How much leeway will i have in suggesting a co-adviser or committee member when i am funded by a professor?

Would it be acceptable if I asked my advisor to bring my master's advisor on board the PhD committee so that she can help me with the statistics material?

You can definitely ask your advisor. Describe why you think this professor would be helpful on your committee, then see what your advisor has to say.

  Will I have any leeway to do something like this especially when he is funding me for PhD

Getting funding from someone doesn't mean they get to dictate everything about your PhD career without any input from you. It's your PhD and ultimately your responsibility to make sure you succeed.

In fact, depending on your department rules, the decision as to who goes on your committee may very well be yours, not your advisor's. Of course, you should consult with your advisor on something like this, because part of his job is to help you make these decisions.

But you should understand that this is your research career regardless of who funds it. And even if your advisor is a great scientist and advisor and you respect his advice, you should always feel that you have "leeway" to make suggestions.

  and what will be the best way to bring this up?

Just set up a meeting with your advisor and say "I wanted to talk about my PhD committee. Here is why I think Professor X would be a valuable person to have on my committee..."

Note: I'm not commenting on whether or not your MS advisor is actually a valuable person to have on your committee - just that it's always OK to make a suggestion like this.


A weaker version of a published theorem with a simpler method; what should be done?

Choice 1 seems pretty clear. It is honest about prior work (existing theorem) and the contribution (new proof).

You could also inform the editor that you have found a theorem that someone else has done, but that you believe your proof to be novel. This will allow the editor to better judge your work.


Translate articles and submit them in other journals

There are a few issues with what you want to do. To translate a work (and subsequently publish it), you need permission from the copyright holder of the original work. Many publishers require you to transfer copyright to them, so you may not have copyright on the works you want to translate any more.

On top of that, journals are interested in work that has not been published before (even if it was in another language).

That is not to say that there is no place for translated works. Some non-english journals regularly publish translations of their articles, and one can sometimes also find translations of important papers in the field. However this is something that is typically done by the publishers.


If your ideas were fleshed out experimental plans that someone else took and used, that's not cool. You should complain.
If your ideas were a bunch of "wouldn't it be great to study this topic" thoughts, that's just not enough to stake a claim. If the PhD student is acknowledging that you're also in that area I wouldn't complain. You should ask her for help designing and executing an experimental plan. The best outcome is that she teaches you some new stuff and you both end up coauthoring something solid.


What is done about academics who do not do research anymore, or who teach badly?

The answer to both your questions will, from my perspective, be "not much". So this answer describes the view from my local point.

As a basis, university positions in my realm are teaching positions, 70% teaching and 30% for admin, personal development and research. The 30% is very quickly consumed by everything but research. On top of that one can "buy" oneself out of teaching so that the research time essentially is based on soft money. If you do not do research well, then no money comes in and your teaching load increases towards the 70%. So as long as you do your job in some way there is no mechanism for "correcting" a lack of research. On the other hand senior academics often get involved in higher and higher level administrative work at university, governmental, etc. level so a lack of research as such may be replaced by benefits gained in other ways. But, basically, a lack of research simply means teaching more.

If your teaching is very poor there is not much that can be done. Employment laws are very strong. The only way to sack a person would be if they, for example, drink at work, or blatantly refuse to accept orders from the "boss" (head of department etc.). It is also possible to remove someone if it can be shown that there is no need for whatever profile the person was employed under. I really cannot provide a detailed description of employment laws here but they make sacking people a difficult way out. Persons failing with teaching will most likely first be placed to do other duties. I have experience with one such person and it is hard to find tasks where this person can function and contribute.

So the "not much" is largely explained by employment laws in "my" case. The problem cases, which do not easily contribute in alternative ways, will cause lots of work for the department to find ways in which they can be made productive to the department. This will be successful in most cases but not so in the odd case.


Must a tutorial TA resolve any questions from the students?

My job as an instructor is to help the students learn, and I try to do so to the best of my abilities.

If a student is asking very basic questions (don't call them lame ever), help them to get up to speed pointing at some reading. You should pay attention to this, since for every student that asks questions, there may be several silent ones, and it may be an indication that the cohort is missing some knowledge your course is assuming.
If they ask questions for which they know the answer, but are unsure, teach them how to validate and verify their answers.
If they ask every little step of the way, the Socratic method is an option: ask questions back, make them work for the answers. But make them helpful: use them to guide the student towards the answer.
The students that just ask very many questions, just get lower priority, since I have to take care of the whole group, but I do still help them.
Questions that are off topic can be either gently shot down and redirected, or quickly point them at some references. If you find the question particularly interesting, you can offer to give more details after class. Make sure they don't get lost in the sidetracks, though.

In general, the goal should be to try to make yourself redundant by teaching them how to not need you you. This is never going to actually happen, but it is a worthy sky to look up to.


Mimic lecturing on blackboard, facing audience

Do not assume that facing the audience is actually better.  It depends on the type of content.  For example, if you are explaining a diagram (detailed hydraulic system for instance), you want the audience to concentrate on that, not the presenter.  The audience is still getting plenty of stimulation by having a live human voice along with visual content.  You actually don't want the presenter to distract the eyeballs from the intricate content.  (I see this wrong often with recorded talks where the video operator concentrates on the podium versus the charts, or shows both but with inadequate scale to see the slide charts.)  If you are doing math (as opposed to history or literature), the content is more intricate and you should have the audience concentrating on the formulas, not the speaker.
Take some occasional time to address the class when that is appropriate.  Examples are a "sea story" about test performance or industrial application of the math.  But these will be a minor amount of time within a math lecture.
I mean, if you really wanted to, you could write backwards in grease pencil on plexiglass like in an old Navy combat information center.  But really what is the point.  People concentrate on the status (content), not the writer anyways.  The one advantage is that you don't have a body blocking part of the board.  I believe there are now electronic versions that would flip this around for you (or you can use an OHP).  But still I think you lose a lot from having a lot less screen space than board space (especially with sliding boards).  So, the small advantage of facing is at the loss of huge amounts of content physical space.


Art Major to Physics/Applied Mathematics, Advise?

If you have taken courses in Coursera and are comfortable with continuing doing so, you can actually get a degree through Coursera. Here is one option. I do not know whether you completed any courses, and if you did, whether they can be counted towards that degree, but it should be easy enough to find out.

I would focus on getting a relevant bachelor's degree. No (reputable) university I'm aware of will take you into a graduate program without one.

Good luck!


Getting into a mathematics master's program from engineering?

"Force = Mass * Acceleration."

You appear to be worried about your inferior "mass." What you may not realize is that you have superior "acceleration" to compensate, probably bringing up your "force" level to at least average.

I entered a math-oriented PhD program with someone who had only one year of calculus, but whose "acceleration" you remind me of. Within a year, he equalized in "mass." Then his superior "acceleration" took him to the top of the class.

The same could happen to you, if you have the natural gifts and "bent" that you say you have. Your engineering gives you enough "background" to get in the game.


Undergraduate prerequisites for a Ph.d. in combinatorics

The prerequisites in combinatorics will not be significantly different from the overall prerequisites in the program to which you are applying.  Having taken a combinatorics course would be beneficial, but there is no need to take many of them as an undergraduate.  You mention Budapest Semesters in Mathematics in a comment.  They offer a lot of combinatorics courses, more than some U.S. universities, and there is certainly no expectation that a typical applicant will have completed this many courses.

In your case, I expect the main issue will be whether you are applying to pure or applied math departments, since combinatorics could be located in either.  For pure mathematics, the admissions committee will wonder how many of your courses were based on rigorous proofs (for example, applied complex variables and mathematical methods for sciences courses might not be), so it would be best to be clear about that.

I would recommend applying broadly and seeing what happens.  Even if your coursework is not ideal, you may still be admitted, with the expectation of having to catch up in a few topics.  Ultimately, it depends on how compelling your application is overall, and your transcript will be just one factor.


How might I improve my math department as an undergrad?

Is there anything I could do as an undergrad to help improve my department? It's hard to say exactly what would make my department "better", but to be somewhat vague, I would consider research productivity and funding to be important factors to improve on.

There's not much you can do as an undergraduate to help improve research productivity or funding.  It's not clear whether the department wants to improve in these ways, or should want to: there's nothing wrong with focusing on teaching.  Even if the faculty do want to become more research active, or the administration wants them to, it's not easy and there's little you can do to make it easier.  I'd be careful with how you frame things, since you could easily cause hurt feelings by giving your professors the impression that you consider them substandard.

Instead of focusing on what might improve the department in some abstract sense, I'd focus on what would create a stimulating, exciting environment for the current students.  You don't want to be too demanding, and some things just might not be feasible, but it can't hurt to ask what could be possible and what it would take to make it happen.  You could look into various sorts of activities:

Advanced courses or independent study.
Undergraduate research supervised by faculty.
Informal mathematical activities: math club, Mathematical Association of America student chapter, Putnam team, etc.

If all of these things are regularly available, then your department is doing pretty well.  Otherwise, you could try to initiate or reinvigorate some of them.  You aren't likely to get clubs or courses for just one student, so you'll probably have to gather some other enthusiastic students.  This may be the biggest way you could contribute, as a catalyst to bring together a group of students the department hadn't realized wanted or needed these activities.


Is it ethical to have two (undergraduate) researchers in the same group "compete" against one another for leadership/credit of a research study?

Let me try with an "onion-answer", one layer at a time.

It is certainly not unethical to have several undergraduate students work on the same project. This is how most people get by, as there are simply not enough interesting and unique projects at undergraduate level that everybody can get their own. (And if there are, it would take too much time developing them.)
It is borderline unethical to set up a competition between students in your lab, dangling the prize of a conference presentation or a publication ahead of them. The focus should be on how to do good research, not how to get ahead of your colleagues - even though it is sometimes also part of research. I can see how this could be done in a somewhat fun and productive atmosphere, so I will not dismiss it off hand. But I would much rather have the students work together, than against each other.
It is blatantly unethical to have a competition among your undergraduate students without informing them, that they are in a competition, first. I assume from your post, that you have never said yes to be in such a competition, and that you in good faith assumed that your chances of getting the "prize" would be based on your performance alone, and not how it compares to the performance of other students. This is a kind of "bait and switch" strategy, also often used for job interviews, where you get a person in the door by promising them a reward - but at the end of the day there is only one reward, and many people competing.

Finally, you mention that part of the prize is also "credit". Here I want to tell you, that if any scientific work is done towards a specific publication as part of the non-winning studies, the authors of said work should be credited as co-authors. Even if they don't win the competition.


Is there a service that can store and mail recommendation letters to schools?

Many schools offer such a service. For example, UC Berkeley

  The Letter Service will send letters to educational institutions to support your admission to graduate and professional school. We will also send letters to educational institutions for the purpose of supporting your applications for academic/educational and research employment, i.e., teaching positions.

You should check with your school/department to see what is offered.


strange potential plagiarism case(missed the acknowledgement page)

First of all, the Ph.D candidate is always considered the only author of the thesis and the only one to respond legally in case of plagiarism. Despite all the input introduced by your supervisor along your research, he will never be entitled to accuse you of plagiarism due to the lack of acknowledgements. This is just an impolite thing to do, nothing more.


Different types of conference publications

For the value of the publication, it will matter more how it is published than whether it's a workshop or conference. If the proceedings are published by a well-known publisher (i.e. with ISBN/ISSN), a workshop paper might be as "valuable" as a conference paper. If on the other hand there are no formal proceedings or just something like a folder, it would be less "valuable". That usually leaves the opportunity to publish the same paper elsewhere though.

Most workshops in CS don't have formal proceedings, so in general it would be better to publish at a conference. That said, in some cases the reviewing process for a workshop/symposium might be more stringent. As smaller events are more specialised, the feedback you get on your work might be better than at a bigger event.

I personally would always go for publication at a conference if I thought the content of the paper to be good enough.


Should I quit or leave my current PhD and find another one?

You seem to be in a box that is difficult to escape. You need funding and it sounds like you can't continue without it. So, think about that first, not about changing places.

I think the way to approach it in the short term is to sit down with your advisor (i.e. face to face) and say just that: I need funding or can't continue here.

After the conversation starts let it flow. Give the options you think you have, but ask if there are other options. The advisor probably has more experience with this.

Perhaps the advisor can either find you that funding, or suggest a way, or suggest a better place to continue your education. They can be a resource in figuring out what to do. Perhaps there are TA/RA positions open. Perhaps there are grants that apply.

If that fails, then look for another place, but make sure you have adequate funding before you jump.


Dealing with rejection anxiety as a reviewer

The role of the reviewer is not so much gate-keeper, but rather your role is to help the authors get the paper to a position where it is publishable. So I very rarely recommend outright rejection at the first round.
Once you have written things down what it would take for the paper to be publishable, it maybe the case that this is clearly unachievable and that this author will never get this paper to that level – but that is for the editor and authors to decide.
Reviewers are normally asked to judge two things:

Is the paper sufficiently novel and exciting to be interesting to a large enough fraction of the readership of the journal.

Is the paper sufficiently rigorous to demonstrate the claims it makes.

If the paper is not sufficiently novel or exciting I say:

To make this paper publishable, the authors must explain the additional advances made compared to Smith et al. and Jones et al. and why their work would be of interest to a reader of the Journal of Things, beyond those connected with the sub field of very small things.

Methodological or interpretive flaws I will simply point out and say they must be fixed.
So for example, I recently had to review a paper for a software tool. It unlikely to get published, but instead of saying “reject” I said:

The tool does not appear to implement any new functionality compared to  Jones et al and indeed is missing several of the functions in that tool. The authors should explain why their tool is an advance in comparison, and provide benchmarking data comparing the performance.

The tool was not installable on my system, the authors should ensure that there is a robust installation routine and that it functions on representative range of systems. {goes on to list the problems with the installation}

The tool has several bugs and conceptual errors in it that must be fixed before it was published. {goes on to list them}

In conclusion, the tool has several usability and functional shortcomings that must be fixed. Even if these were fixed, the authors must explain why their tool is superior, or even equal in performance or features to Jones et al.

Now I was 80% sure that this wasn’t going to happen – the amount of work required to bring the paper up to a publishable standard was probably more than had been put into the project up until that point – but if they wanted to do it, I’d be happy to recommend publication. I never saw another revision of the paper – I don’t know if the editor decided to reject it, or the authors decided it wasn’t worth it –, but I fulfilled my role: to say what it was that was necessary to bring it up to standard.
If the authors do decide to try for a resubmission, without fixing the problems I identified, I will just say that:

The authors have not addressed points A, B and C, and I cannot recommend publication until they have done so.

There are several "Peer Reviewer's Oaths" out there. The one I like is from here:
http://www.opiniomics.org/the-reviewers-oath/

I, the reviewer, promise:

to not hide behind a screen of anonymity
to be open and honest with you (the authors) at all times
to be constructive in my criticism
within the rules given to me by the journal, to assist you in every way
I ethically can to get your manuscript published, by providing
criticism and praise that is valid and relevant


What do these mysterious numbers in the subject line of arXiv mailing list emails mean?

Straight from the horse's mouth: there is no fix, but an update is on the list of things that "will be done when they're done".

  You may safely ignore the numbers after the text "class mailing" as
  they are used for internal audit code and essentially meaningless from
  a user perspective.

  We do have plans to update the mailing code at some stage, but the
  time-line is unclear due to limited developer time.


Editor assignment pending after "review competed"

It's not certain what it means without knowing the particulars of the journal's internal handling, but a likely meaning is that the paper has been handed off from the associate editor who has been handling the reviewing to a senior editor to finalize the decision.  In many journals, an associate editor provides a recommendation for the decision, but a senior editor actually makes the decision; if there are multiple senior editors, then a brief gap before one of them takes up the paper would create the observed behavior.

Bottom line: you are likely to see a decision shortly.


Should I skip MS in Computer Science and directly opt for PHD? If so, what to expect from a PHD program?

Yes, in the US most students start doctoral studies immediately after a bachelors. Yes, there will be quite a lot of coursework before you get to the dissertation stage. The courses prepare you to pass the qualifying exams and assure that you have a broad grounding in the field.
However, almost all US graduate students work as part of the program, usually as a TA (Teaching Assistant) or RA (Research Assistant). A TA usually does grading and meets with small "sections" of a larger course so that students can get questions answered. An RA works with a professor on research and the tasks depend on what that professor is doing. It might be programming or library research or whatever.
Holding a TA or RA position also means that the student doesn't pay tuition and has enough of a stipend to live (modestly), perhaps even with a family. I had two kids by the time I finished my PhD though my spouse also worked. That would be harder for a foreign student because of visa rules.
You don't need to have a research project in mind to apply for admission, nor do you need to immediately connect with a particular professor. The first year will feel a lot like the final year of undergraduate but with more advanced courses and possibly an introduction to research process.
Apply to several schools, probably in the R1 (Research focused) category. It is best if the general area you want to study within CS is represented there by several faculty so that there is the possibility for a research seminar.
At many such doctoral programs you can be awarded a masters, also, part way through your studies.


What to do if a university is pushing for a response before making a formal offer for a tenure-track position?

"I would like to see a formal written offer before we move forward."

Any department that's unwilling to do that is sending up huge, brightly colored red flags. With fancy gold tassels. And embroidery that reads "DANGER".


How to deal with low quality software project that needs to be evaluated

When I look at the part of the project which should process the
  general_input_file, there is a statement which looks like this: if the
  name of the given input file equals specific_input_file, then return
  specific_output_file. [...]
  Otherwise, try to process the generate_input_file and generate
  general_output_file. At this point the software breaks.

By your description, it sounds like the code you are looking at is cheating by returning a precomputed output known to be correct if the input matches a single sample input the authors included with their code (presumably to demonstrate its correctness and because including a sample input was required to get their paper accepted). For all input instances other than this one sample input, the code does something entirely different, which doesn't produce correct results.

This sort of behavior would without question merit a failing grade in a programming course homework assignment or exam. If done in the context of a commercial product, similar behavior would justify the resignation of the CEO and a multibillion dollar scandal. So, saying that the code is "of low quality" seems to me so euphemistic as to be itself a dishonest statement. The way I would describe it is: if the authors are claiming that their code is correct, then they are lying.

Now, I could discuss your actual question of how to discuss this situation in your follow-up paper "without being offensive to the authors," but honestly, I don't see the point. I would ask instead, why would you want to not be offensive to the authors? It's not just that the authors' algorithm may be wrong and that their code is of poor quality; they are seemingly committing academic fraud by submitting an incorrect algorithm with code dishonestly tweaked to make it seem like the algorithm is working. I'm willing to leave a 3% chance that some other more innocent explanation can be proposed, but given the description you've provided I really can't think of one. I'll be happy to reconsider if you provide a bit more detail on how the authors' claims are presented in the paper.


How can I cite a previously given, unavailable talk without self-plagiarism

I think the right action hinges on this point:

  It is outside the scope of the current paper paper to present those ideas as a new thing, but it would be something that would be appropriate to reference as existing.

It seems like you want to reference your past work because it is out of the scope of the new work and yet still relevant. If this is correct, then referencing the talk will not help the reader, who may (or may not) need to know about the past idea, concept, or whatever it was. Therefore your only option would be to publish the ideas in some form (paper, blog, etc.) or explain them briefly in the new paper.

If you simply want to show the history of your ideas, but it is not important, then I would leave out and simply acknowledge whoever helped you out.

If you are worried primarily about self-plagiarism, I do not see how not citing a non-published talk, that you yourself gave, is much different from not citing some thoughts you had in your head two years ago. It is a bit different, but not to the extent that it would constitute self-plagiarism, which is really about making it clear what is and what is not new in a paper as it is assessed for novelty during peer-review.


What is the point of a cover letter in journal submission?

Prior to online submission forms, cover letters let the authors communicate information to the editors. Information I have included in covers includes:

Why the manuscript fits into the journal (if i recall correctly, Ecological Indicators explicitly requires a statement of what "indictor" you are addressing in the manuscript)
Potential reviewers and blocked reviewers
A statement that the manuscript is not under review elsewhere
Other pertinent information for the editor such as why the manuscript is timely (for example, perhaps you are studying a species that is under consideration for listing as an endangered species, and the information may be public, but not widely known)
Responses to reviewer comments
How I am meeting the journal's open data/open code requirements

With current online journal submissions, all of this information can be captured in online forms. Hence some journals either no longer require cover letters or outright do not allow authors to upload them. Conversely, I have seen other journals that still require cover letters.

I suspect journals use of cover letters depend upon the history of the journal, their current online publishing system, and the culture of the editorial team and office.


Starting of cover letter for academic jobs

Probably not. I doubt anyone is going to catch it and, if they do, they probably won't care.


Is it possible to spend a couple of years after a post doc working as a bioinformatician and then return to academia?

As long as you are doing your own research and publishing, I don't think this should necessarily be a problem. If the position is de facto similar to a post-doc with a higher salary you should be fine and it will probably just be treated like a second post-doc.

However, if you are just giving services and not leading any research project that can be a problem.

So the bottom line is what matters is mainly what you actually do and less the title of the position - I know of someone who after completing his PhD took a bioinformatician position in academia, rather than a post-doc, and used that to get a faculty position.


Should I 'admit' a weakness of a paper even if it's 'obvious'?

I wonder if your research is ready for prime time. Not getting consistent results and not knowing why is a fault. Maybe you should continue work for a bit.

But for the question itself, it is better that any shortcomings come from you rather than from someone else.

At a minimum, you have an interesting "future research" section to write. Maybe you should find a way to look at the larger data sets or others that will give you better insight into what is really going on.


If a professor is not offering funding to a PhD applicant, does it mean that he doesn't really want to be his advisor?

It could be, as is usually the case in the UK, that the Professor has no direct influence on the awarding of scholarship money. It would, therefore, be irresponsible of him to mislead you about your chances of obtaining funding. I certainly wouldn't take it as a sign that he doesn't wish to supervise you.


Research Methodology Books for beginners in Computer Science research

Research methodologies are usually independent of your area. Often, the application of some methods and the examples used to describe them differ depending on the area. For example, empirical research is a methodology that can be applied whether you do research in CS, psychology, or physics. This methodology teaches you how to conduct experiments that are sound (by minimizing different threats to validity) and how to analyze the data in a statistical way (e.g., when to use which statistical test to accept a certain research hypothesis).
In medicine, you might conduct experiments to analyze the effects of some drugs whereas is CS, you would do some performance experiments to analyze the effects of some optimizations. The methods used in both areas are the same, the application might differ largely though.

Hence, it would not harm to study a text book from psychology / statistics, because the tools you learn there are also valuable for CS (e.g., knowing the difference between qualitative and quantitative research or descriptive and analytic). Furthermore, there is no CS-methodology (at least I am not aware of).


Will a mail to the journal asking about the status of my article have a negative effect on the decision of the article?

It most likely won't. I think it is normal to push the editor if there is a significant delay. Check what the average time for receiving reviews is first.

I have done it when there has been a significant delay and it hasn't been a problem.


Do my articles published in local newspapers count as publications?

It's not uncommon to have subheadings for different kinds of publications. "Peer-reviewed journal articles", "Proceedings", "Monographs" and so on. For a journalism program, "Newspaper articles" seems like a completely appropriate subheading.


Is asking questions with very short answers on major exams recommended?

There's a bit of a false dichotomy in the way you present things. Exam questions can have a long answer without being hopelessly vague and subjective. In college-level math, one usually can't avoid asking some questions with long answers, whether they're problem-solving, proof-based, or conceptual. Partial credit is just part of the deal, as is handling the occasional student seeking more partial credit. (You have to at least hear them out, because it's always possible you've made a mistake.)

However, there are different views on this; I once had a professor who gave an entirely true/false final exam, with no explanations or partial credit, in an abstract algebra class. His reasoning was that over an exam with say 40 questions, the effects of random guessing would average out to a roughly equal small bump for everyone. I was skeptical, but after taking the test I was confident that the same people did well on it, as would have done well on a traditional "solve this problem, prove this small fact, etc." exam. But this may have worked because abstract algebra has a lot of questions with a concise statement and answer, but that require real understanding. (One T/F question I remember: The Galois group of the fifth cyclotomic field is cyclic.) I don't think it would work for every course; at some point in your math education, someone needs to read the gory details of your solutions and give you feedback.

By all means, look for opportunities to make good questions that can be graded quickly and objectively, but a lot of the time, there just aren't many questions like that.


What does "awaiting reviewer selection" really mean under the "minor revision" scenario?

Try to recollect how the statuses changed when you submitted the paper the first time.

Scenario 1: with editor/under editor evaluation >> awaiting reviewer selection >> under review
If this is how the status had changed the first time you submitted the paper, then chances are that your paper is actually being sent for a re-review.

Scenario 2: awaiting reviewer selection>> under review
If this was the way the status had changed, then it is possible that the online status tracking software uses the status "awaiting reviewer selection" to indicate that the paper is with the editor.


How we can look active both in class and after class in our supervisor's mind?

Try not to "show yourself as an active student", be it! There is really a difference in it.

As an active student, you are genuinely interested in the field, you are asking question no mtter how stupid they seem, you are going an extra mile in assignments, be helpful to others (even if no one notices it), be active in students activities, ...

In fact there are way too many things you could do to do them all. So try to be you and pick what's best for your personality. Then you will shine.


Is there an alternative to traditional exams?

One alternative that's been gaining momentum in actual classroom use is standards-based grading (SBG): http://www.fwps.org/teaching/sbe/grading-system/

In SBG, the instructor establishes a list of milestones that students are expected to attain throughout the course. The students then can provide evidence of any sort -- within parameters set by the instructor -- that prove they have met the standard. Student evidence of attainment of a standard is marked on a scale usually from 0 to 4 (unacceptable, novice, progressing, acceptable, and mastery -- or something like this) and grades are assigned at the end of the semester based on how many of the milestones have been met at "Acceptable" level or above.

For example, in calculus, one standard might be "Take the derivative of a second-degree polynomial using the limit definition". A student might show that they know this by doing a problem on a standard timed test. But maybe they don't have it down as well as they should, and on the test their work is marked as a 2 out of 4 (progressing; maybe they got the definition right but did some of the resulting algebra wrong). This isn't the end of the story. Later in the course, the student can show evidence again that they've learned what they need to learn -- for example, they can schedule time in office hours to come work a problem or two to show you they've met the standard. Or maybe take a short quiz in class, or work a problem during unstructured group work time in class meetings, or whatever avenue the instructor allows.

The point of SBG is that we want to assess students based on what they know, and give them multiple ways to show that they know it. SBG can therefore be a superset of traditional timed testing -- students that do well in timed situations will do fine in SBG, but students who struggle with timed testing can have multiple chances to get their act together, and as long as they can prove they've mastered the material by the end of the course, that is what matters.

I don't personally practice SBG but I would like to. I'd suggest this blog post by my colleague Jon Hasenbank who is a big SBG proponent: http://profjonh.blogspot.com/2014/02/sbg-mia14.html


How to report spam pdf links in Google Scholar?

After a little more hunting, it seems that there is a general "contact us" support page where issues can be submitted.

https://support.google.com/scholar/contact/general

Presumably, this would be a way of notifying Google Scholar about spam PDFs.


I find Latour and Woolgar's spectrum of "facticity" a useful tool for thinking about these questions (a nice summary can be found at this link).  It breaks scientific statements into five rough categories by level of certainty in the assertion:

Speculations - don't have to be backed by anything
Descriptions - not established, so need to be directly backed by evidence
Tentatively established - need to be backed by citations
Well accepted - should be stated, but don't need evidence or citations
Tacit - should not even be stated

Where exactly a fact lies on this spectrum depends on the community and state in discussion.  In general, the broader the audience, the less well accepted facts should be assumed to be.  I think the notion "Should everybody reading this have been taught in a class?" is a good one, though undergraduate is not necessarily the stopping point.  For a machine learning audience, for example, you should assume everybody has had graduate level machine learning courses, while for a biology audience you should not assume they have even had undergraduate computer science.


Why aren't all research articles on PubMed?

Because PubMed is about biomedical literature and life science journals. Things are blurry, however, because of two factors:

Obviously, there is no strict definition of what is (or is not) biomedicine.
PubMed does not select “article by article”, but has a list of indexed journals, from which all papers are indexed. Yet, a single journal's scope can be very varied.

Combine the two, and you get the idea that there is a lot of variability in whether an article on a given topic is published. For example, my own research field is materials chemistry, and about two-thirds of my papers appear to be indexed in PubMed: probably because those were published in generic chemistry journals, which also happen to publish some papers of relevant to life science.


How do you prepare to attend a conference where you may have trouble following the talks?

Nobody can know everything. Even just in mathematics the last time it was possible to literally know it all was early in the 20th century. Things have advanced too fast and too far for such things now.
A conference might be expected to present the latest ideas in a sub field. If that is your specialty you would be expected to follow "generally" but would probably require additional study afterwards if the subject of a talk was important to your work. But a "general understanding" and a few notes about how and where to follow up is probably enough for most people.
I doubt that your education, as you describe it, puts you at the research edge in graph theory. If you are doing research in that, then a quick literature survey of closely relevant topics would be good preparation, but I'd guess that few  people do that. If the proceedings are available in advance, skimming the papers will give you an idea of where the holes are in your understanding.
But at the conference take a few notes, especially on topics that are not known to you, as a guide for further study. If you attend (physically or virtually) with colleagues, start a conversation over coffee/tea/whatever to ask others for their insights.
On the other hand, if one of the speakers is your dissertation advisor, you'd probably be expected to understand most of it. Or at least grasp the general trend of thought.
Math is pretty esoteric at the edges.

Another kind of "preparation", however, is to prepare to meet new people and share a few ideas. Harder now with thing mostly virtual, but a great way to build contacts.


Particular tone or rhythm in academic presentations

Everybody has to find their own style and "voice."  Perhaps in some people, that might come out in a sort of rhythm or tone.  In my own talks, when I am comfortable and happy with my material, I often settle into certain characteristic pattens of emphasis and pause, fast and slow. Watching people give good talks and studying their style can be a useful tool for figuring out how you relate to various tactics, and perhaps give you more comfort in their diversity, by showing that you do not have to strictly conform to any particular pattern. Your "voice," when you find it, however, will be uniquely your own.


How do I go about publishing a paper without a university affiliation?

Is it possible to publish a paper without a Professor?

Sure.  Nobody gives a rat's patootie about the academic ranks of paper authors (at least in my field).  I published sole-author papers as a graduate student.  I have colleagues who published as undergraduates, and others who published with no university (or research lab, or corporate) affiliation at all.

  How to choose a research topic?

Choose something you're good at, that you're passionate about, and that other people will care about.  If you're not good at it, you'll never get anywhere.  If you're not passionate about it, you won't put in enough effort to succeed.  If nobody cares, then, well, nobody cares.

  Should I read all the papers on this field?

No.  Reading all the papers in any field is simply not possible.  But you should read a lot.  A few hundred papers should get you started (ha ha only serious).

  How to decide which problem to work on or which is not obsolete? I don't want to work on something which no one is interested in.

Read lots of papers; talk to lots of people; go to seminars/conferences and listen to talks.  Or decide that the topics that you care about are so fascinating and your results are so compelling that you'll make other people interested (but be prepared for disappointment).  Or—my personal favorite—just make up something cool out of thin air.

  Should I read and study all the prerequisite material, or fill in the gaps during research efforts?

Yes.  Both.  (Except not all the prerequisite material; that's impossible.)


Can I use images from an arxiv paper (and some others) in my undergrad thesis?

There are at least four things to consider:

Is it allowed by academic ethics?
Yes, if you cite appropriately and make it clear where the image came from.

Is it allowed by copyright law?
Maybe.  You'll have to look at the license that the arXiv paper is released under.  If it is copyrighted and not under a license that allows reproduction, you may have to get permission from the copyright holder (could be the author, or a commercial publisher who published the paper.)  On the other hand, there could be fair-use laws in your jurisdiction that allow it; see  Academic fair use and using publication images in your thesis.  But that question is not strictly on-topic for this site, since it's more about law than academia.

Is it acceptable under your university's thesis regulations?
You'll have to read them.

Is it acceptable to your advisor?
Ask him or her.  Excessive use of material from outside sources, even if properly cited and permitted by copyright, may suggest that your thesis does not contain enough original work to merit a passing grade.


What tools do you use in academia to jointly review a thesis?

This is a good question and I don't want to discourage you, but let me explain what you will likely find most of the time.

They each already have a preferred way of giving you their feedback and some or all of them will not want to use whatever tool you choose.  Since they are doing you a favor, you will need to respect their preference.  For instance, I prefer to take a hard copy and a red pen and go to a coffee shop or library in order to focus.

Also, when I review a thesis I do not want to see comments from other reviewers before I form my own opinion.


From blog posts to research papers; successful cases?

First, it totally depends how you define the term “research paper”. Some people uses a blog in such a way that (some or all) blog entries are actually akin to minimal-size “research papers”, albeit with a nonconventional publication mean and possibly nonconventional format.

Secondly, it also depends where you draw the line between “turning X into Y” and “writing X based on Y”. Obviously, many journals would object to publishing material that has already been published somewhere else, including on a personal blog. Moreover, publishing identical content in two very different media probably means that it is not fully adapted to one of the two (or both): to give only one example, you don't typically have the same language level on a blog as in an academic paper.

Finally, an example: scientific writer Philip Ball has a blog on the topic of Water in Biology, and he also regularly publishes “News & Views” articles for Nature (one example there). In both cases, he writes critical reviews the recent literature on the same topic: there is wide overlap, but he does not publish his papers by directly converting blog posts.


How can I view the license information of preprints on the arXiv?

Below the download options for each article (i.e. "pdf", "postscript", etc.) there is a link in very small print labeled "license".


Actually, these are not titles.

The only academic titles that are used in Germany in writing or conversation are Dr. (also Dr.-Ing.) and Prof. (sometimes MSc and more rarely BSc and also there has been Dipl. which, of course, is still in use).

No one would ever use certificates or memberships in their name. This would look extremely strange in Germany. Also, one usually does not introduce yourself as "Dr. X" or "Prof. X" (you may want to use these on letters or emails signatures, though).


If I were in your position, instead of submitting a 'cold' re-application, I would first contact the committee and ask them for advice about what I could do to improve my prospects of being accepted as a PhD student. I have seen people do this a few times, and the strategy receives positive responses from faculty; but of course you will then have to do the work and actually improve on the things they suggest.

Re-applying with exactly the same material will probably not get you anywhere. However, if you get advice from the committee and/or from other people who are experienced in the field about what to improve or what skills/experience to acquire, and if you can demonstrate the results well, it will be noticed.


Is there a name for the inverse of the impostor syndrome?

I have on occasion felt the same myself (sometimes still do), and know of many disillusioned PhD students who felt exactly like that. There are dark moments in the night, when you are wondering whether funding for CS will be cut down entirely eventually, when funding agencies also get to the conclusion that CS is one big science of imposters.

However, what you need to realize is that this is in fact impostor syndrome - only that you are not comparing yourself to your peers, but rather you and your peers to e.g., other sciences. However, the reason why it happens are the same: you have unrealistically high expectations of the research community, which it cannot possibly live up to in reality. You know the shortcomings of your community all too well, but do not have enough insight to see that other research communities or professions are also far from perfect. Yes, all the crap you mention happens on occasion, but guess what? We are all human, so it is simply unrealistic to assume that every professor will always be a good manager (or even a decent human being), that every dean will always still be an active and good researcher, or that every paper is always published with the most noble intentions.

I should also mention that your conclusion that, if you are not alone in this feeling, you surely need to be right, is fundamentally flawed. History has shown all over again that many people can be wrong in the same way at the same time.

Edit:

By the way, I think your question title is wrong. The opposite of the impostor syndrome is, as you say, more or less the Dunning–Kruger effect. What you are referring to is not the opposite.


If it has been published, ask the author for a pdf of the published version (from your question I got the feeling that the paper has been published). This would also be easier to share with your supervisor later on. It makes no sense to cite or quote a draft version if the paper has been published. At least ask if the draft has identical content as the published version. If so, you could maybe get away with using the draft but citing the published version in your reference list (not ideal though).

Otherwise, cite it as a working paper/draft, by including author, title, and the date when you recieved the paper, see e.g. Chicago manual of style online or MLA style guide.


As a tutor, should I encourage exploration at the risk of incorrect information?

Short version:

Encourage them, definitely encourage them.

Long version:

First of all I have to say that I am not familiar with Scheme, so in my answer I will assume an arbitrary coding project. Now, you have to consider that coding, especially a bigger project, is much more than just typing the code. As you said the class is quite difficult, I assume the students to have some experience already, so they should know it. Here, they can learn all the things that matter: A structured plan on what they want to code, good documentation of the code, time management, etc.
Be honest about what you can and cannot do, tell them that you will not look at a few 100 lines of messy code to find an error. Tell them for you to read their code and to look for errors in there, they should properly document it such that it is readable and understandable to an outsider. Tell them to differentiate between logical questions ("how to solve this problem?") and implementation questions ("I have this idea/algorithm, but I don't know how to call function XXX, which I need to implement it." ). Not only will this help you with helping them, it will also help them to look at their problems more structured. If a student comes to you and simply says "I don't know how to do this, tell me please." then don't just tell them how you did it. Take a little time to make a plan (on paper first maybe?) together with them of how this part of the program might look like, how to best do it, then let them implement it. If they run into problems with the implementation itself, they can come back again.

The same should go for errors in the program: You should not be the one to run tests, to do simulations or to input special cases in every last function to find the error. Tell and teach the students how to find errors, show them how to (if possible) narrow it down to a single function, maybe to a single part of this function (a good documentation of what a function or a code fragment is supposed to do helps here). In most cases they will find the error themselves, feel happy and motivated and go on. If they still can't find it, well, at least they can show you the wrong output that function F generates and you can take it from there and point them in the right direction.

It would be nice if I could stop my advice here, but unfortunately there is still one more point: motivation. The above might work well with a motivated student who knows what he is doing, who sits down at home to work on it and comes to you for help if needed. However, this is not the only kind of student. There are also students who are in the course just for a passing grade, who don't go to the lectures, who just want a step by step instruction on what to do to not fail and don't want to put any effort at all. If you don't have any of these in your class then congratulations, consider yourself lucky. But if you want to try an approach as I sketched above, you should consider such students in the plan and should think of what to do with them: Do you just tell them what to do? Do you let them fail the class? These points should be discussed with the instructor, as he or she might have own ideas on what to expect of the students. You should not just act on your own, especially if you might fail some lazy students you need his consent. After deciding on a plan together, make it public to the students, tell them exactly what you expect of them to do on their own before they come for your help, how they should properly prepare their project for you to be able to answer efficiently.


Does work experience in non-related field help in grad school admissions?

It might have been useful to state the country you are inquiring about as this may be different all over the world.

However, in my experience, the people who oversee the admission process are not at all related to the people who create the statistics. They admit you because they believe you could handle the program - not because of some job prospects. Relevant job experience could be one factor which makes it more likely that you succeed (or not).

Indeed, most professors I know see their programms not as a way to obtain a (non-academic) job, but rather as a way to spread deep academic knowledge.  (I don't disagree with this view.) I don't see how a good academic program would by itself mean a job guarantee.

Edit: I just saw that you write "non-related" field in the title. Again, there is no yes/no answer to this question. Some professors might see this experience as positive since it might show that you have certain skills, others may see that you are not loyal enough to their field..


Firstly manuscipt 'rejected' and then status changed to 'revise'

It is not really clear what happened. It sounds like the 25 days it was "with editor" it was actually out for review (possibly the editor does the review). It then sounds like the editor looked at the review(s) and decided the manuscript was not "new work". Instead of coming to a decision then, he ask you if the work was new. Your initial response did not convince him, so he rejected the work for not being new. He did not send the reviews, because the issue was the work was not new. You then convinced him the work was new, so he changed the status and gave you the review(s).

  Is it a good sign or editor is just passing time ?

I can assure you that the editor is not just passing time. I think you have an uphill battle still to convince the editor and reviewer that the work is new. It also seems like you may not be as clear as you could be.

As for whether it goes out for review again, that depends on the editor.


As a student, how much time should I spend helping other students with research?

You forget one consideration: do you enjoy using that skill? To take your own example, I enjoy programming, and even though I might not learn or get anything technical from it, I enjoy solving someone's else problem with some lines of code :) Of course, one should be careful of the time spent and the reward you can get from it, but doing something you enjoy is very different than doing something you can, but don't particularly enjoy doing.

For instance, I can probably install a server and manage a website (with a CMS) for someone, but I don't enjoy it, so I would be very explicit about the benefit (I do that for you if you do that for me). But I could do some cool coding on my free time.

On a completely different aspect, it also depends if you intend to stay in academia: it's a very small world, and the person you're doing a favor to today might be the one sitting on your tenure committee in 20 years (if you work in the same department and all stay in academia, it's quite likely that your paths will cross again at some point in the future).


Do reviewers of research proposals for a fellowship read the whole application, or only the scientific part?

From my experience, reviewers get the whole proposal and also read the whole proposal. Reviewers try to get a complete picture of the applicant and skim the proposal for all relevant information in this regard. This means, that probably no reviewer will read every word of the proposal, but potentially, every word will be read by some reviewer. The reviewers base their review on the whole picture they get, but usually their feedback is only for the part for which they are specialists (e.g. the scientific strength of the applicant and so on…).


How to find the best journals or articles to read

This depends on your field. In mathematics, physics, and a few related areas there is arXiv.org. From which you get rss feeds or e-mail announcements for individual research areas. This is particularly helpful because there are a huge amount a journals in mathematics and physics and you could never keep up with all of them.

The added benefit is that most of what you run across on arXiv hasn't made it to a journal yet so it is relatively new and free. Then after you find useful and interesting articles you can keep track of them and find out where they were eventually published.

Another set of tools that can be useful is a good indexing service that lets you trace backwards and forwards the references from a paper that you know is important. This lets you see not only what the important paper references but also who has referenced it and where they did so.

Because of the fact that my research field does not yet have a single journal dedicated to my field these are the tools that I use most to find new literature and see what is going on. Of course if you are still looking around for a research field to get into there are the big general topic journals in each area which are a good place to start if you want a big picture.


Strategies to plan research and make the maximum out of it

Since scientific and math writers are writing for experts, and in fact specialists, it can be very difficult to read papers as you are getting started. Specialists share a mindset that implies that they can leave a lot unsaid. The author of a paper is likely very familiar with all of the papers cited, and you are not. This makes it especially difficult.
To understand a given paper it may be necessary to review many of the referenced papers first. At least the abstracts of those papers. It might be necessary to become familiar with some terminology that you aren't used to. Wikipedia can be a big help in many fields, actually.
But if you are starting out as a masters student then your education up to now has been mostly as a generalist, not a specialist. Don't get overly discouraged, but it takes a lot of work to build up your knowledge base to the point that you can understand a paper.
Dissertations are usually a bit easier, since candidates are expected to be a bit more complete than is true for published articles that depend on earlier work.
It is probably easier now than when I needed to spend hours in the math library, searching for referenced papers and then the papers referenced in those, etc, until I got some idea about what was being said. Now you can find a lot of those older papers online. The understanding hasn't gotten easier, of course.
But eventually, you grasp the specialized language and also the way of thinking of experts in your field. Lots of hours.
If you can ask questions of your advisor or others you can shorten the understanding process quite a bit.
As you read, take a lot of notes. Write down key ideas, of course, but also write down questions you still have. Then try to answer those questions either with more reading or by asking of others. If you find an answer in written work, it is good to write down the citation. You may want it later.
An effective researcher will also write down questions that aren't answered in the paper being read. This gives you an opportunity to extend the work.
Think of the knowledge you need as a tree that you need to explore. You need to go both wide and deep to acquire the understanding.


Writing a short paper pointing to a mistake in a 2012 journal paper that got significant citations, while discussion with the author not successful

If you are sure of your work, there is little reason not to write the paper and submit it. Cite the other work properly, of course, and make your case clear. If the editor of a journal doesn't reject it out of hand it will be passed to a couple of referees who will give their judgement on the work.
But you don't jeopardize your career by doing this. Your paper isn't public until it is published. But asking the editor first is probably a  mistake, since you can't develop your argument without writing the paper.
And, it isn't impossible that in writing it up formally you will find an error in your own work. Make the case. Submit it for publication if it is strong enough.


How to reconnect a relationship with a professor

I think you have gotten yourself into a pretty deep mess if it is really as bad as you suggest and not just a sense you have of the situation. But, the only way to proceed is to go visit the professor in person and steel yourself for whatever occurs. I'd make an appointment first, to give the other person a chance to think about their own response.

You may well owe an apology, so prepare to give it. But, as long as the prof isn't a monster, it may well turn out better than you fear. But it may also take a while to completely dispel any bad feelings if they exist so a single meeting may not turn things around like flipping a switch. But a face to face meeting will give both of you a sense whether a continued professional relationship is possible and desirable.

It may be the professor was disappointed when you left, but also possible that he/she is so busy generally that it didn't register too much.

The past is what it is and can't be changed. The future is up you you. But expect that the transition may be uncomfortable.


Do American students enroll in unaccredited universities?

There are two very different cases that should be distinguished.

You might have a brand-new university that is seeking to become accredited, but needs to be operating (with students) for a few years before accreditation is awarded.  An example is Olin College which enrolled its first class in 2002, and received accreditation in 2006-2007.  The first few classes of students do have to consider the risk that the institution might never receive accreditation, or might not establish a good reputation, or might shut down completely before they graduate.  So the school has to do a good job of building a reputation fast.

Prospective employers of the first students could conceivably be bothered by the fact that the institution is not accredited; however, reputation typically counts for much more than accreditation per se.  Also, in the case of Olin, note that accreditation came through just shortly after the first class graduated, and after that, nobody is really going to check whether they got their degree before or after accreditation.

The other case is universities that are not accredited and do not want to be.  There is nothing illegal about this; in the US, accreditation is a purely voluntary procedure.  However, most such institutions have a poor reputation or none at all.  A few have genuine educational programs but prefer to remain independent of the accrediting process for philosophical or religious reasons.  Others are mere "diploma mills" with no real educational product whatsoever.  Students should be very cautious about choosing such non-accredited institutions, but they are free to do so if they want.  Employers are likely to view such degrees with skepticism; however, this would be based more on the institution's lack of reputation than its lack of accreditation.


How common is it for a science research paper to include direct quotes?

I guess I disagree, but you have to think about what you are doing. Anytime you use another's words directly you should quote them and indicate explicitly that it is a quote. This can be done with "quote" marks or otherwise, such as indentation. You also need to provide a reference to the source, say, in a footnote.

However, perhaps your professor is saying that, rather than quoting people's words directly, you paraphrase their arguments, etc. instead. Then you don't quote them. You still need the  reference, of course and need to be sure that your paraphrase is accurate. Your formatting, etc. needs to make it clear that the words are yours, not theirs.

But I would suggest you explore it further with your professor. Perhaps he or she has another idea in mind.


I want to be a researcher but I don't think I'd be any good at teaching. What do I do?

Staying at the university, i.e., eventually becoming a professor, will be hard / impossible without teaching. There are, however, research facilities that are usually financed half by industrial projects and half by funding from the state. If you get a job in one of these, you will have to aquire money by getting research projects accepted, and are then free to do research without any teaching obligations. Note that your contract there will probably never be any longer than 2-3 years at once. I will then hopefully be refreshed, but you will not have a lot of stability.

The main question may be whether you think you can do your PhD. That involves giving several presentations (at conferences and during your defense), a rather high level of stress tolerance, and probably occasional preassure from your advisor, especially during the last year.

I had a colleague who might have a slight form of Asperger, and he quit about one year before finishing his PhD, because it got to overwhelming. But there were several factors involved there, including him not being happy with the direction his research was going. So that might have nothing to say!


How do I/should I convince my advisor to let me transfer with her blessings?

Keep the trust of every party involved. Don't lie! Don't disappoint them. Assume all of them are normal and honest and adult persons.

Ask, if you have a written offer, permission to forward it. Then do it. That might trigger direct interaction between past and future advisors.

Your actual (and soon past) advisor will understand that it is not his/her interest to keep you against your will.

Your relation with your past advisor is not a slave -> master one. Both of you are adults.

From the point of view of your past advisor, you are quitting (or giving up your PhD). That happens many times.

Of course, do respect the usual prior notice.

You want to be respected, and you should respect all others

BTW, notice that if you get (it is hard) some research funding, you can chose its topic. But that observation is even more relevant for your postdoc than for your PhD.

PS. The trivial point is that nobody is working well under constraint. You need passion to work on any PhD


Is the prestige of a university correlated with how rigorous its undergraduate courses are?

Your intuition is correct; I nevertheless do not think is it easy to quantify how much harder (or easier) is one degree compared to another. It is imperative to also define how we measure "hardness"; eg. hours per week? success rate? span of material covered? etc.
Clearly one adapts the difficulty of the lecture to the audience. I am not talking about trivializing a topic (that can happen too and it is wrong) but actually as an educator you have to strike the right balance.

To give a small anecdote from Greece:
My very close friend graduated Physics and decided to go a second degree afterwards in EECS in NTUA. EECS in NTUA in Greece is one of the most prestigious and hardest to get in schools in the country (occasionally it is actually the hardest). In this programme he had to do a particular Physics class and while he was good, he had to put a lot of effort on it. So at some point he asked the lecturer (I am paraphrasing) : "I am a physicist, I know this stuff and I know you give them really hard problems on this subject. I see the class fighting to keep up; is it worth it? It is extremely unlikely they will use this material." the answer was : "Yes, you are right; but they are the best (theoretically) in country so I need to drill them the hardest." The lecturer was adapting the lecture to the audience. And I have heard complains from academics in minor schools for the exact opposite thing (under-qualified audiences).

To recap: Yes, the same class taught in a top school and in a average school will almost surely be harder in a top school. That is natural and should be expected to a certain degree. Quantifying the difficulty of it though is useless unless you have a particular "yardstick*.

Disclaimer: I am not a physicist nor did I attend the institution mentioned above aside a few lectures here and there.


Establishing the list of authors for a comprehensive/review (conference) paper

The way that I think about this sort of situation is that co-authorship of an abstract and talk is very low-stakes, and there's little reason to be stingy with it.  The most important thing here is to preserve a good relationship with collaborators that you value, and so I would recommend asking your collaborators.

If it's a collegial group with good working relation, then you'll probably get a quick consensus on one of the three options.  My own experience with many co-author situations like this is that many collaborators are happy enough to go along for the ride; a few will make constructive (or at least neutral) suggestions, and most just want to make sure their name isn't getting associated with anything embarassing---most people will only try to micromanage if you invite them to.

One important note, however: if the consensus ends up going with option #2, where some people get designated as "important", then let your collaborators decide if they should be on that list.  Again, the authorship of an abstract and presentation like this is pretty low-stakes (unlike for journal papers, where it's good that it sounds like you've already got clear boundaries drawn).  It's extremely dangerous for good relations if you put yourself in the position of telling Juan that he's less important to you than Marie.

Now, if you've got a problem collaborator who is not likely to be collegial or who is going to try to operate you like a puppet on stage, that's a different problem, and one whose resolution is likely to require very specific help and advice from some of your senior collaborators...


How to write a reminder mail to a Professor asking about the application?

Professors forget to reply to emails all the time. (I think they get trained in email forgetfulness as part of the tenure process) As long as you aren't demanding or insulting, you should be fine. I'd suggest sending something like this:

  Dear Prof. Awesome,

  I haven't heard from you since I sent in my Postdoc application on January 3rd. I wanted check on the status of the application and see if there were any other documents you need.

  Thank you for your time,

  Kunal R Shah


What does "Application review begins ..." practically mean in job ads in computer science in USA?

It means that, shortly after date Y, the committee in charge of reviewing applicants will meet and discuss the applications that have been received up to that point and, if they like some of the candidates, they will be invited for interviews and, depending on how it goes, may get an offer. They committee may revisit the applicant pool at a later date and, if the position is still open, they may consider further applicants. So, in principle, you can apply whenever you want but if you wait until after date Y, you may miss out. Of course, it can happen that all good candidates are late but you shouldn't count on that.


Problem of mentioning the department affiliated with PhD degrees

My question is, what is the best way in our cases to "market" our research focus and experiences to other people?

Marketing is all about knowing your audience. And thus you may market your PhD to different audiences in different ways.

If you're talking to a person on the street, you could say "PhD in Computer Science".

If you're talking to a Computer Scientist, you could say "PhD in Quantum Information".

If you're talking to a specialist in Quantum Information, you could say "PhD in X, Y & Z" where X, Y and Z are detailed topics.

The truth of the matter is that a PhD is a PhD. Officially speaking, there's no such thing as a "PhD in ...". So for the given person in front of you, try to communicate the area of your PhD as best as you can.

And as for the "IT guy" stuff, if that's how they chose to stereotype what you are doing, then that's their problem, not yours/your boyfriends.


Does copyright restrict how I can adapt papers when compiling them into a thesis?

I disagree with part of the other answer, in that the copyright holder of a work is not always the creators/authors. For some journals when you publish with them and sign the licensing agreement, you transfer the copyright of your work to the publisher. Then it is up to the publisher to decide how you can reuse your paper. I would advice reviewing the copyright/licensing agreement you signed with your publisher for limitations for reuse, and if still in doubt, contact the publisher.


I do not see anything unusual or particularly alarming in this situation. Your first review arrived very quickly — compared to Mathematics, where a first review can take 15-18 months in some journals.

It is not unusual for reviewers to make remarks which appear contradictory. Sometimes it is possible to find a compromise to pacify both; sometimes (as in your case) it is necessary to rebut the criticism. Rebuttals are never easy and the suggestion of the first reviewer to reject a paper is not completely unexpected. Now the decision falls on the Editor, who has to either side with you (and potentially lose their Journal the Reviewer One) or side with Reviewer One and reject your paper. It is not an easy decision, and it requires for Editor to personally read the paper, or to invite another reviewer to join the fun. Whatever they are doing, three months does not seem overly long yet to me.

tl;dr: It's best to wait patiently.


Is applying to 20 graduate schools too much?

Just my opinion: Do you really need to apply to 20 schools? I think it is very hard to be focused when applying to many schools. You also have to spend lots of money, and more importantly, you have to find referees willing to write 20 recommendation letters!

I have read many articles and most of them suggest 6-8 school: 3 reach schools, 2 match schools, and 2 safe schools and that seems reasonable.

20 seems to be too much and a waste of your time and money.


Getting married abroad on August 21st, job begins on August 23rd. What do I do?

The best way to handle a situation like this is to get in touch with your Head of Department / Director of Teaching in advance (perhaps, after you receive a formal offer) and discuss your situation. Make them aware of your wedding date (congratulations, btw!) and explain that you can arrive to your post right in time for your first class, but you would be grateful if your first lecture can be rescheduled to give you a bit more time. In many Universities it is customary for colleagues to step in for each other in case of sick leave or important family events (like wedding). It is much better to arrange a replacement / rescheduling in advance, rather than risk not showing (or showing not prepared) for your first class.


Academic occupation options for foreign visitors to the USA?

If you want to work or study in a program, you must change your visa type. You can file for an adjustment of status once you have found a job that will sponsor a different visa type or matriculate into a program that will also sponsor a visa for you. Tread carefully in your job hunting as job-hunting itself may be interpreted as a violation of your status -- it would be good for you to consult with an immigration attorney (or barring that, your university's foreign student's office) before you initiate this.

Otherwise, you are unable to work or study formally. The things that you can do:

Use your spousal ID card to study in the library
Use your spousal ID card to audit classes for non-credit
Enjoy hobbies -- join a maker club and make giant fighting robots, learn to fly a kite, etc.
Take part in the activities organized by your university's foreign student/scholar office (there are many spouses in your same situation, so they tend to offer things to help pass the time)
Cook, clean, take care of the children, and otherwise be a fantastic spouse to your wife


Supervisor using my dataset without my consent to submit papers with his other students

I don't see anything problematic here, unless the papers that your advisor wrote with the other students take credit for developing the dataset (which would be a clear ethical violation).
Many papers in computer science use one or several datasets developed by other authors, and it's not a standard practice that the dataset developers are invited to contribute as authors. In fact, doing so may lead to vastly inflated author lists for papers that use many datasets.


How much money do universities pay to access datasets?

I can not offer you research, but I can tell you that when I was touring the library at SFSU, the librarian said that they pay something over $200,000. for access to their complete list of journals and databases. I imagine it varies considerably from one to the other university.


Should I feel bad for applying to two postdoc positions?

Everyone who is hiring knows that applicants are applying for multiple positions. This covers everyone from McDonald's to Harvard. It's expected. They will get multiple applications and will only take one, so you must apply to multiple positions to have a chance of landing one. Unless you have an offer in hand which you have already accepted when you apply for another position, you haven't done anything wrong. I'm surprised you've only applied to two.


How to address reading courses in cv for Phd application for pure math?

It would be helpful to list the topics you looked at, and their sources. Even "standard" courses, with standard names, vary wildly depending on the choice of textbook or other sources, and depending on the instructor (who may be the author of notes or textbook for the course!)

Similarly, "reading course in X" tells far too little, just as saying "standard course in X" would. Prior to the enforced uniformization of applications to our grad program, as occasional Dir of Grad Studies in Math, I required applicants to not only tell the course name, but also, even more importantly, the (title and) author(s) of the text(s)/source(s) for the course. Reading courses treated the same way.

To repeat: the standard catch-phrases/labels of course names absolutely do not describe the content... so, yes, please do give more details. These details are not at all implied by the general, vague, cliched titles.


Doing a master's degree after PhD. Is it advisable?

I think a postdoc would better suit your purposes. The benefit is just not there to pursue a masters degree. Further, unless you are trying to go into a field that requires that specific degree as a prerequisite for entry, you can easily teach yourself from open source material.

The benefits of a postdoc are that it allows you to make a transition in your academic career while getting paid better than a graduate student. You also do not have the pressure of course work or degree requirements.

I used my postdoc to strengthen my programming skills, begin work in machine learning, and to expose myself to bayesian statistics. This sounds pretty similar to where you are at.


Should I admit that I can't find a solution to a math problem?

I don't know why you think there are any options other than both.  Of course you shouldn't just say "I'm having difficulties, full stop" without talking about what you have tried.  Of course you shouldn't just say "this is what I did" without also talking about where you're stuck.

You sound like you're worried about making the best impression on this professor.  The best impression you can make here is showing that you have the maturity to deal with doing research: to work hard on a problem, be aware of both what you've accomplished and what you haven't, and be able to ask for help where you need it.

There are bunch of things that could be happening:

You went off in the wrong direction, or missed something, and the professor will be able to help get you back on the right track.
The problem is actually harder than the professor thought, and explaining why you're stuck will make that clear to them.
The problem is harder than you thought, and the professor expected you to need some help.

In all of those cases, the absolute best thing to do is honestly present the work you've done.  The less you worry about framing things to make you look good, the better you actually end up looking.


What could be incentives for publishers to waive fees for reusing figures?

I've never had a problem getting permission to use a figure with proper citation – ideally such a usage drives traffic back to the original article / source too.  So that's one incentive right there.  Be sure to let them know you will send traffic / credit back and ask how they want to be cited and / or linked.

But authors ordinarily do not really expect to lose control over their IP, so authors would probably avoid such publishers if they found out that a journal "jailed" their figures. This is obviously a stick not a carrot, maybe saying something like "I think the authors would be very disappointed to find out if they have been disadvantaged by publishing with you, it might discourage them working with you in the future."


Good at coursework and learning background material, but attempts at original research go downhill. How to overcome psychological block?

It is hard to give a good answer here, but it seems to me that you, despite being a good student, haven't learned to do research yet.

When you describe what you are good at, you describe all the things you need to be a good student. These things are all necessary to be good at research, but alas, they are not sufficient. To do research, you need to shift to a different gear.

For example: Do not read a paper thinking "How does this work?" but more "What does that mean? What can I do with it? What could be done differently?". Learn to read articles and books through different lenses, e.g. with a lens that focuses on broad understanding of concepts, a lens that focuses on fine details, a lens that focuses on open problems or possible improvements,…

Also, find a problem to work on, not a topic to learn. Ask some supervisor to provide a problem to work on at the beginning, but note that later on you should come up with interesting problems on your own.


Include author after revision in IEEE journal

Yes, you can update the author list. Depending on the system, you might be able to update the authors in the submission system directly, or you may have to contact the editor to have them do it.

One caveat, there is the possibility that a new author changes the people conflicted with reviewing it.  For a minor revision, which probably only goes back to an associate editor, this may not matter much.  Plus, it's already essentially accepted.  If it were a major revision that would get reviewed again, it's possible someone who should reread it is now conflicted. (More likely if the new author is with another institution, but even if it were a student, a summer internship could have that effect.)


How inclusive should my CV's publications be?

Typically, your C.V. is expected to contain a fairly complete accounting of your life's scientific work (unless you are so advanced in your career that you can do a "selected publications" CV that just lists your greatest hits).

As such, it is generally best to list every publication on which you are listed as an author, no matter when it may have been published.


How to manage lot of random yet potential ideas for research and startup?

For your first question, here is the workflow I follow:

Write them down (as @JeffE mentioned)
Organize them in order of viability/ease
Take the most viable idea and do a (very) quick prototype
If prototype is successful, develop it. If not, iterate.

From the prototype you probably have a better idea of how much work it would take to fully develop the research idea. If it seems like you won't be able to handle it in the amount of time you have, or if the outcome is not worth the effort, I usually archive that idea for later. For a  prototype I usually try to do the bare minimum to produce the simplest result possible. A common trap is to start from the complex before you've mastered the simple.

The second question depends a lot on your personality, so don't take the following advice much too serious. Personally, I have a very hard time focusing on two things at the same time. What I would do is focus on my PhD. You'll surely get many more ideas as your work progresses. For every problem you solve, you'll generate 10 new ones. Be sure to write things down so that you don't forget them later on.

This is a very personal question and you have to see what works for you.


Is it important to include my supervisor name in research paper

Authorship should be decided by who made intellectual contributions to the work, not by feelings that three is or is not a better number than two.


Should I tell one of my recommenders that his notes are at a level beyond me?

Instead of saying

  These notes are far beyond my level, do you have other suggestions?

Consider something like

  What level of detail do you recommend for me when going through these notes? What kind of things should I be looking for and taking note of?

to gain a better understanding of what he intended for you when suggesting that you read these notes.

It's possible that he expected you to understand the notes, and that your inability to do so is a worrying sign.

It's also possible that he didn't expect you to understand them fully, but suggested them for other reasons: to gain an idea of overall trends in a particular field, to get a sense of what advanced coursework in the field looks like, just to find an idea that inspires you, etc. If you read the notes and skip the details (the derivations, the proofs, etc.) and look up unfamiliar terms as you go, can you understand some of them? Most of them?

It's also possible that these notes are at an advanced level, but that your inability to understand them is not necessarily a worrying sign. Perhaps he expected for you to spend a lot of time studying them in detail (probably using external resources to fill in gaps in your background knowledge) before you can begin to understand them.


I think your SOP should focus on that, not your past record. The committee will have access to your grades and will focus most on the subject grades in any case. There is no need to waste words on things that can better support your candidacy. Yes, you are proud of your past work, but your CV already shows that.

Write about what you want to do in the future, how your interests and skills align with that purpose. If necessary, talk about how you fit well into the program you hope to join.

Make your SOP work to complement your CV, not to repeat it.


I suspect that this is strongly culturally dependent.  In the American tradition of egalitarianism, my C.V. has never had any titles in it at all, following the example I saw amongst my older peers and professor.  On the other hand, I suspect that a German C.V. might be much more particular, since academic titles are considered important enough to be protected by law there.

My suggestion to you, then, would be to look at the CVs of people with a position similar to that you aim to obtain, and to adopt the style that they have used.


Master's at Undergrad University Then Pursue PhD Elsewhere

My answer reflects the situation in the US and Canada.  In the US, most Ph.D. programs accept people directly from undergrad; at a few US and most Canadian schools you'll be expected to start in a master's program, but it is generally relatively easy to move up to the Ph.D. program (not significantly harder than avoiding getting kicked out of most US Ph.D. programs).  Whether it says "MS" on your degree will matter less than what courses you have taken.  Having another year of coursework will probably strengthen your application (or at least gives you a chance to), but if you have to pay a significant amount of tuition, then I have serious concerns about whether it will be worth it. If you can get into a funded master's or Ph.D. program, then that will save you a LOT of money, and you can get roughly the same boost to your future applications spending a year there that you would by being in the BS/MS program.

EDIT:  Since the OP has clarified that the extra year would be funded with a stipend, my comments above aren't really applicable.  In that case, it probably is the best plan to stay at the current university and get the BS/MS.

Maybe I'll just make a general comment here which seems relevant: its generally pretty advantageous to stay longer at the current stage of career where you already are, as opposed to moving on in a rush.  Our culture makes a powerful mystique around completing things quickly, but all other things being equal, it is to your benefit to be a little ahead in actual accomplishments of where you are in your career (which extra time is one way of accomplishing).  You get "clock resets" at various points of your career (when starting or finishing a Ph.D., for example), if you can get more done before those, all the better.  Of course, often financial or personal considerations have to be weighed against this.


Copyright for creating a video that is a chapter-by-chapter Analysis of a Technical Book?

Disclaimer 1: I am not a lawyer, I know sh*t about law, it is not a legal advice and you should consult with a professional.

Disclaimer 2: ethics and law are two different question, this answer tries to give ideas about the law part (and you should not fully rely on it, as stated in D1)

If you using substantial amount of the book (its code, its ideas), especially blatantly copy its structure making it obvious what you copied, then you are way beyond fair use and you are in a gray or even red copyright area. Depending on publishers they generally put some short examples in their copyright session what constitute fair use, you can check those. What you describe here goes far beyond this. Also the whole purpose is to spread it to wide audience on youtube, so publisher can claim that they suffer significant loss of revenue, because the whole thing with all the details and secret sauce is on YouTube.

What you can do about it?
You can try to get a permission from the publisher (most probably the author himself cannot give this). It may help if you have a reasonable discussion with the author / publisher about your idea and tune down the "I will discuss every little details of your book and copy out all the codes" part. For example it helps if you have your own intellectual effort in this whole stuff, e.g. analysing problems not presented in the book and show how the books method can be used, and not just reading/summarizing the book on video.


My university requires that I take attendance. How should I treat students who arrive late to class?

This is an answer to a previous version of the question, where it was not clear that recording attendance was mandatory at the asker’s university. Therefore my answer does not cover the specific situation of the OP, but may still help others in a similar situation.

0)  Allow all students in class and do not monitor attendance.

They are adults and they come to learn. As long as they do not disrupt the class they are free to come and go as they please. I do not see which purpose the monitoring of attendance serves. It sends the wrong signal and focuses students on signing the register sheet rather than on the objective of the class.

I do, however, start each class by thanking students who attend and come in time. Latecomers will miss this part.


No, unless your institution has a specific policy on grade cutoffs.

Grade cutoffs are arbitrary. You cannot compare a % grade in one class to another, because the assessments are going to be different.


Microsoft Academic
Microsoft Academic does show such information: Click on a researcher profile, go to the tab Cited By, then look at the column (to the left of the screen) titled Top Authors. Here is an example for Christian Drosten:

If you have a profile at Microsoft Academic and claimed your publications, you can see a similar list regarding your own 'citers'.

CrossRef
An alternative approach would be the following: You could gather all the DOIs from the papers that cite you, loop through it to access CrossRef's API via https://api.crossref.org/works/{DOI}, and extract the respective author-field.


Unproductive in dissertation research (mathematics/statistics)

Some problems are just hard, and insight can't be scheduled. So, yes, others have had similar problems. Good problems, by the way, are hard to find. They can be too easy and have no real significance. You don't gain much by solving them. Others are just impossible, possibly theoretically, or possibly just at the current state of knowledge.

My field is different, but one thing I'd probably think of trying if I didn't understand a function would be to model it computationally. Another thing I'd probably want to think about is my partial results. Are they meaningful? Can the be used for other things?

But the best help will probably come from your advisor. If you can explain what is blocking you, maybe the two of you can find a crack to exploit. Just trying to explain your problem and your issue can sometimes free a block, if that is what it is.