journal cost money to submit to, and if so, do I have any funding for said submission? Is there a means of waiving that fee if I don't have funding?
Is the journal read by the people I want to read my paper? This I'd gauge by talking to my colleagues - for example, if no one in (hypothetically) infection control reads F1000Research, then I'm not publishing there, because the point of my paper is to be read and advance the field, and it can't do that if it isn't where relevant eyes will see it, whether or not the journal gets an ideological checkmark.
Similar to readership, when this journal is looked at by a promotion committee etc., will it matter?

The latter two are, in my mind, not yet settled, and that makes me a little hesitant - bold ideological stands are for people who aren't on the job market. Beyond that, I think the primary problem with post-pub peer review is that I'm not convinced it will be at all uniformly distributed. My suspicion is that a few prominent papers will be heavily reviewed, and then the rest will have either middling, or no reviews beyond what is mandated by the journal. I'm also not convinced it's a terribly fair system - it's relatively easy to attack a post-doc or doctoral student's work, while you might hesitate to do so for Important Person In Your Field, and similarly, said Important Person may be able to be fairly rude with impunity, especially if the journals aren't terribly well known.

For what it's worth, several major journals in my field are double-blinded. I have no idea who the authors are, there are actually instructions to remove clearly identifiable information (change "Brigham-Women's Hospital" to "A major regional hospital in the Northeast United States", etc.) in the manuscript, and the reviews are anonymous unless signed.


In the universities I've been affiliated, conditions are strictly enforced. If you fail to meet the condition, then the offer is withdrawn. You can appeal the withdrawal, but an appeal will be granted only insofar as procedural irregularities were judged to have taken place. The conditions itself can't be appealed.

I do not know enough about your personal circumstances to comment on the issue of repeating a course. However, it seems to me that repeating a course means that you won't be available to accept the offer and most offers are time-bound.

Good luck to you.


Has there ever been a trend in academia like the one we're experiencing with Data Science?

Does any field in the past compare to the current field of Data Science, in terms of trendiness and importance?

Yes. It has happened before, it is happening now, and will again.  There was programming in the 80's and 90's.  Then Software Engineering...
Back in the late 40's and 50's there was a big boom in nuclear physics, and nuclear engineering.

Don't get a degree because you think that there might be good jobs.  Do what is interesting to you (and something that is likely to get you a job.)  If you like Data Science, then do it.  If you don't, then don't.  you are going to have to live with doing the work all day, every day for many, many years to get a PhD.  If you aren't in love with it, then you will not succeed.

Since a PhD is a long-term commitment, takes a lot of patience, costs a lot of money and takes a lot of time during the term, it is not to be undertaken by an answer on the internet. It is your decision.


Funding during graduate study (phd, masters) in math in the US

When somebody says a program is "funded", does that mean the money is conditional (whether he TAs or not) or unconditional? Or is it clarified in context?

The vast majority of funding is conditional on some amount of teaching, TAing and/or grading.  The exact amount varies from program to program and, often, within a given program, both from student to student and from year to year.  Various government-sponsored fellowships will cut out all teaching obligations for entire years, but there will be other years in which teaching is required.  Most students spend five or six years in a math PhD program in the US, and most prestigious fellowships don't fund all of that time: e.g. the NSF graduate fellowship provides three (very highly paid) full years of support.  You should also be aware that some teaching experience is desirable bordering on mandatory for future career success, so even a candidate who needs to do no teaching whatsoever (e.g. a foreigner supported by their own government) usually does at least one or two classes.

  Is there such a thing as entirely unconditional funding? If it's not tied to teaching, will it always be tied with progress (or something else)?

NSF funding is not conditional on teaching (the above link makes this clear).  Yes, all funding is conditional on satisfactory progress.  It has to be, because continuation in a PhD program is conditional on satisfactory progress and funding is conditional on being in the program.

  Are there programs that will ask you to take out loans? In other words, do (most) schools generally have some sort of funding available? How does this depend on rankings/tier? Is there a specific ranking, say 50, below which you'll mostly likely need money through loans? Does it depend on type (masters or phd)?

The majority of PhD programs in mathematics only want to admit students who have (in some technical sense, anyway) full funding, through a combination of stipends and teaching.  Students who want to pay their own way are generally admitted in "non-degree programs" or in ad hoc temporary situations.  I don't know of a PhD program that advises students to take out loans.  In fact, I would advise the contrary: you should not attend a math PhD program unless you have full funding.  What constitutes full funding may be higher at a top program (but also depending upon the location of the program, the wealth of the institution and other factors) but so far as I know, less prestigious programs are no less likely to fund their students.

Master's programs are different: in many cases, it is harder to get funding for a master's program, though it is certainly still possible.  In some cases there is an across the board raise from the master's program to the PhD program: e.g. the same TA duties done by a master's student may earn less than if done by a PhD student.  Still I would not advise any student to pay tuition to enroll in a math master's program in the US.

  For the sake of avoiding confusion, what are different sources? Fellowships, scholarships, the department, "TAships" (what is an exhaustive list?)

There is external funding and then there is internal funding.  External funding comes from a variety of sources, especially the government, especially the NSF.  Internal funding comes from the department and/or the university.  It is usually divided into a stipend -- which is what you get paid just by being there -- and an instructorship, which is what you get paid for doing tutoring / grading / TAing / teaching.  For more precise information you should consult the individual department.

  My personal concern is whether or not I can depend on being funded, even if I'm not a very strong student (or if I'm a student coming from a different discipline).

The entire funding package should be given to you in detail when you are admitted.  It will not be a year-to-year deal: it will be guaranteed (conditional on satisfactory progress, which essentially means not getting kicked out of the program) for N years, where N is a number that will be given to you in advance and usually lies in [4,6].  Asking how often students get funded in years N+1, N+2, N+3 are good questions, by the way.


Should I cite my supervisor in a thesis?

I think it is common and well-known that the supervisor sometimes helps the PhD student. In fact, the main work of the supervisor is giving ideas that they come up with due to their experience and knowledge. In many cases, this ideas will not work, in some cases they may. It is up to the PhD student to work out the details and see what comes out in the end.
Thus, I don't think that you should cite your supervisor at every idea she came up with. It should of course be clear in the document who supervised you and you might want to add an acknowledgement.

Two small points to finish:

If the result is important enough for a stand alone publication, i.e. if you are writing a paper out of it, your supervisor deserves to be one of the authors (then again, this should be rather common for most papers written by a PhD student...).
If you are in doubt, ask your supervisor about it. She will know how to write it and you can be sure that she agrees with your choice.


Do professors get paid for supervising students?

In the US, supervising graduate students is generally considered part of the normal workload of a faculty member and there's no extra pay for doing this.

The number of students supervised is typically a factor in tenure, promotion, and pay raise evaluations.  Not supervising enough graduate students can hurt your evaluations and might possibly result in your not getting tenure or promotion or a pay raise.


How exhaustive should I be when enumerating works in a State of the Art

It is difficult to give a general answer to "how much detail do you need to summarize", since that depends on a lot of things, but you should first of all ask your supervisor what they expect. That is always the definitive answer to "how much is enough" regarding a thesis: it doesn't really matter what answers you might get at Academia SE; what really matters is what your supervisor (and thesis committee) accept.

That said, if your goal is to provide the most useful information for researchers that might read your thesis, then I would suggest that you be as exhaustive and detailed as possible. If you have gone through the trouble to read these articles (at least enough to actually understand the differences between various Muffin equations), then it would be very helpful to others for you to spare them the read by summarizing what you have read and understood.

From what you describe, though, I don't think writing a textual paragraph would be the most helpful way to describe this information for your readers (nor the easiest for you). I recommend that you present these details in a table which cuts out all the fluffy words and just gets to the point: the name of each variation; the citation of the article that presents it; the key details that distinguishes it from other variations; the pros and cons. In addition, if you could group the 20 variations into three to six categories that are similar to each other, that would be a further helpful layer of synthesis.

There are two further advantages of using a table:

For yourself, a table helps you focus on what is essential in each article. By carefully thinking about the structure of the table (mainly, which columns are necessary), you help yourself to better understand what you're reading and to focus on what you consider important.
You don't need to worry about which ones are "worth" summarizing or in how much detail: you just simply summarize everything, briefly and to the point. That said, if a few variations stand out to you as important, then by all means write as many paragraphs as you want to that discuss these ones in detail. But then you won't need to do that for any of the others that you have already briefly summarized.


Why do some conferences ask authors whether a paper they are submitting to the conference was published in arXiv?

Presumably some reviewers check for plagiarism, so it is useful for them to know that there exists a preprint out there that is expected to significantly overlap with the submission they are reviewing.

From the CFP for the conference you gave as an example:

  Reviewers will be told: “The author(s) have notified us that there exists a non-archival previous version of this paper with significantly overlapping text. We have approved submission under these circumstances, but to preserve the spirit of blind review, the current submission does not reference the non-archival version.” Reviewers are free to do what they like with this information.


Master's thesis - lack of evidence, possibly poor topic choice

Don't panic. It's quite normal for the direction of the research to shift a bit after the initial proposal. It's common to find out that for one reason or another it's not feasible to do exactly what was proposed. After all, if you knew exactly how to do it in a way that's guaranteed to work, then it wouldn't be research!

Unless your funding is tied to a specific project, you can probably broaden the scope or make other adjustments. I'm sure your advisors will have some specific suggestions for you, but in the meantime, think about what you could do with the types of materials that you have been able to find.


How to handle the plagiarism on references?

25% similarity is low. Similarity in references should also be discounted. I suspect it's either a mistake or something you don't have to pay attention to - you mention that your manuscript's already been accepted, and they might just be sending plagiarism reports with the acceptance email as a matter of course.

If the editor also said something like "please correct these plagiarized text", I'd write back saying that the similarities outside of the bibliography are minute, and ask for clarification.


Participants had to be rejected - where and how do I explain that in my paper?

It is very simple: you just need to (1) be honest and (2) explain clearly what you did, just like in the question you are asking here.

The explanation why there are two different values of N belongs in the "Methods" or "Participants" section. But it will most likely be necessary to add (N=...) in a few other places in the paper (eg. in figures), to make sure that there is no confusion over which of the two was used.

To mention N in the abstract, if you have to choose between the two, the lower value would be preferred (in general, people like modesty and statisticians like to "err on the side of caution").


Are there any journals that pay reviewers?

It's not a myth. There are/have been some journals that pay peer reviewers. For example:

The New England Journal of Medicine used to pay $5 per review, until some reviewers complained that "if that was the price that this eminent journal placed on their opinion, the New England Journal of Medicine should seek referees elsewhere"
The Lancet reportedly pays for peer review "sometimes"
Reviewers for journals published by the American Economic Association earn $100 for each "timely" review.
Zentralblatt MATH (zbMATH) pays 2.56 EUR per review, although this is for post-publication reviews that are then published.
The Journal of Medical Internet Research offers "a review model in which selected peer reviewers may be paid to deliver high-quality and speedy peer-review reports" (if authors pay an extra fee for the fast-track option)
The Arabian Journal for Science and Engineering has offered an honorarium of $100 for each "timely" review
Drugs in Context pays its peer reviewers an honorarium of unspecified amount, supposedly "to motivate rigorous peer review"
The International Institute for Science, Technology and Education (which is on Beall's list of allegedly predatory open-access journals and publishers) pays reviewers for its journals $60-$100 per review

Whether the reviewer being paid, has more obligations to provide thorough in depth review is true or not is entirely uncertain, though.


How much should we trust that the approach described in a paper solves the problem that it addresses as well as it claims to?

I think there is more than one type of "trust" here: "trust" as in whether to believe the authors are being honest, "trust" in terms of the state and certainty of knowledge in a field, and "trust" in the value of the peer review system.

Although misconduct is possible, and it is worthwhile to consider, another possibility is that the approach used in a paper relies on assumptions that were either taken for granted or are stated in the paper but you have overlooked them. For a signal-processing algorithm, for example, there may be an assumption that external noise has a particular color (white, pink, etc) - with a different color noise, or with real world signals, the algorithm may not work as well; for code optimized for a particular architecture you might get different results with different hardware or a different software environment. You shouldn't "trust" that a result in one context will apply to all other contexts that have not yet been tested.

Peer review is meant to improve the quality of and confidence in published material - it is not a flawless fact-checking system. Even when everything in peer review goes perfectly, the best you can assume from a peer reviewed paper or presentation is that the methodology is sound and the conclusions are reasonable based on the data. You should never "trust" a published work as the last word on a topic, and be wary of far-reaching claims - these are often stated for the potential of the technique, not necessarily the implementation as presented - these statements are intended to gain support for further work on the topic, so feel free to treat them with some skepticism. I wouldn't classify any of these as misconduct, just a potential for miscommunication between what is written and how you are expected to interpret what is written.

Lastly, the issue of sharing code differs by field, but at least in the biological sciences it has become standard for journals to ask authors to make analysis code and raw data available on request. I am not sure about the norms in computer science, and it certainly might depend on the potential for commercial application. It seems unlikely that someone would truly have "lost the code" to a recent paper, but if you are going back more than a couple years it is certainly possible that was indeed the case.

It is also possible, if you are a student, for example, that the authors felt your request was bothersome. How did you ask? "Can I see your code?" is a lot different from "I implemented the algorithm you published in 2014, and I got a different result from what you published. Here is the code I used - would you be able to share your original code, or have a look at mine to help find the discrepancy?" If you are truly skeptical, this is the approach I would suggest - science would benefit greatly from these types of replication and confirmation attempts.


Access to good research communities without being in the university

One of your best bets would be to find some active SubReddits, Discord, and GitHub communities. Without university infrastructure, it’s a very steep challenge. Even with my suggestions, you become increasingly limited by what you’re able to do.


What can we do about being dissatisfied, morally and practically, by the business-like tactics shown by Universities (in the US and elsewhere)?

Before this question gets closed for not being an answerable question, let me try to give some personal life advice, which might sound frivolous but is serious:
Start your own monastery.
Sure most professors care about the quality of their universities, but they also want time and energy to do their research, or they want to have some perks in their life, or they have families they need to support.  They also realize that, even if they did take over the university, most of the problems would still remain; they still wouldn't have the funding to provide the small classes and individual support and research opportunities their students need, at least if they wanted to pay themselves above minimum wage.
Forget about industry; it's an order of magnitude worse in industry, where there is no way of making enough money to survive, never mind make a profit, without lying to everyone else left and right.


Is it peculiar for a department not to have any of its own PhD graduates as professors?

It's common in computer science for a university to have few if any of its own graduates as faculty, and should not be taken as a bad sign by itself. This low representation is for two main reasons:

The best five or ten universities in the United States produce a disproportionately large number of strong academic candidates. In practice universities that have research departments at all (let alone the exceptionally strong ones) tend to be filled with professors with Ph.D.s from the elite few.
Going somewhere else leads to cross-fertilization of academic thought. Presumably after 5+ years of graduate school one has spent a lot of time learning from the expertise available in their department. Going somewhere else allows a professor to transfer her knowledge to a different group of researchers, and to get fresh insight from them in return.


If you downoload the templates for Communications Society Journals and open the README, you will find the following note

  This package contains the IEEE Communications Society subset of the full
  IEEEtran package and is intended for use with IEEE Communications Society
  publications. The included version of the IEEEtran_HOWTO.pdf has been
  specially formatted in IEEE Communications Society (comsoc) journal mode.

and the disclaimer

  NOTE: Take care not to confuse the "comsoc" and "compsoc" class options/modes as they are very different:

  comsoc  ==> IEEE Communications Society

  compsoc ==> IEEE Computer
  Society

The IEEE Transactions on Pattern Analysis and Machine Intelligence is not published by the IEEE Communications Society but by the IEEE Computer Society (compsoc). Thus, I think that for this you should use the templates for Computer Society Journals.

The IEEE Transactions on Multimedia seems to be published by both societies and by others too. The IEEE Transactions on Multimedia home page links at the information for authors page which further links to the author digital tools page, but saying (bold mine):

  The style files are available on the web at the IEEE Author Digital
  Toolbox (link is external) under "Template for all Transactions."
  (LaTeX and MS Word).


How should a PhD student approach a collaboration?

The best way to start a collaboration is to engage in a face-to-face brainstorming/working session so that you 1) formulate a problem of a mutual interest, 2) jointly sketch a scaffolding of a joint paper, and 3) come up with a plan to proceed, or at least agree on how to arrive to such a plan. Before the meeting consider the topic semi-open (unless you are dead-sure you know what you want to work on with the person), you never know what new/interesting/unexpected will come out of your discussions.

Now to get to a meeting/a few days stay, you need to arrange for a visit at the (future) collaborator's place and it seems that what you are asking is about a particular way to do that. From my personal experience, there is no right, nor a wrong way to do it. I understand these things in terms of signalling. That is, the form is less important that the signal you are sending. In my opinion/experience it does not matter whether you write a short notice like

  Hello Joe, we met there and there and I got intrigued by the topic we discussed. Would it be possible for me to visit your lab/group and expand on those ideas? Fred.

or expand in a two-page argument about why it is beneficial for both of you to meet. In both cases the signal is the same: would you be willing to speak to me? and that is the only thing which matters.

And you should read the reply in exactly the same manner. Whatever is written there, the only thing which matters is whether the answer is yes, let's see what comes out, or no, blah, blah. All the rest can be discussed during the meeting, given the reply is positive. If it's negative, most probably the collaboration wouldn't work out anyway. Being open-minded is a state of mind, a personality trait.

Now to your concern about the collaborator's higher rank/position at a prominent university: I do not know about the culture and social interactions in communities concerned with humanities, but my general observation is that the better a scientist (whatever better means), the more humble and modest the person is with respect to the corporate structure and seniority ladder. That is, the majority of really good/respectable researchers in my experience do not care for your rank, they care for what you say.

The point I wanted to convey above is the following:

  if the person you want to collaborate with is open minded and thus a potentially a good collaborator, it does not really matter how you approach him/her, just do it. In the case you have something important/significant/novel to say, he/she will engage you and the collaboration will start. Just remember, it's you who approached the other party, hence you want something from her/him, therefore it is important that you understand that you will be the driver of the collaboration, at least at the beginning - the ball is initially on your side - unless you touch a topic the other party is working on and has some solutions for anyway.


Should I inform my old supervisor of new insights that lead me to think his hypothesis must be adapted?

Definitely seems like something worth mentioning.  Regardless of whether this leads to any edits in the final version of the paper, presumably your old advisor cares about the question for its own sake and not just for publications and so would like to know if there's new information that pertains to your results.

Your old advisor will be in a good position to decide whether any changes need to be made, and if so whether it's fine to just wait until the reports come back for the minor changes.  Sometimes it's fine to have a paper that reflects your understanding at the time it was written.  Sometimes you can just add a small remark in the final version mentioning that new things have come to light.  Sometimes it might be that you should update the referee immediately.  It's hard to know without knowing more about the details of the situation, but usually it won't require pausing the review process.


Should I mention in my statement of purpose that I am applying because of my girlfriend

I can't see any scenario in which that would help and can see many in which it would hurt you. The first question asked would be "Is this guy serious???" People are looking for people dedicated to the academic process, research, learning, etc. Personal reasons such as this, and many others, shouldn't be mentioned. Take about why it is that you want to work with this faculty and what  your long term academic goals are.


Is it possible to finish PhD quicker than formally possible?

I don't understand what you want; do you want us to contact your supervisor for you?  We can't find some magic exception in the rules for you.  Either you need to suck it up and accept this won't happen, or you need talk to your supervisor and convince them that this is a good idea.

Let me just add that this sounds like a terrible idea to me.  UK Ph.D.'s are way too short anyways; rushing through one will just throw you out into the cold hard reality of the job market totally underprepared.  You don't seem to have thought about the "If" in "If I can finish my PhD thesis earlier, and then move to a preferred place for a postdoc, I do not see a reason to delay." or thought about what happens at the end of your postdoc.  If you are really finished with your thesis at the end of 15 months, then it's not as though you'll twiddle your thumbs for the next several months; you'll have an incredibly valuable chance to start some other projects, and get a bit of a head start before heading into your postdoc.  That's time you'll never get back, and which you want to strain your relationship with your advisor in your rush to throw away.


Publishing vs. putting work online under a free license

There are two separate questions tangled together here.  The first is whether scientists will cite something that has not gone through a traditional peer review process, and the second is whether a copyleft / open source repository project is a good way to manage such a non-traditional publication.

To the first, the answer is most certainly yes.  Many non-peer-reviewed publications are not just cited, but highly cited, particularly technical reports and standards.  These do not undergo peer review, but if they are useful to people, they will cite them---sometimes thousands of times.

For the second, well, consider the fate of most free and open projects, whether on GitHub or elsewhere.  Almost every project of this type dies quietly in the dark, because nobody notices or cares about it.  Some, of course, succeed, and a few have massive impact.  The question is: why should anybody care about your project?  If they do, then copylefting in a git repository is no better or worse a way to manage the document than any other way that communities manage non-peer-reviewed documents (though make sure you do it with a CC license, not a code license).  If they don't then the technological or ideological elegance of your approach will make no difference.

The bottom line is: you are focusing on the technology, rather than the community.  You need to understand how your work will interact with your community, and then the technology is a secondary issue that will follow from that interaction.


How appropriate is to make multiple submissions of research findings to same venue/conference?

You cannot submit both papers.  As others have pointed out, most venues explicitly forbid simultaneous submission of substantially overlapping papers.  The answer to your first three questions is the same: Immediate rejection.

In fact, I would go further: Neither PA nor PB can be submitted alone.  It is unethical to submit a paper without the explicit consent of all authors, because authorship implies endorsement of and responsibility for the content of the paper.  On the other hand, it is unethical to revoke authorship from someone who has made a substantial intellectual contribution to the work.  The two authors must work out their editorial differences, like grown-up professional adults, before they can submit anything.

If they can't agree on what to submit, then tough noogies — no paper.


Can I submit more than 3 reference letters with my grad school applications?

No!

US institutions expect that you have never seen your recommendation letters; your references are supposed to upload/submit them directly to your target departments.  But presumably you are uploading/submitting your own supporting documents.

If the application web site somehow restricts you to naming only three references, then you only get three letters; choose wisely.  If it's a paper application, just ask all your references to mail in their letters.

(I assume you are applying to a graduate program.)


can I reuse Coursera material for my lecture notes?

Coursera's terms of service state that students can only access course
  materials for their own purposes; they are not meant to be distributed
  more widely.

Also they have

  Even if you are the creator of published content, you do not
  necessarily own copyright.

This means that you have to directly contact Coursera and ask the question from them.


Is it worth enrolling in a Ph.D. program without employment?

Europe is not a country but a continent. The links you gave are from the university of Vienna, and the example of employed PhD students refers to a special program from the University of Vienna, so that is not even Austria-wide.

Enrolling in a PhD program without employment can mean many things, for example it could mean you get no financial support what so ever, i.e. you are self-funded (but even there is variability depending on how much tuition you pay). Being in a PhD program without employment could also mean you receive a stipend instead of wage (which has consequences for your eligibility for social security, pension, health insurgence, etc. This varies to a huge extend from country to country).

In general a PhD degree is a PhD degree regardless of how it was funded. It may be that some programs are more prestigious than others, but that is country specific: It may be that in some countries particular stipends are very prestigious, while in other countries employment is so rare, that getting it is considered prestigious.

I would be weary of self-funded PhD programs, but otherwise stipends and employment contracts are both fine.


This is a common problem that researchers face. The fear of being scooped partially explains the publish or perish culture in academia. This is definitely a setback for you, but there are a few options which you can consider to make at least some use of all those months of research:

You can try to build on the published paper. If required, conduct a few more experiments and move over to the next logical step in the idea.
Using your original idea as a base, try to come up with a related but new research question that allows you to use some of the old data.
Go through your paper again and see if there is any secondary finding that you might not have focused on at that point of time, but which could be developed into a new research idea.

Now that you have been scooped once, you should try to get your results out before anybody else does. Since the publication process of journals can take up a lot of time, one thing you can do to avoid getting scooped is post a pre-print or present at a conference as soon as you finish your research. Also, make sure that you do not take too long to write your manuscript. You should actually start writing certain sections, such as the methods and results section as and when you perform the experiments. That way, you will be able to save up on the writing time.

Most importantly, do not lose motivation. The fear of being scooped is part of a researcher's life and there is no foolproof system in place to avoid it. So just keep your spirits up and move on.


Can I hide my bachelor and master degrees in CV when I apply for a PhD position?

No. You should not hide anything that you have done -- in academic programs or in work experience.  It doesn't matter whether you think that it is or is not related to the PhD application.

If you made mistakes, then address them directly in your application essay.  What were the mistakes? What did you learn from these past mistakes?  Who are you now, given your experience in these mistakes?

In my opinion, if you aren't able or willing to talk about these "mistakes", then you aren't ready to enter a PhD program.

EDIT

My suggestion reflects a particular moral and ethical code, and it also reflects a certain culture (US Science, Engineering, and Social Science programs). It may not be appropriate in other cultures, and it may not suit your morals and ethics.

To the folks who recommend "only focus on the positives", my reply is "good luck with that".  In my experience, admission committees (and hiring managers) are keen to find any weaknesses and problems.  If none are apparent, they will ferret them out.

If OP leaves these off his/her CV, then there will be holes.  If s/he doesn't address the holes in the application essay, then you are leaving it up to the admissions committee to fill in the holes with their imagination.  I presume they will assume the worst.  (In my experience, this can happen even with evidence of accomplishment.)

If these are included in the CV, then official transcripts will have to be submitted (this is standard in the US), and thereby the committee will see the full record, not just GPA for each degree program.  And if s/he doesn't say anything about them in the application essay, the committee will probably draw very negative conclusions from them.

Finally, my suggestion to address the problems and learning in the application essay doesn't mean that it needs to be long or detailed. It could be a couple of sentences: "These degree programs were not as successful as I would have liked, and but thankfully I'm much the wiser now.  I learned what I'm good at and what I'm not good at, and I learned what I really want to do in my career."


Does it matter if you have three or four possible answers when making a multiple choice test for learning?

The standard for multiple choice questions is normally 4 answers. However, there is research that indicates that three choices is optimal. Three choices seems to increase the reliability of the test and decreases the number of poor distractors.

If you are worried about the difficult of your assessment. Instead of developing questions with four choices another strategy would be to increase the number of questions with three choices. This will allow you to cover more content.


Sending a second reminder to a professor about LORs, after the first reminder

A week since your first reminder is somewhat on the short side - personally I would wait a couple more days (maybe two weeks since the last email) to send another email.

A week before the deadline is a good point of time to send a reminder. There is no need to state that this is a second (or nth) reminder. A short email, roughly of the form 'thanks again for agreeing to write a recommendation letter for me. I just wanted to quickly remind you that the deadlines are one week away. Please let me know if you need any more information from me. Thanks again for all your help, etc.' is sufficient.


How to gracefully exit my postdoc position with 1 year left in contract

Tell him you want scientific variety, geographic variety, etc.  I wouldn't get into the "he doesn't have time for you".  Just indicate you are interested in new things.  Tell him this is a natural break point since you wrapped one thing up, so it's not even like there is a huge dislocation.  Tell him you plan to continue working on current contract but looking for other things, very actively, at same time.

[Keep soaking up the current salary. Do some things to keep him/you happy, but it doesn't sound like there is huge supervision, expectations, anyways.  Assuming there is no new major project, figure out how to dust off some minor aspects and get some "cheaper" papers done that pad out your resume, build off of last project.  Helps you out and the advisor at least sees some pub count even though you aren't solving more Millennium Prize problems. If he gives you a new big project, I would be OK doing that, but keep looking for next spot and be willing to ditch it if you need to hop to another assignment.  Be able to write up incomplete work...there is an art to this and it is not as sleazy as it sounds.  In fact a lot of work is wasted because people don't write up incomplete work and it sits for years instead or gets redone.]

Ask for his assistance.  He'll either give it or won't give it.  I suspect he will at least give his blessing.  In any case, once you have told him, you just execute your plan and start looking for things.  2:1 anything you come up with ends up needing some time to develop and there is a natural dovetail with current contract end and new contract start.

Personally, I think a postdoc (or senior grad student) should be relatively independent and capable of starting, executing projects on own.  And of writing papers that just need a rubber stamp from the advisor who attaches his name to pad his CV.  (Definitely work on your paper writing...publications are how people keep score in academia and a PI is expected to be able to write a paper without someone above them.)


If you only adjunct at the other two institutions (my assumption based on saying you do it part time), I would list your affiliation with your doctoral program. Of course your CV should include these adjunct roles as well, they just aren't your main affiliation.

If you have developed a more intimate relationship with either the two institutions you teach part time at (like say you've been an adjunct for many years) you might consider listing them as an affiliation. Those part time adjunct gigs though don't typically support research activities that would result in outside roles such as a reviewer (for anything) or even being considered a specialist in the field.


How to cite an authorless report in JabRef/Bibtex

In the end, you should format your citations according to the style guide of the journal you are targeting. Which BibTeX fields you have to use depends on the bibliographystyle you are using in your document.

For example, IEEE journals require that the name of the institution appears after the title of the report, see here on page 7.

With the ieeetran bibliography style, the author field is printed before the title, while the institution field is not printed at all. In order to fit the journal style (institution name after title), one needs to remove the author field and enter the institution in the type field, which is a bit of a hack:

@TechReport{USACE2015,
    title       = {{North Atlantic Coast Comprehensive: resilient adaptation to increasing risk physical depth damage function summary report}},
    type      = {{US Army Corps of Engineers}},
    year        = {2015},
    file        = {:10A_PhysicalDepthDmgFxSummary_26Jan2015.pdf:PDF},
}

produces the desired output:

In short: check the citation style of your target journal and try to mimic that. If you also want JabRef to sort your references properly by institution, you will also need to include the institution in the institution field.


Academic Writing: Numbered points in text etiquette

They're both acceptable, nobody except very careful English fanatics are likely to care, but the latter is preferable. Reasons:

Periods are more "final". They indicate the end of the sentence. That implies that you should instead use capital letters if you stick with periods:

The loser will: 1. Get laughed at, 2. Pay for drinks and 3. Have to run outside naked.

Because periods indicate the end of the sentence, one doesn't expect to see multiple periods in a single sentence. Using ) avoids this problem.

As for whether or not to use a semicolon, again it's up to you, but the comma is fine here. That's because the three things listed are all pretty related, short phrases, and on an equal footing. Semicolons are better when a sentence is complex or has other punctuation symbols. Example of something where I'd prefer the semicolon:

This new year, I resolve to: 1) cook 100 breakfasts for my wife - she deserves it; 2) set tests such that 50% of the class fails to shake my reputation as an academic Santa Claus; and 3) run for president.


What is considered "completed work" for a conference submission

Completed work consists of work where you've gone through all the steps of formulating your research question, applying a methodology, and generating and analyzing results. Incomplete work is where you're still in the phase of applying your methodology, or you haven't fully analyzed the results to figure out what they mean. A paper or poster on incomplete work might focus on the methodology or preliminary results, but it doesn't fully answer the questions posed when the work began.

There's definitely a judgement call when you can consider work "completed". Oftentimes, the answers to research questions lead to more questions, creating a line of related work that's never really "finished". In this case, you'll need to compartmentalize your results into digestible chunks that can be considered "completed". Describing future work planned on a project doesn't mean that a work is incomplete.

For a work to be "completed", it doesn't necessarily have to have been written up already. That said, you'll probably have to write up the work before submitting anyway. You almost certainly shouldn't be submitting the same work to a journal and a conference. You could try to submit "incomplete" work to the conference, since it's a somewhat fuzzy line, but don't be surprised if you get a rejection if all you've got is the methodology and no results at all.


Penalties for disclosing student grades without consent

In the US the Family Educational Rights and Privacy Act (FERPA) protects the privacy of students. This "act" is not a law (on further reading it is a law), but rather a stipulation by the Department of Education that universities must obey in order to receive funding. As such, I do not believe that violations are classed as a criminal offense and hence cannot lead to jail time. Universities which violate the FERPA can lose their funding and likely have grounds to dismiss employees who violate the act. The university might even be able to seek damages against those individuals, but again, not jail time.

I would suggest that you not violate FERPA. If you intend to, or have done so (accidentally or otherwise), I suggest that you seek legal advice.


Would I fail if, for example, during the discussion a mistake in my comparison and evaluation approach is discovered which makes my results meaningless? Although I discussed my approach and everything I did with my advisor (postdoc not the prof), yet I still fear that I might have done something wrong and then everything collaps.

This should not happen unless:

The mistake is blatantly obvious and something you should have really known better. And with blatantly obvious, I mean something that somebody who has not even studied computer science or a related field could easily spot. Even then you may have chances, if the rest of your work is appropriate – almost everybody brainfarts now and then.
You made not only one mistake but a lot of big mistakes.
It becomes obvious that you deliberately ignored that mistake, to avoid being stuck or to get “nicer” results.

(In the first two cases, your advisor is in big trouble, too.) The point of the master thesis is that you should demonstrate that you can investigate a scientific question under supervision (or something similar – check the regulations, if you wish to know). One mistake does not change this.

Moreover, in some examination regulations I am aware of, there is a procedure for the case that some important but localised flaw is detected in your thesis. For example, you could be given a month to amend your thesis.

  How would one fail a master thesis defense?

I have not experienced or heard of such a case but from what I have gathered, you pass if you:

Give a talk about your thesis.
Be able to answer questions about it.
Are not detected to have been cheating.

Even if you suffer from a mental breakdown due to nervousness or similar, you probably can repeat the defense – at least with any reasonable examination regulation and examination committee. I am aware of one case where somebody had a nervous breakdown for understandable reasons¹ and the examination board let him repeat the exam. If you look into your examination regulations, there are probably some clauses that allow the examination board to do some things at their own discretion in exceptional cases.

Be aware though that being very difficult to fail does not make the defense unimportant. A bad defense may seriously (and in particular more than nominally) affect your thesis degree, which in turn has a huge impact on your total degree. In particular having passed a thesis with the lowest possible degree (or something close to it) is something you definetely do not want to have in your vita².

¹ It’s very complicated, but you might compare it to the following: In the middle of the defense, somebody who was the defender’s girlfriend until six months ago enters the room being obviously pregnant in her ninth month.
² Unless you are in one of those few disciplines where this is the norm.


Applying to graduate programs unrelated to undergraduate degree

You should definitely apply. I have seen many cases where individuals with degrees in tangentially related fields not only are accepted to, but excel in, graduate programs in different fields.

Do note, though, that if you're applying to be a PhD, it's expected that you'll be doing research in the new field, and you'll have to demonstrate to the application committee that you're up to the task. You may have to be creative about this, given that your background is very different from what they're used to seeing; consider emphasizing any possible applications of computer science to literature (ngrams, maybe?) or anything else which may strengthen your application.


Effect of bland cover letter for journal submission in biology

All journals I have come across their guide for authors require a cover letter. Although it's probably partially a remnant of older times, where letters and manuscripts were mailed to the journals, it does have functionality.

The cover letter is a quick way for the editor to decide if it's even worth opening the full article. For this reason, arguments on the novelty, findings, importance, challenges and perspectives of the work should be demonstrated. In practice, it might not be much different than the abstract (different structure of course), but some journals also ask for specific questions to be answered.

It also helps the editor, who might not have the same expertise as the manuscript, to decide whether it's worth sending the manuscript to external reviewers. It also saves him a few hours of work from reading the whole article to understand its value.

It also adds a degree of personal communication between the corresponding author and the editor, rather than being a automated, impersonal submission process.

Finally, I usually add sentences like "all authors have agreed to submit the manuscript in this journal" or "no conflict of interest" etc, which adds a signature under the statements.

In the case a cover letter would only say "here it is", I think the editor would probably drop it in the trash bin, unless:

The title (and the abstract) conveys a subject so important that any editor could not bear not to check it out more thoroughly.
The corresponding author, or one of the co-authors, is a really big name in the field, that (even if the article is not that important) the editor cannot just reject it.

So, in mathematics, maybe just saying "Here is the solution of the problem X" and everyone knows the problem and die to see the solution, then you don't need to add much. But in sciences where a problem doesn't have a name, a more detailed explanation might be required.

Lastly, the manuscript is indeed evaluated by the manuscript itself. However, a good cover letter might make the editor check your submission more thoroughly, out of the tens or hundreds of manuscripts they may receive.

I think of it as the trailer to a movie. If you like Batman and you see Batman on the title, you will check the movie a little more before deciding if it's a crap movie or not. If you see a movie is directed by let's say Spielberg (and you like him), you may do the same. But if you are unsure about the title and you don't know the actors and directors, a trailer might convince you to watch the movie.


You will not find such information as there is no standard process in the UK. The best people to talk to are your supervisor (who should have knowledge of both examiners, and can tell you what they're like) and the internal examiner (who should be making sure the exam follows your institutions' regulations, and guiding the process).

In UK vivas that I've been involved with, the process is to keep going until the candidate has proved they

did the work that the thesis in their name describes;
can say why it's important;
can say why it's original;
can convince the examiners it's correct.

Typically the external examiner will take the lead in asking questions; they can go into as much depth as they like. The more confident you can make them that you know what you're doing, the less likely they are to drill into tiny details (unless they are particularly interested, in which case it's more a chat than an exam).

Finally, it's now become standard in the cases I've been involved with that the candidate has a few minutes at the beginning to summarize what they did - typically 2-5 minutes. If you get this chance, make sure you take it and can immediately (and I mean, in the first or second sentence out of your mouth), cover the "important" and "original" points above. A confident (in appearance) statement of "This is the important, interesting stuff that I did, and we're now going to have an exciting 2 hour chat about it", gets everybody started on the right footing, builds confidence in all, and usually leads to a good result.


How can I post my own version of a published SPIE paper on arXiv?

So is there a way around it for me to submit my article to arXiv?

It's reasonable for you to ask SPIE for permission to post the paper to the arXiv (under conditions (a), (b), and (c)).  They might not grant permission, but it can't hurt to ask.  Even if they deny permission, at least you've given them feedback about what authors like you want.

One possibility is that they actively object to posting on the arXiv.  In that case, you are probably stuck.  Another possibility is that they don't specifically object to the arXiv, but don't want to authorize arbitrary websites they are unfamiliar with or other websites they object to.  In that case, they might grant you permission.  If they do, then that should suffice for the arXiv administrators.

  If not, I think I can surely post it on my own website, right?

Yes, assuming it is controlled exclusively by you or your employer.  (That's true for most people's websites, but it could fail in unusual cases, for example if you are treating a social network page as your home page.)


Plagiarism of Research Proposal Idea by Potential Supervisors

I understand and completely share your frustration here. It feels awful when your application is rejected but later the same idea is used by a person you put some of your trust in.

I don't have a universal answer which helps to avoid such things. Sometimes people suggest to be vague in your proposal, but I don't think this is really a good idea. After all, when you have an idea, and you think it is good, you don't want to sound like you don't know what you're talking about. So, I don't think you should somehow tweak your proposal to make it less easy to plagiarise.

Instead, I would suggest to maybe do better research of potential supervisors before you send them your detailed proposal. Perhaps, do a small polite exchange of emails and check if they are even interested to have another PhD/postdoc at this moment? Look at their history of publications, read a few papers - are they really working in the area you want to work in? Look at author's lists - is there evidence that a potential supervisor  was a guest/gift author in many papers? Are there cases when they re-claim someone else's idea as their own (by doing minor modifications and changing the name, etc.) If possible, get in touch with their current postdocs/PhDs and check what they think about the transparency and ethics of the research/publication process in their group. Or simply try to arrange a small chat with the potential supervisor - sometimes five minutes face-to-face tell you more about a person than a year of email exchanges.

Good luck.


My professor is using questions from other colleges for an assignment. Is this plagiarism?

No. Unlike for students (who have to demonstrate their understanding) and for research (which has to demonstrate an improvement to the state of the art in the field) there is no expectation of originality in homework questions, and there is no ethical problem with having multiple classes work through the same problem set. There are even arguments to be made that it is a good thing for students to be judged on a uniform basis.

It would only be a problem if your prof represented these questions as his own work e.g. when highlighting his teaching contributions in his evaluation or in candidatures for a new position. As a student, you wouldn't be in a position to know about this.

There might also be a copyright issue if your professor did not ask for permission to use these questions. But there is no reason to assume that he didn't.


Letter of Recommendation from PhD Student for Masters

I think your potential writer (1) gave you good advice: look for a professor first. However, if they can write a strong letter for you then certainly it's better than nothing; your second choice may not actually be a choice if they never respond.
I think if you were submitting at least 3 letters of recommendation, it would be less of an issue for one of them to come from a non-professor, but with only two letters I would suggest you think hard about other options for the second letter. If two letters is only a minimum and you can submit a third, then I think including your option (1) as one of those would be totally fine.
It's important to recognize that recommendations for graduate school aren't primarily about your performance in an undergraduate class, they are about your potential as a graduate student. Professors are more likely to have experience teaching and mentoring graduate students, so they presumably have a better background to evaluate potential in that area.
I did write some recommendations as a graduate student for my undergraduate students, but I wrote them in concert with a professor who also signed the letter.


Do professors work through all the homework problems they assign to students?

For many professors, undergraduate courses are simple enough that when they go over 1-2 problems, they can grasp them quickly. For others, they go over solution manuals and previous notes to recall and remember how to do them. Some assign office hours to TAs, where the TA deals with students and their homework. Keep in mind that many schools do tell the professors which courses they will teach next semester/year, so they have plenty of time to prepare and develop their notes and slides.

I would be more worried about professors teaching graduate level courses that are not familiar with. It seems that many issues/inconsistencies occur at this level.


Multiple (two) undergraduate degrees in Phd application

You need to follow the instructions on the application.

However, most applications will want transcripts for all prior degrees. One good thing: you may not have been successful before but you were when you tried again. So, you've shown that you can be successful. That improvement is important to be able to demonstrate (as you've done).


Can one get a faculty position by posting CV on job websites?

For entry-level junior faculty, the likelihood is almost none unless you are already a superstar.

People get invited to apply based on their prominence/brilliance in the field or through personal connections.

While it doesn't hurt to have your CV uploaded to a job website, the likelihood that a hiring department will use it to pick you up is not very high.

The reason is that for most job postings in this economic / intellectual climate is that any single job posting will get over a hundred applicants, if not more.

Even small schools can get over 200+ applicants for junior faculty postings.  They have no need to solicit additional applicants.

[Note this is the case for the humanities / social sciences in the United States based on my experience. Your mileage may vary.]


Using an alternative name part of the way through my academic career

A difficult question to answer as, ultimately, this is quite personal. It is "what are you willing to put up with" mixed with "how much of your own personal identity do you ascribe to your name"?

I have a colleague who has had (at least) three different names during their academic publishing career and no one knows how to cite their work: do we convert publications under old names to new names? I also constantly have to tell students and other scholars "that's the same person...". It isn't great. Perhaps if you have a colleague that has changed their name due to marriage or other circumstances, you might discuss with them their experiences of building a profile anew.

One thing is for certain: if you don't change the name you use, you'll be memorable to the readers of your work. You'll come to mind before Jane Smith and John Jones.


Can I get into a top school C.S. Ph.D. program with a Master's from a lower ranking university?

There are some academic-cultural differences between US (where I live) and Canada, so take my answer with a grain of salt.

Top CS PhD programs in the US are looking primarily for concrete evidence of research potential in PhD applications.  This is especially true in machine learning, which is by far the single most popular research area for PhD appicants.  (At least a third of last year’s PhD applicants at Illinois listed ML or some close variant as their primary research interest.)  I cannot emphasize this enough—competition for PhD programs in ML is incredibly fierce.  ML has become the default area-of-interest for smart people who like CS but don’t really know what they want to do.  High grades and test scores might be enough to get a human being to look at your application, but they will not be enough to get you in; classes ain’t research.

In addition, since you’d be applying with a masters degree, you’ll be compared with other applicants with masters degrees, many of whom will already have ML publications. (Unlike Europe, most PhD programs in North America require only a bachelor’s degree to enroll, and most new PhD students in those programs do not have master’s degrees.)

On the other hand, a strong background in functional analysis, differential geometry, and probability theory is extremely rare among computer scientists, and could be a huge advantage, if you can leverage that expertise into concrete evidence of research potential.

Some specific things to aim for in a master’s program:

When you apply for PhD prorgams, you will need recommendation letters from well-known researchers researchers in your target research area.  Make sure the department where you get your master’s degree has those researchers!  You should be thinking in terms of potential faculty mentors/references, not departments.
In your PhD application, you must be able to talk about your research interests using the idiomatic language of a researcher, not just as an interested student.  Moreover, your recommendation letters must present concrete evidence of your research potential.  Make sure that your masters program gives you an opportunity to do research (or at least indepedent study projects) with those well-known researchers in your target research area.
A purely course-based master’s degree will work against you; classes ain’t research.  Similarly, using MOOCs as evidence of your expertise in ML will work against you, because we only have your word for how well you did, and MOOCs definitely ain’t research.  That doesn’t mean on-campus courses and MOOCs are useless, but you should use them to enable your research, not as end goals in themselves.
Leverage your strengths.  Look for MS programs that will help you develop research expertise that takes advantage of your particular skills.  In particular, look for potential faculty mentors who have, or at least appreciate, a similar mathematics background to your own.
Sadly, the name of your school does matter.  There are too many good applications; people apply all sorts of stupid filters to limit the number of applications they have to read.  (It might matter less coming from Germany, where there’s less variance in quality/reputation.)  Wherever you are offered admission, ask for data about PhD placement before deciding which offer to accept.