How to keep track of deliverables for supervised students when you supervise many students?

When teaching undergraduates, before my retirement, I tracked/supervised student research/capstone projects with two methods.

1) I required the student to prepare an Excel document with their timeline for completion and the milestone dates.  After a joint review (and revision(s)), I then had the document which I kept in a binder (later on a shared server) which I could track completions and keeping of suspense dates.

2) The other method which I usually used for team projects was a written ONE-PAGE weekly activity report.  (And even up to 1 year ago, they were to be submitted in hard copy.)  The report included a summary of work done in the last 7 days, what is planned for the next 7 days, what were the next 2 milestones and their due dates.

Additionally, some of my colleagues were in the last few years using a shared Google gdrive folder for a shared calender for each student and project.  I did not do this because I actually wanted a record of how milestones were revised as the project processed.  (Part of good research is being willing to revise the plan in an appropriate manner, keeping all parties informed, and accomplishing the task at hand in the time required)


I recently enrolled in masters in AI after doing my bachelor in CS, I'm overwhelmed how to start research

TL;DR. Search this forum, and beyond, for impostor syndrome: What you're experiencing is perfectly normal.
At masters-level, you're just entering the amphitheatre arena. Of course everyone looks better, you haven't started yet. I see outstanding papers published round the clock, that's great! You're looking in the right places, finding the best stuff. It really makes me feel how anything I would do would even match the lowest standard worthy of publishing, that's impostor syndrome. Hang around, absorb the knowledge, learn how to compete.
[N]ot to mention the single biggest problem I don't have a problem in hand, many students get handed problems by their advisors, only later do they identify their own problems.
Look in the mirror, ask yourself, do I want to do research? If the answer is yes, go learn how to do it. Don't worry about not being able today.


Can I be successful as a lone wolf researcher in mathematics?

Plenty of mathematicians are introverted, quiet, and typically prefer to work alone. (Also, plenty of mathematicians are extroverted, boisterous, and prefer to work with others -- but I believe the profession does a reasonably good job of welcoming various personality types.)

All successful mathematicians whom I know spend some of their time and energy engaging with the mathematical community. Going to conferences or chatting with colleagues are good ways to do this. There are also ways such as MathOverflow to interact with mathematicians online. And simply reading the (contemporary) work of other mathematicians is also a form of engagement.

If you want your work to be appreciated by others, then I recommend taking the time and energy to appreciate others' work. For example, are there any questions asked by others, for which your work gives any insights? If you can help people answer questions they are interested in, then it is quite natural that they might take an interest in your own work as well.

Good luck!


Am I supposed to understand my training dataset for a machine learning project?

From the point of pure exercise in machine learning, you do not care whether the data is reliable and whether it was collected or taken from the ceiling. Your task is just to design a recognition algorithm that classifies the objects into groups based on the numbers associated with them. If you can do it, you pass, if not, you fail.

From the perspective of practical recognition of rocks, your algorithm (if it works) will be useful only if you trained it on accurate data or data with not too much noise and if you know what the numbers mean, so if you later are given the information in different units or on an altogether different scale (say, logarithmic instead of linear), you'll know how to convert before feeding them into the machine. If your algorithm is intended for real use, the people who requested the work should be most interested in getting things right, so you should be able to ask them as many relevant questions as you want. If it is just a practice problem, just forget about "rocks", "radiance", etc. View all that as an abstract classification problem about objects and numbers without any meaning whatsoever.

From what you are saying, it looks like you are in the first case scenario. I agree that the exercise is about as meaningful as the exercise in computing the area of the triangle with sides 6,7,8 and the altitude of length 5 drawn to the side of length 7. My daughter really had that as a problem on one of her exams and her teacher replied to my objections that at that stage of learning he just wanted to make sure that kids knew which side to multiply by the height. He wasn't a bad math. teacher overall, by the way, just a bit reckless about the details that weren't directly related to the current topic. Apparently, your professors have a similar attitude.


How to cite my own code in an academic paper?

As you suggested you can create a GitHub repository for your code. There is also the possibility to create a release of your repository. Then you can get a DOI for that release using Zenodo:

Zenodo How-to

You can then put that DOI in your paper as reference and do not have the problem with changing code, because the DOI is associated with the specific release.


Can I claim authorship on work I wasn't personally involved in, that uses a framework I developed for my research?

Disclaimer: This is somewhat field-dependent. I'm answering based on what I believe to be the current situation in computer science / related fields.

1) Can you claim authorship given the way things have evolved? Probably not.

2) Would it have been a good idea for him to find a way to include you in the research collaboration so that you could get something out of your work? Yes.

The area of academia in which I work (*) is structured so as to value ideas over implementation. In practice, that means that it's not uncommon for people who write large amounts of code for a project to get little credit for it, which seems inherently unjust.

The way sensible people usually handle this is to make sure that people who do a lot of implementation work are given an opportunity to contribute scientifically over and above that - that allows them to justify their authorship in scientific terms, regardless of the fact that they also made significant non-scientific contributions to the overall project.

It's certainly possible to take advantage of implementers by not doing this, but people who do that tend to find themselves doing the implementation work themselves.

Bottom line: He should have had the common sense to include you in the scientific collaboration, and if he didn't have that common sense then his supervisor should have suggested it.

As an aside, I would view the situation somewhat differently if you already had a publication as a result of your work. In that case, you've already got the credit for working on the framework, and there's less of a moral obligation to include you in the new collaboration: instead, they can simply cite you. I'm certainly not of the view that writing a framework entitles you to be involved in every paper that is ever built on top of that framework - indeed, I've written frameworks that other people have continued to use for later research, and I wouldn't expect to be involved with the papers in question.

(*) As pointed out in the comments, this may not be the case in other fields.


How do I continue my PhD research project as a Postdoc?

In the UK there might be one or two early career fellowship schemes that you could apply to. Some have restrictions on when you finished your PhD and require the hosting university to provide some percentage of the funding. They are competitive of course but it sounds like a good fit for your situation - you have a good idea and relevant experience and all you need is someone sensible enough to fund you.


I want to review my old college applications via FERPA - is this possible?

Can people [request their records under FERPA] for schools to which they were not accepted?

No. From the FERPA text, education records are defined as:

those records that are:
(1) Directly related to a student; and
(2) Maintained by an educational agency or institution or by a party acting for the agency or institution.

and a student is defined as:

any individual who is or has been in attendance at an educational agency or institution and regarding whom the agency or institution maintains education records.

Since you have never been in attendance at the schools who rejected you, you have are a not considered their student and FERPA does not accord you any protections.
This accords with most "plain English" descriptions. For example, it agrees with this description from PrepScholar and this explanation from USC.
As Nate points out in the comments: "section 99.5 (c)...says you don't even have the right to view your application records if you applied to a different component of an institution you were already attending." So there is no loophole if you applied to grad school at your undergraduate institution.
There is therefore no question of "choosing not to honor the law" -- rather, the law does not impose any obligations on the school until a student-university relationship is formed.

What is the retention period? I would think that if I applied over four years ago, they might not have my record on file...?

FERPA does not specify any retention period. As noted here, however, state law may impose certain retention requirements.
In a larger sense, the goal of FERPA is protect privacy and allow students to correct errors in their educational record. It is not concerned with the admissions process directly (until the point where admissions documents become part of the student's educational record).
I agree with the commenters suggesting that you would do better to ask professors you know to review your application materials and give you feedback. I admit I am also a little concerned that you are still seeking "closure" five years later, but that is perhaps a separate matter.


How is it possible to get into PhD in a different institute than Masters when publications take so long?

There are two ways to look at this question, both of which are answered in the comments. The first of which is just you asking, "I have submitted for publication, but they haven't been accepted yet." As Per Alexandersson said, make a list, write submitted, and if it's in mathematics, you can even link to Arxiv.

But addressing the implication of the question that it is required to have publications to matriculate, I'm not sure that's entirely accurate. Many Ph.D. Programs accept students directly out of their undergraduate degree, and so to expect them to have published research would be generally unfair. It makes more sense for Ph.D. programs to be looking for students who have the capability for research. This capability can be shown through projects that go beyond the scope of the classroom, research with professors that didn't necessarily result in publication, or as astronat mentioned in the comments, by strong references letters from supervisors, professors, etc.


How do I replicate simulations on a research paper?

If you don't have the original code, you need to use the experiment descriptions (the methodology) to create your own code, and perhaps data. This is much harder, of course, than if you had the code. But it is much more valuable for science as a whole. If you come to the same results (statistically speaking) then you have evidence that the original hypotheses stand up. But if you get different results you have to question why. Either the original result was false or your own work misses something. Both cases lead to advances in science.

And, running the same code on the same data is a bit boring, actually. Hardly something that can be published.

But point your own efforts at the hypothesis in the original paper, not at the results specifically. Then, you have something publishable whether you confirm or refute the original results.


What is common in most PhD application procedures in the UK?

Unfortunately the system in the UK is not uniform. You will really have to read each individual department's web site to know how to apply. There are, for example, Centres for Doctoral Training http://www.epsrc.ac.uk/skills/students/centres/ which you apply to like a US graduate program.  I don't know if there is a good one that covers stochastic analysis but it seems likely.

It sounds like the list you give is for people who want to apply for a specific supervisor.  For this route, your main issue will be funding as there is very little funding for non-UK students these days.  This will also vary wildly between different universities. There may be deadlines which you have missed already if you want to start in 2015.  However, simply for being accepted by a supervisor without funding the list you gave is fine.

Overall, read each department's web site on their PhD programmes, don't forget to look for any relevant Centres for Doctoral Training and good luck.


What are the advantages and disadvantages of doing research without studying for a degree?

Your question is a bit underspecified, but if I understand it correctly, perhaps the following will help.

Research is about learning what is true about some aspect of the world or the mind. Carrying out research is good mental training and gives you the basis both for future study and for a profession. So, it is worth doing, just for that, without regard to any results. Doing it in a group, as you suggest, is also good as you can help teach each other as you go.

On the other hand, carrying out research without professional guidance, as a beginner, can lead you to waste your time, both in understanding what is important to study and what is already known. One reason for beginning a research career as a student of a degree program is that your advisor can keep you from falling into such traps. The advisor can, most likely, point you to resources that would be difficult for you to find on your own. There are specific techniques used in research in specific fields that you may also not be aware of without access to an experienced guide.

It is also, arguably, easier to publish if you are associated with a known institution. This isn't a requirement, actually, but it has some effect.


If an author does not intend to make much revenue from a book, why not make it open-access?

There are a number of reasons why not to, and they stem from the reasons one might want to publish a book, even if you aren't making much if any money:

The prestige of the publisher matters. For many tenure committees, professional organizations, etc. "A Book from BigDeal University Press" > "Some Markdown Files on Github" or what have you in terms of evaluation. In effect, you are getting paid, but in prestige and reputation rather than money.
Publishers take care of a number of things that, if you're self-publishing an open access book you have to do yourself, including copy-editing, layout, and most importantly, finding peer reviewers.
Seeing a book adopted widely (another part of the whole prestige aspect) will likely be more difficult for an open-access book, at least at present, where they are fairly common. Who is going to do the marketing? Has it actually been properly peer reviewed? Are there nice, hard-bound copies available (some of us like reading things on paper), etc.

That is not to say that there are not some very successful efforts in my field to do open access books. Hernan and Robins causal inference book, for example, has drafts and code available online: http://www.hsph.harvard.edu/miguel-hernan/causal-inference-book/

But neither one of those authors is in the position to need much benefit from a book publication, and it's still being placed in a traditional press when it's finished.


What percentage of a professor's salary is paid for by tuition?

I think that you'll never be able to sort this out. Most universities cross-subsidize departments to the point that even individual departments don't know how much of their own faculty lines come from the tuition of students majoring in that subject vs. tuition from other departments' students. Does the English department fully fund itself through the fees students pay for English classes? I doubt it. State funding, though a diminishing portion of most state universities' budgets, picks up some fraction of the costs.

Also, departments see level funding in the face of modest fluctuations in class enrollments. If 45 students took Calculus I last fall and 52 sign up this fall, the department doesn't see increased revenue for that. The department has a number of faculty lines coming from the dean's office to teach the projected enrollment. If that spikes or drops off substantially such that more instructors are required, then the department has to negotiate more or fewer lines with their dean.

That being said, I think that most departments negotiate expected breakdowns in effort with the faculty they hire. Of a typical 9 month appointment, a faculty member might be expected to do 35% teaching, 35%  service, and 30% research (or whatever), and that might be the expectation regardless of whether the teaching load is a 1-1, 2-1, or 2-2. Where, again, it's entirely unclear whether that 35% teaching is completely funded by tuition or partly funded by tuition, central endowment, and/or a local named chair.


Multiple submission of same work for different audiences

This is actually something my group also deals with extensively. A lot of the work we do is focused on improving existing computational methods to improve their efficiency or extend their range. A lot of the time, the actual work done is of very little interest to the end-user audience, but quite significant from a computer science perspective. So a lot of our recent work has been divided in exactly the manner you propose: we present the basics of the method and some end-user applications in papers geared toward the application community, and specialized papers for the methodology that are directed toward the CS community.

The main thing to remember is that the publications should stand independently of one another as much as possible. Some overlap will of course be inevitable here, but you should strive to make the "stories" they tell as distinct as possible.


How significant is it to publish a scientific "review paper" in 6–10 impact factor journal?

This really depends on the field and the venue...
In my own field, book chapters are almost useless for your goals - they come in two flavors: those where already accomplished authors write reviews of a subject and are considered highly but are written by people who do not need an introduction, and those solicited by publishers looking for cheap content they can resell. There are other fields where book chapters are a pretty central part of publishing.
That said, review articles can be basically the same: those where established researchers convey their wisdom are highly respected, but typically the authors have sufficient credit already. In my area, an impact factor of 6-10 is pretty good, though also low for a journal that trades in the review arena: highly influential reviews in review journals get tens to hundreds (sometimes thousands) of citations, so those journals have inflated impact factors.
With the limited information you've provided, I'd assume the review article is better, if indeed the journal is a good journal and not somehow inflating an impact factor with false citations (not an uncommon thing). The more important advice I would offer is for you to check the specific circumstances with an advisor you trust. Your thesis advisor would be a good start.


How common is it for journal to reject a solicited paper?

This is not common, but it certainly does happen.  I know a small number of people who have had their invited submissions rejected.  Whether it is a likely possibility in particular instance will depend on how many invitations the editor(s) send out—and, correspondingly, how well they know the potential contributors and their work.  If the invitations are kept to a relatively small group of individuals familiar to the editor, it is less likely that anyone will submit a manuscript that is of low quality or is not topical.

Whether this is likely to happen also depends on how the submissions are being evaluated.  Sometimes, an expert guest editor for a special issue may take care of all the refereeing themself.  However, this will not work if the topic is too broad or there are too many submission.  I was actually responsible for getting a low-quality invited paper rejected from a special issue once, when I was asked to referee it.  The work was simply too shoddy to merit publication in any venue.


Are there any benefits for a researcher or university in terms of number of grants submitted?

There are no direct benefits if the applications are not accepted. There might be some indirect benefits, if during the writing process the researcher gains feedback on their ideas and plans from colleagues or reviewers. Or, it might be useful to show evidence to your boss that, in the absence of grant income, you are indeed attempting to secure some.

But one important benefit is mentioned in your question already:

  in fact, one of her grants was accepted

You've got to be in it to win it. There is definitely some unpredictability in the grant application process, in terms of who reviews it, who is on the panel, what mood the panel are in on that particular day, etc. So, (all else being equal) the more you submit, the more chance you have.

Importantly, there are also potential disadvantages of submitting large numbers of low quality grants. For example, NERC UK has instigated a "demand management" system for its standard grants, such that if an institution's success rate drops below 20% they will be limited in the number of applications they can submit the next year. The NSF (which is tagged in OP's question) places limits on the number of applications from an institution for a number of its grant schemes. For an individual researcher, this means that they probably need to get through an internal review before they can submit a grant application. In both internal and external reviews, it may not go down well with your colleagues/peers if you regularly submit low-standard grant applications, resulting in reputational damage.


Segregation rules for females studying in Saudi Arabia

I myself study as a PhD student in King Abdullah University of Science and Technology (KAUST). It's a mixed-gender university. A single woman can study here without being accompanied by a husband.

It is a graduate-level university, that is, you can study only for Master of Science (MSc) or Philosophy Doctor (PhD) degrees here.

Regarding programs we have applied mathematics, computer science, electrical engineering, material science, Earth science, marine science, environmental science, statistics, mechanical engineering, chemistry, and many others (I'm not aware of all possible fields that are studied here).

You can find more information on the official website (https://www.kaust.edu.sa/en).


Should I accept an invitation to give a talk from someone who might review my proposal?

It's the potential reviewer's responsibility to declare or avoid any conflict of interest, not yours.

If the potential reviewer isn't asked to review your proposal (or declines for other reasons) then there's no conflict of interest.

If the potential reviewer does end up reviewing your proposal and you've declined an invitation to speak at his institution that potential reviewer might hold it against you.

If you do accept the invitation, this wouldn't by itself be sufficient to create a conflict of interest that would prevent the potential reviewer from reviewing your proposal.

Thus I wouldn't hesitate to accept the invitation.


Where can I study what I really interested in as a postdoc researcher?

As a tenured professor you can choose your research area basically as you want (sometimes there may be some pressure from above to go into specific directions but where I am (Germany) there is freedom of research). However you will have many other things to do which can not always choose (particular courses to lecture, administration, meetings, committees...). So it is not like you can do the research you want to do all day.

So, staying where area may not be as bad as you think now: You are assigned to project B now but 1. you may ask to also contribute to project A at the same time or 2. do a good job at project B and then ask your advisor to work on the project you would like.

Personally I don't know anybody who funds his research on some private basis. One guy I know works in some company where his work is a bit close to research and he manages to teach courses at the university and publish papers and books. I don't know if he works part time or not...  In Germany you need the title "Privatdozent" to do so or get a "Lehrauftrag" each term.


Can I use decompiled source code for research?

Using a decompiler, you can work with the restored source code as good as if the authors had made the code available in the first place.

Not even close. Try running the decompiler on a free software program (to avoid any ethical tangles) to see what it generates. The output of a decompiler, especially when run on an optimized binary, is horrendous.

  Is it OK if I decompile the code to do my research?

Legality depends on the jurisdiction you are in. Ethically, my view is that there is no difference between decompiling an executable to see how it works and taking apart a mechanical device to see how it works - both are perfectly legitimate means to learn about the state of the art.

  If yes, then how do I deal with the fact that I decompiled the tool in my paper? Would it be considered rude/sketchy to say that I did it?

I don't see how it could possibly be rude. Your paper should accurately outline your methodology, so I would say you ought to include this information.

  Can I make the modified tool available to other researchers (and yes, as executables and/or source code)?

No, as it would clearly be a derivative work. As you don't have any license to use the original work, I think this would be illegal in most, if not all, jurisdictions.


Must I list my committee members as co-authors on a manuscript after being dismissed from grad school?

Unless they made scientific contributions, do not list them as co-authors. Proofreading and grammar help is cause for an acknowledgment, not co-authorship. If they contributed scientifically, then you have an ethical obligation to list them. If it is a borderline case, I would err on the side of not including them, given that they basically fired you.

You do need to list that institution as your affiliation. Even though you are no longer there, they funded you while you did this research (presumably) and deserve to have the attribution. Further, your contract may require this.

Edit: there was a (now-deleted) follow-up question about whether it's necessary to seek permission to acknowledge someone. My gut feeling is no, but check out: Is it necessary to ask permission before including someone in the acknowledgements of a research paper?


Some questions about math postdoc offers

Here's a little more detail about timing of math postdocs offers, since that seems to be a particular focus of this question.  What I'll describe applies only to research-oriented postdoctoral positions offered by mathematics departments in the U.S.  Tenure-track jobs and anything teaching-focused are on a somewhat different schedule, and positions outside the U.S. may be totally different.

Everything is synchronized by the AMS common deadline, because most or all of the top candidates (depending on how strict your definition of "top" is) will have accepted offers by then.  In particular, just about every position will have been offered to someone by then, but many of those offers will be turned down.  Most departments will not set an earlier deadline than the AMS deadline, but they nevertheless encourage earlier decisions if possible.  When a position is turned down, a competent department will try to make another offer as quickly as they can.  Who gets the next offer depends not just on relative rankings of candidates, but also on factors such as research specialty and game-theoretic issues such as perceived likelihood of accepting the offer.  Administrative dysfunction may limit how quickly offers can be made, but it's not uncommon for a department to go through several rounds of offers in January.

In practice, it seems to work out more or less as follows:

A few people get offers in December, but this is rather unusual.  You shouldn't worry at all if you have no offers as of January 1.

The people perceived as top candidates generally start to get offers in early January.  If you make it a couple of weeks into January with no offers, then you probably aren't going to end up getting tons of offers, but you shouldn't feel discouraged.  All you need is one offer you're happy with.

As January progresses, more and more offers are made.  Quite a few candidates, but certainly not all, will get an offer in the second half of January.

If you do get an offer, you should immediately do two things.  First, you should withdraw any applications to (or turn down offers from) places you are no longer interested in, so they don't waste time and so you don't tie up offers someone else is waiting for.  It's reasonable to hold onto several offers at once if you genuinely can't decide between them, but you do this only when truly necessary.  Second, you should write to any departments you would prefer to your current offers to let them know about your upcoming deadline.  The competition may increase their interest in you, and in any case they need to know they'll miss their chance at you if they don't move fast enough.

If you haven't yet received an offer, the second half of January is a good time to make inquiries.  You can do this yourself, but it's sometimes better if your advisor looks into it.  (All you can do is express interest, but your advisor can put in a good word for you and try to find out how things are going through back channels.)

As the AMS deadline approaches, there's a flurry of activity.  Many offers are turned down or accepted around then, and departments are eager to get their favorite candidates before they accept another job, so there's a lot of turn-over for offers.

If you make it past the first week in February without an offer, it's a bad sign.  It's certainly not a disaster, and plenty of strong mathematicians have gotten offers later than that.  However, this is the point at which you need to start taking action, with your advisor's help.  You need to figure out which positions are still open, and make sure they are aware that you are still interested.  It's really useful if your advisor can work his/her contacts to help figure out what might still be a possibility and to make sure you don't fall through the cracks.

The more times passes, the more you need to actively search for a job, rather than just waiting to see what happens.  If you hit March, then you're in trouble.  You can still find a job then, but you need to be open to possibilities you weren't originally hoping for.  For example, there are often late job postings for unpredictable openings, such as a temporary replacement for someone on sabbatical or leave.  In March, you should be applying for every new opening you would be willing to take (and you should have a backup plan for what happens if you don't get a job at all, to help you decide where to draw the line).  This is also a good time to review options with your advisor.  Could you delay graduation for a year, or spend the next year as a lecturer?

I don't mean for this to sound discouraging.  It's certainly possible to get a job quite late in the season, and you might even get lucky and find a really good job.  However, I think it's worth having an overview of what the plausible outcomes are at each stage.

TL;DR: If you are hoping for a research-oriented postdoc in math, don't worry until late January, worry somewhat in February, and worry a lot in March (but don't panic).


Having Public Consumption on my record to greatly affect my PhD applications?

I would do everything I can to prevent this going on my transcript. The first thing I would do is write a letter of apology to the cleaning crew for my misbehaviour. Do not approach the cleaners directly, but rather through their boss. Then I would contact the head of the MS program to explain what happened. While waiting for that meeting I would schedule a meeting with an alcohol counsellor so I could demonstrate I do not have a problem drinking. You may also want to enrol in a workplace sensitivity training course.

I cannot recall seeing an application with anything like this before. I don't think people would really hold it against you and you could explain it in your cover letter. That said graduate school admission is competitive.


How far back should one go in citing classic works?

The ultimate question is what would the average well-informed bachelor's or master's degree-holder in your field be expected to know.

Something that comes up in an undergraduate textbook, or is a commonly known and easily demonstrated fact (for example, the definition of the error function), probably doesn't need to be cited, because everyone in your field would be expected to know it. On the other hand, if you're publishing in a "general interest" journal, then you might want to assume a lower "base" of knowledge, and cite a commonly available source.

However, if it's something that's a very specific tool or fact (or a derivation, etc.), then it probably merits a citation in any case.


Solo publication in a low-rank journal or co-authored with a famous professor in a high/medium-rank journal?

Technically, this probably isn't an answer, but information that I hope will be valuable to you in your early career.
It isn't really a matter of either-or, here. But, you want to publish "good" papers in "appropriate" journals working with "helpful colleagues" when possible. What is "better" is better papers, actually.
Publishing low quality papers, in whatever journal, does you little good. The "fame" of a co-author might actually cloud your participation/contribution and might, when taken to the extreme, result in misconduct: i.e. "gift" authorship.
But collaboration is good. Not because it "puts points on the board" (which is IMO a foolish quest) but because it leads to better papers, deeper insight, and the faster advancement of a field. The collaboration can be, and usually is, among peers, though student/advisor collaborations are also common.
So, the advice is to write the best papers you can, collaborating as appropriate and as valuable, and submit to the best journals that you can. Think more about the fun of research and the advancement of the field and less about "winning" some imagined game.
Write a lot of good papers, singly or in collaboration, send them to good journals and your career has a good chance to succeed.


How can I up my confidence level in my technical skills?

My advice is to focus less on the abstract unknowable questions "how good am I?", or "am I technically skilled?" - and instead focus on the concrete things which you've actually done. Focus on the achievements you made in your education. If you like, make a list of all the problems you solved and things you did in your PhD. When you get asked questions in your interviews, don't think about whether you are "good", just think about all the things you did and (metaphorically) give the interviewer that list, and let them judge for themselves if you are a good fit. The other clear solution to having nerves during interviews is simply to do a lot of interviews. Try to schedule some "easy" ones early, so that when you get an interview with a company you really want to work with, you have a bit of practice under your belt. You can also of course have mock practices with your colleagues and friends.


What happens if your manuscript is accepted as a filler?

Yes, this is different from being accepted for publication (instead, it's closer to not rejected).  It means they might publish it soon, they might publish it at some point further in the future, and they might not publish it at all.  I have no idea what the statistics are, and they may vary depending on the current editor in chief.

Here's some background:

The Mathematical Association of America publishes several widely read, high-quality journals that focus on exposition rather than original research (most prominently the American Mathematical Monthly).  There's a lot of competition to publish in these journals, which means they reject many submissions, including almost all submissions to the Monthly.

The Monthly has a tradition of using short, interesting submissions as filler (and I think other MAA journals do as well, but I'm not certain).  This tradition arose in the print era, when it was more important to ensure that the number and layout of the pages came out right, and it has continued since readers enjoy the filler and there aren't many good places to publish pieces like this.  The filler articles are generally not considered particularly important, and they are chosen to fill the available space, to complement the main articles, or just because they caught the editor's eye.

So why would someone allow their submission to be used as filler?  One reason is that there may not be other good opportunities for publishing it, but I think the general reason is that the author doesn't consider it a big deal.  The typical filler article is short and entertaining, but not a major part of the author's career.  If your submission really matters to you, either because you would feel insulted to see it used as filler or because your career would benefit from having it published soon, then the filler archives are probably not a good place for it.  (You might get lucky and see it published immediately, but probably not.)


Can I publish an article or thesis about my research without supervisor?

You definitely submit a paper by yourself and if you write a high quality submission, it will be accepted.

When I was early in my research career I found it very helpful to have a collaborator such as a teacher/professor or a postdoc student with publishing experience to collaborate on papers. This often helps catching points or issues that you may overlook within your research as well as providing advice and guidance.


How to quit/put on hold a PhD program due to personality clash with advisor?

Five publications? Good God, you deserve a PhD more than me and anybody else I have known. FábioDias is absolutely right. I know of an identical case where the advisor wanted the student to do more work after six years and four publications...and refused to fund him AND wouldn't get him a TAship. He finally, talked to the graduate chair in our department. He was ready to go to the department chair and even the dean of the college...but it didn't come to that. The graduate chair immediately took charge, switched his advisor, emailed his thesis to three other faculty members to judge if his thesis was sufficient. He scheduled a defense. Half of the department (students and faculty) showed up. The abusive advisor was also present because he was kept as part of the committee, he was just not the chair nor the "advisor". He successfully defended and even the abusive advisor passed him.

He defended and left within a month.

You have done a lot of work and invested a lot of time and you definitely deserve your degree if you have so many peer-reviewed publications. I wouldn't recommend taking a leave because only rarely I have seen someone coming back after a break (whatever the reason may be for the leave) and finishing. And as you said, it will have financial complications and NSF wouldn't like it very much. In addition, would you quit your job a year later to come back to school? Or work part time? Start fresh with a new advisor, or continue the same project? Will you spend another four years with the new advisor? I would say that finish this as quickly as possible in your own favor. And how specifically would an email to the department chair reach the advisor first? Does he or his/department's secretary play golf with your advisor?

I would say, without writing anything, just drop by the office of the grad chair. Talk to him first. Tell him everything verbally. You should think very hard before putting anything in writing as in an email. Ask him for help. See what he does. If he takes control, then good. Otherwise just drop by the department chair's office and talk to him. This also avoids the danger of your advisor seeing your email first because there never was an email.

At the very end, I would compose a very careful email and send it to the dean of the college and/or the dean of the graduate school, making sure to CC both the department chair and the grad chair.

These are all different levels of escalation. You should start at the bottom, give them a fair chance and a reasonable amount of time to resolve this in good faith. But if it doesn't work, then don't be afraid to escalate it to the next level and repeat.

If you want to take it even further, there is the division of student affair and conflict resolution which is usually under the chancellor or the vice-chancellor. There is also the ombudsman office. At the very end, I would talk to the legal counsel at your school. In the US, even the hint of a possible litigation can have miraculous effects. The school's counsel will of course look out for the school but they might convince the school/college/department to behave rationally because the bad publicity is not worth a grad student.

I'd say hang in there. Research these offices in your university. Read up on some of these policies. Be reasonable and fair but also firm and assertive. I know you have put up with so much abuse but you have to start at the bottom and move up fighting for what's rightfully yours.


What is the most likely cause of short, quick, and useless reviews?

The basic idea is simple: reviewers have no incentive to write good reviews apart from their desire to see the conference succeed. Seeing an abundance of short, superficial reviews with a high acceptance rate indicates a low quality conference.

An alternative explanation might be that this is a non-archival conference, often referred to as a workshop. In that case reviewers mostly care about the general problem the paper presents and whether it sounds interesting/relevant. Program chairs are usually those who go through the papers to see what fits (and there’s a small number of submissions).

If it’s not a workshop, the program committee/organizers aren’t well-respected researchers, and they charge you a lot of money in registration fees, I’d consider retracting.


A PhD program recommendation fell through. How do I deal with this?

Get another letter. Grad app deadlines are many times not as strict for letters as they are for your application materials.


I did an MS in math.  My tuition was waived and I received a stipend that was enough for me to live on (albeit very cheaply).  In return for this I taught one class of either business math or college algebra every semester I was there.  I think everyone that was there with me at the same time was on the same deal.

It shouldn't be hard to get this information from the school or schools of your choice.  If they have a program like this they probably recruit for it.

This might be different from what you are asking, since it more or less involves working for the money, but for anyone that needs a way to pay for a Master's degree, this is definitely a way to explore.  I can't say how common an arrangement like this would be outside of mathematics, however.

You should contact the school(s) you are considering attending and find out what kind of arrangements are made there.


How do you come to terms with the fact that you might never be among the best in your research community?

If every swimmer were to compete with the latest 20 year old Olympic gold medalist, they would soon give up. That's why we have different leagues. They provide more relevant frames of reference to compare different athletes. Thus you need to:

Shift the frame.

Adjusting a bad frame:

You are a PhD student who completed some regular college and an outsider to your field. But you are comparing yourself with your supervisor and with "the brightest kids" in the world and, what is more, with scientist who specialized in your field from the get-go. How can that not be disappointing?

What about: You are an up-and-coming young researcher with real-world experience and a background that is not the usual run-of-the-mill in the field you are working in. You have an amazing supervisor who trusts your work and you are at least as successful as the other PhD students in your cohort. Perhaps you are the only one from your college who made it to graduate school in the last couple of years. You still have plenty of time as a researcher to develop your own profile according to your interests. Don't be fooled by the impostor syndrome.

Dropping a bad frame:

Never mind what I said in the beginning. Science is not a competition -- at least it shouldn't be.

If you're doing research mainly to outcompete your colleagues, to improve your social status, to feel pleased with yourself: you're doing it wrong. Then you are extrinsically motivated, and this is neither sustainable nor does it make you happy. Have you ever delved into a problem and forgotten to drink or eat until the sun went down? Have you ever felt deeply frustrated because you just couldn't wrap your head around some strange finding, only to realize later that it completely makes sense when you look at it from a different angle? Experienced the enthusiasm that came with that discovery? Do you deeply feel that you have to understand this? Then you know the feeling of flow that really only comes from intrinsic motivation. Forget the competition; enjoy the game.


Can I still ask my prospective advisor (guide) for a confirmation letter in the middle of Covid-19

It is fine to ask. Life goes on as best we can manage. The situation is worldwide, of course, and we don't yet see the end of it.

In a letter, you could, if you wish, say you are sorry if the request is coming at a bad time and that you understand the global situation.

You may not be able to get a reply in time, of course, or at all. But there is no problem asking. There is only a week left.

And note that people will want to start up as normal again as soon as the situation allows. Things may be delayed.


Are there general guidelines for order of front and back matter sections in a thesis?

One of the wonderful things about your thesis is that it is one of the few documents that there is very little constraint on how you are allowed to arrange it.  Once you have satisfied the university's formal requirements (of which there are often few), it is up to you (with, of course, the consent of your advisor).  So arrange things however you feel makes the most clear and accessible presentation, and it will be OK.


Applying for PhD as a transferred undergraduate: do I need transcripts from my previous institution?

They will probably ask for it.
That being said this is a question for the institution you are applying to. Send an email or call their graduate college to figure out what is necessary in your particular case.


How common is it that professors have their students write textbooks?

Amongst the number of professors I have known who wrote textbooks, I have never known this to be the case.  Of course, I have only a small sample...

I have however, known professors to trial run their textbooks on the students in the appropriate class.  I would consider this entirely reasonable and appropriate, as in many cases it would probably be more accurate to say that, in fact, the textbook is a condensation and evolution of the lecture notes of the course that the professor has been developing in any case.


Terminating with Master's after several years in a PhD program. How to indicate on CV/Resume?

Personally, I would just put the M.S.  People might assume that you were working towards a Ph.D. and decided to leave with a Master's, or they might assume you were working on it part-time; if you think it is important to distinguish, then you can mention it in a cover letter.  But I would guess that, while dropping out of a Ph.D. program might not necessarily look bad, working towards a Ph.D. that you didn't complete isn't something you want to put on your CV.

(Disclaimer: I've never been in a position where I have evaluated people's CV for hiring, so this is just my guess).


Google Scholar Syntax quirks: results depend on order of search strings

If you want to use google scholar as a means of measuring the number of papers on a certain topic: don't.

Contrary to what we often see in reviews or other publications, you did some more research than simply copying the number of results from a naïve search, and that research indicated that this number is highly unreliable (as should have been expected). Conclusion: Google scholar is not the right tool for the job. Its algorithms are unknown, and the sources it searches are unknown as well. Maybe it even counts the same paper multiple times, depending on which words you search for, who knows?

Having said that, in practice nobody really seems to mind an introduction stating "a Google search for XXX returned N results", but the question remains how useful such a statement is, given your findings.


What to use instead of academic 'we' when describing an experiment?

The use of the authorial 'we' is very common in academia even for single-author papers, as argued by many and properly referenced in the other question that you mention.

Personally, I would keep 'we' also for the thesis without bothering. I doubt anyone would misunderstand, but if you wish you can include a quick remark in the introduction: something like Despite the use of the 'authorial we', common in academia, this thesis is the sole work of its author. In many cases you are required to state that you are the only author anyway in some boilerplate forms in the front matter.

This looks much better to my eye than changing every sentence to a contorted passive form. Readability matters.


Master thesis is reaching a dead-end and supervisor doesn't seem to understand?

I'm halfway...through my masters thesis and the problem involves using a few open source software libraries to the analyse data[, which I've completed already, what should I do for the next three months?]

You could analyse the data using different techniques, draw conclusions from your analysis, ...

  [My supervisor wants me to] explain why it performed so well, but [this is well-known].

Perhaps your supervisor wants you to demonstrate that you understand the well-known method, i.e., to explain the statistical model, the algorithm, etc.

  I am just stuck and worried on how I was going to write a thesis on this.

You haven't mentioned the requirements for your thesis (they vary between universities). Perhaps you can edit your question to expand upon this.

  my supervisor still wants me to go deeper
  to find a link, even though there may not be one.

Discovering the absence of a link is a research contribution (albeit, such research isn't considered so highly)

  Should I ask an [administrative] supervisor for advice?

I don't see how an administrator can help.

  Should I just stick it out and develop a weak link between those two?

That's one direction. Alternatively, find a better direction (and negotiated with your supervisor that you'll study that).

  Should I swap projects to something more experimental where at least
  the results are original since it was self-measured?

Your halfway, swapping projects would be risky. Perhaps you can perform experiments on your data?


My grade was penalized because of a technical problem. Who can I contact?

I fail to see how a teacher could give you what you want, while remaining fair with respect to all other students.

I taught a course where I made clear from the start to everyone that late submissions would not be graded and would not receive any points. Around one deadline, one student decided to take a holiday in Portugal, which is located one time zone to the west of most of Europe. They submitted their homework three minutes before midnight in the Portuguese time zone, which was 57 minutes late in our time zone.

If I now stretch up the rules for this student, why would any other student ever take my red lines seriously anymore? Moreover, other students who remained in the central European timezone may have missed the deadline by, say, ten minutes, and just decide not to submit given that I had been clear that late submissions would not be graded. If a professor writes down a hard, clear rule, they cannot make technical exceptions for that rule without un-leveling the playing field. It would be unfair to other students, to make an exception for you.

It would be different, if the university's online course tracking system to which you allude, has a formal role in the examination regulations. If there are university or department regulations that stipulates that the system administrates, then you might be in your rights. But barring that, the teacher sets the rules, and is responsible for upholding them in an objectively fair manner. Objectively fair would be to not grant you the technical exemption that other students would also not be granted.


Assistant professor position in the USA. Can any leftover startup money for equipment be used to pay students or my summer salary?

This varies not only from university to university but from department to department. In some places it wouldn't be a problem, and in others it may even be impossible.

I recommend you get in touch with whoever your point of contact is (whoever extended you the offer) and ask them directly. It is important that they know you want to do this as this will naturally affect how much startup funds you are liable to need.


Can I disclose a conflict of interest with some professors from a particular university in responding to comments?

I'd advise against such a move, which can be seen as a way to avoid a complex revision.

Usually, at the time of submission, journals allow the authors to specify non-preferred potential reviewers, either directly through the submission management system or through the cover letter. If you think that someone can be strongly biased against your work due to a conflict of interest, that's the time to voice your concern, not after the review.


Any risks down the line choosing maths vs. stats PhD programme?

Provided one can find a supervisor who has the background and research interestes that would allow one to keep extending ones pure mathematical toolbox are there any major risks in going for a PhD in stats?

There's a small risk, but it can be managed.  The first issue is that you need to make the mathematical content of your work very clear, for example by publishing in journals that could be considered both math journals and statistics journals (e.g., IMS journals).  However, if you're interested in math departments I assume you'd be doing that anyway.

The slightly more subtle issue is how mathematicians view statisticians.  There's sometimes a mild prejudice that people in mathematical statistics are overly specialized and outside of the mainstream of mathematics.  For example, it's possible to get a Ph.D. in mathematical statistics while having considerably less breadth of mathematical background than would be considered acceptable for a math grad student.  (Of course, the flip side is that you are expected to know other things instead.)  There's sometimes a fear that a statistician would be unlikely to talk much with other math department members, or might be unwilling or unable to teach anything but statistics.

Plenty of statisticians have found jobs in math departments, so I don't want to be discouraging.  However, I'd recommend focusing on mathematical breadth.  For example, if you work with people in combinatorics or algebra, then it will be clear to everyone why a math department is a natural fit.  If you talk only to statisticians, it will be less clear.  It can still work out even then, but generally when the department either has a thriving statistics group or has decided they really need a statistician (and either way this cuts down on the flexibility of your job search).


I think that this can be clarified with a thought experiment.  Let's say that rather than observing a Twitter conversation (or other social media), you were part of a three-way discussion with the two experts in the hallway at a conference.  During the course of the conversation, some key facts and sources are mentioned, and this inspires you to look them up.

Would you cite the hallway conversation?  Absolutely not.  At most, you might mention your source of inspiration in an acknowledgement, if it was particularly important to your work.

Likewise, I think that you should feel no obligation to cite a conversation that you observed on Twitter, which is effectively the same thing in an electronic hallway conversation.  (You can, of course, cite Twitter as a primary source, e.g., if you want to give an example of Twitter conversations, but that doesn't seem to be particularly germane to this question).


Can I have two system models in the same paper, for the same research?

Yes, you can. But be sure to follow the common structure of a scientific article. That means that you have to have 2 subsections at least on the procedure section (AKA materials and methods) as well as on the results section and on the results discussion. These sub-sections are those related to your 2 systems.
I would conclude about the paper as a whole. Also, be sure that your introduction states at the end the interest of studying two separate objects: if the first object is more general, is the idea to apply the methodology to a smaller system in order to validate it. Or is it the idea to get a generalization of the findings obtained for the smaller sub-system? Usually the latter is widely better accepted. In that case, you should put the smaller sub-system first.

I hope I have helped you,
Cheers,
Miguel Andrade
Mechanical Engineer,PhD


How to review similar academic papers for a literature review?

It looks that it is an example of two independent studies that obtained similar results so you might comment that this reinforces the claim that the reported results are correct. However, most probably the studies weren't exact replications so it might be good to mention the differences between the studies.

It is also a good idea to investigate the journals they were published in - maybe the earlier paper was published in some obscure journal and the second one appeared in a high impact factor one? Have you looked at 'cited by' numbers (in Google Scholar)? Which paper got more citations? Maybe there are some publications that mention both papers? This might give you a clue how the community finds both papers and which one made more impact. It is also plausible that one paper got bigger publicity simply because of more known authors/research group.


Referees ask for more content but this lengthens the paper dramatically

First, share your concerns with the editors. The reviewers may not have realized the extent of the work. If they agree that a long paper is fine, then write the long paper. If they don't want to do that then consider breaking the work into two papers with one referencing the other. You could even submit them simultaneously to the same journal.

But it would probably be worth checking that with the editors also. I'll guess they would consider that to be the better solution, but it is their call.


Is it OK to use bullet points in the statement of purpose for graduate school applications?

Both Buffy and JoshuaZ raise valid points:

One of the things that [some] reviewers will be looking for...is your basic writing ability.
The reaction [to bullet points] seemed to be all over the place. One person thought bullet points stood out and were great. Another considered it to be unprofessional.

I'll add: Used well, bullet points can convey your message succinctly, which is a skill reviews are looking for. Used badly, they suggest a poor writing style. You, yourself, can perhaps determine whether bullet points are working. Give it a try. You can also ask people what they think.


First: the usual (read: boring) way of writing academic paper titles is indeed without verbs:

  A study of acquired growth hormone deficiency
  and hypogonadotropic hypogonadism in a subject with repeated head trauma

or using gerunds (which is a verb form, but in that case is used to construct a present progressive but a noun phrase):

  Understanding acquired growth hormone deficiency
  and hypogonadotropic hypogonadism in a subject with repeated head trauma

However, I think include a verb is possible, and oftentimes makes the title much catchier and appealing to the non-specialist reader. For example, the titles I “quoted” above are of my own making, but the real title for the article (and believe me, you want to read it) is:

  Acquired growth hormone deficiency and hypogonadotropic hypogonadism in a subject with repeated head trauma, or Tintin goes to the neurologist

There: even if I know nothing of “acquired growth hormone deficiency” and “hypogonadotropic hypogonadism”, I know what the paper is about.

Now, if you use verbs in article titles, they are mostly going to be about established facts, generic questions, mathematical proofs, … which means you should write in the present tense.

  Vitamin C enriched diet can prevent scurvy
  Minesweeper is NP-complete

I particularly like to use questions in titles, as they make quite clear the problem you're tackling:

  How hard is the measurement of quartz hardness? A review of the commercial available apparatuses and their robustness
  How fast does the swallow fly? Reexamining the impact of the bird's geographical origin

In a few cases, you would talk about a historical event, and then you'd use the past tense:

  How World War One was won: the role of time travelers from the twenty-second century
  The CERN measurement was not a fluke: finally establishing the Higgs discovery at the 10-sigma level


Mathematician John B. Conway has written a book: On Being a Department Head, a Personal View.


Supervisor insists on writing a manuscript, yet procrastinates on writing for years

In my opinion, if your career is dependent on publication, which is most often true in academic settings, one should just "keep on writing" regardless of conditions.

Due the time the superviser delayed the writing, if you would have parallely kept on updating the manuscript, two things would have happened.

Supervisor does not write:
You would have your updated manuscript as a factual proof that you can manage to writ the manuscript by yourself. May be then supervisor may back down and allow you to writ the manuscript. This would be a very helpful exercise for you because writing is arguably the most important and challenging skill in academia. You would get an opportunity to improve your skills further through practice. In future, that would indeed would help in your career.
Supervisor does write:
Your parallel updating of manuscript would only accelerate the writing process. The supervisor may probably feel a sense of competition (!) and may do write the manuscript.

Both cases would have been eventually beneficial for your career. So I would say just "keep on writing".


Language of reference entries for sources in a foreign language

Citations follow templates, e.g.,

  A, B, & C (YYYY) Title. In BookTitle, volume X, pages xx-yy.

To cite a particular work, you fill-in the place holders, e.g., A, B, C, YYYY,  Title, BookTitle, X, xx, and yy. Hence, words such as "In", "volume", and "pages" can remain in English.

When a template does not specify how to include translations of titles/booktitles, I think it is reasonable to include bracketed translations, e.g., original title (translated title).


How to explain an unofficial research sabbatical on my CV?

Given that it sounds like the university was aware of your plans to come back and seems to have kept your original faculty position for you while you were on sabbatical, you don't have to list this as separate employment. Sabbaticals are well understood within the academic field; listing it separately is just confusing things.

You may want to put the sabbatical as a sub-bullet under your academic position on your resume just to emphasize that (1) you're a cool enough person that your university allowed you to take sabbatical (and held your position for you until you came back), and (2) you have experience doing research outside the university setting.


How do junior faculty in the U.S. normally address senior faculty in emails?

In my experience in the United States, most professors invite even their graduate students to call them by their given (first) name.  Junior faculty would be no less invited to familiar address.  Whether you say "Hi, Name" or just dive into communication is often a matter of personal style and communication medium---for example, emailing from one's phone often has much terser communication, and this is generally understood and not taken amiss.

Just because you are addressing somebody by their given name, however, doesn't mean you are actually an intimate or a peer.  Many senior faculty in the United States will still expect deference by junior faculty; they will just expect it to be shown by the tone and actions of interaction, rather than merely the formality of address.


Importance of the current postdoc advisor's letter in TT job search

In my view, strong letters are extremely important. You certainly don't want any letters from people interested in sabotaging you in any way. Even poorly written letters can be a setback. So can letters written by non-native speakers who may not grok the nuances of certain phrases.

There is the concept of Damning with Faint Praise that can be absolutely deadly in a letter. It can be intentional or not, actually.

Get letters from people who know your potential and are willing to speak for it. They need to know about your past work, of course, but people will be looking for potential and how it relates to a particular position.

If you have any doubts about what a person might say, ask them about it, or go elsewhere. In certain situations (non-native speakers, say) you might even request that a letter writer check their letter with a neutral third party, such as a department head. This would have saved me tremendous grief long ago.


I am so tired and un-focused in my postdoc. Is quitting my position a good choice?

It takes years to get over getting a PhD. It sounds like you are having a more difficult time than some. A therapist might be able to help with the issues. At a minimum, tell your supervisor what is going on. You talk only about your work, but you need to think about how the change of city is effecting you personally. Are you living in the lab, or do you have new friends? Often during the PhD process we drop social activities that we enjoy, it might be time to start these up again.

Now that you have a PhD and a Postdoc, it sounds like you are in it for the long haul. The key is to make sure you balance the personal and work aspects of life.


Why do people do postdoc(s) when they can already do research as a professor?

Because the requirements for the majority of professorships are such that very few people can be considered serious applicants right out of their PhD.

Also, the number of PhD holders looking for a professorship far exceeds the number of available positions which creates a "backlog".

The two are obviously correlated since the higher the demand to offer ratio, the pickier the institutions can be.

So even in the case where people developed the necessary skills to conduct professor-level research and teaching during their PhD (which should not be underestimated, that level usually requires more experience than what a typical PhD can give), they usually need to spend some years conducting independent or less closely-mentored research along with students mentoring and teaching as a postdoc until they can secure a position.

Note that the majority of postdoc researchers never get a faculty position.


Judging from your comment, this publication approval letter is supposed to show that your supervisor approves of the publication (i.e. that your supervisor is aware of the publication and has no problems with you publishing it). You'll have to ask your supervisor for it.


Is there such a thing as too much work for a Master's Thesis?

It is not clear how to judge the "size" of a thesis (page length or word count is probably not very good), but one can clearly do too much research for a Masters or Doctorate. That said a factor of two difference is not really that big since there is always going to be a healthy overlap between the "largest" Master thesis and the "smallest" PhD thesis. If your Masters thesis is larger than the average PhD thesis and larger than the vast majority of Masters theses, then it is possibly too large.

As a student you need to be asking yourself why you are getting the qualification. Most students put in much more work than that which is required to simply graduate. You should make sure you push your supervisor to help you achieve your goals.


People usually add press coverage in a note after the publication eg
C. Xavier “On Human Genetic Mutation”, thesis, 1975
Press Coverage: CNN, BBC

Etc


How to decide whether a statement requires citing a reliable source

Yes, there are rules on what requires citation.

Generally, publicly-known information (widely known, common knowledge, etc.) does not need to be cited. Your sentence about Java being class-based would fall under this category.

Information which is based on someone else's work (analysis, research, pictures, etc.), whether quoted or paraphrased, should always be cited. Your sentence about Java being x time slower/faster than C++ would fall under this category.

If you are unsure, cite it to be safe.


reviewing other articles for a conference

Welcome to conference reviewing.  Your situation is unfortunately extremely common.  If the number of submissions in area X is less than the number of reviewers with interest and expertise in area X, then inevitably some of those reviewers will be assigned papers in area Y.  Symmetrically, if the number of submissions in X is more than the number of experts in X, then some of those papers must be assigned to reviewers who'd prefer Z.  Ideally, most papers are reviewed by experts and each reviewer is assigned mostly papers in their areas of expertise, but sometimes the matching system breaks down.

By default, you must review the papers that you were assigned.  But there are a couple of ways to address mismatches.

If your assignment looks like a complete mismatch, you should quickly contact the PC chair and express your concerns, and in particular to verify that they received your preference email.  If you're early enough in the process, the chair may be able and willing to swap assignments with other reviewers with complementary mismatches.  There might also be a mechanism to swap assignments directly with other committee members, but you should always get the PC chair's permission before actually swapping.
Most computer science conference review forms ask for your confidence in your review; fill in this field honestly.  If you really don't have the expertise to understand the paper or make a recommendation, your review should read "I apparently do not have the expertise to understand this paper or make a recommendation."  That's a damning review of both the paper and the assignment process, but that's okay; your job as a reviewer is to be respectful but brutally honest.

On the other hand, as a matter of simple self-preservation, you should not review papers that you were not assigned.  Reviewing well is extremely hard and time-consuming, and you have many other demands on your time.  (And reviewing badly should just not be done at all.)  Generally speaking, doing extra unsolicited reviewing will not earn you additional credit or brownie points.

There are a few exceptions.  If you see a paper that you plan to read in detail anyway, despite getting no credit for doing so, you might as well write a review.  And if the initial reviews of a paper disagree, the PC chair may seek out additional input or even full reviews; if you're asked about a paper in your area of expertise late in the review cycle, you should help.  (If you're asked about a paper outside your area of expertise in later rounds, you should just say no.)


Weightage of a review paper on an undergraduate CV

Yes, it holds a weight.
How much? it depends on the sensibility of the Panel, if no hard-rules are set.
Maybe 0.5 times the weight of a regular paper, because it is missing the novelty? Or maybe 1.5 times the weight of a regular paper, because if you took part in the review, then you already are updated about the State-of-Art on the topic and it can be very relevant to your PhD?
In absence of hard rules, it depends strongly on how you frame it. Be smart.
Then of course it has not much weight in the CV, if it is a 10 years old review paper: in 10 years the SoA changed a lot ... and if did not change much, you can publish an update of the same review paper, updating the content.


Should I write a "proof" to a professor I don't know?

The significance of your additional work is unclear. Have you talked about this with the professor that teaches your class? (s)he – or another prof in the department – should be involved if you want to take this further.

If the additional work is significant enough, you'll be perfectly within your rights to write and publish your own paper that presents the results. Trivial results usually aren't publishable on their own, but if it's a novel approach then it's certainly doable. The original work is old enough that you need not worry about "scooping" the original authors' results. Just make sure to check that a solution to the problem hasn't already been published elsewhere.

In any other case, there shouldn't be any harm in sending an email to the authors (whether or not they will respond is another matter). Don't send the solution in your first email! Just inform the authors that you think that you've solved the problem, and only send them your solution if they agree to let you co-author any publications that incorporate your results. Intellectual property rights are a tricky business, and you should always ask for the help of a professor when doing things like this. The paper's authors will also be much more likely to take notice if the first email is from a well known professor, rather than an unknown grad student.


Research plan vs proposed research for class project?

In general a research plan will include within it a section that deals with the proposed approach. As this University of Michigan page explains:

  Research Plan (Approach)

  This section includes a comprehensive explanation of the proposed
  research, and is addressed to other specialists in your field (not to
  laymen). The section is the heart of the proposal and is the primary
  concern of the technical reviewers. To make it clear and easy to
  follow, you may need several subsections tailored to your work.
  Research design is a large subject and cannot be covered here, but a
  few reminders concerning frequently mishandled aspects of proposals
  may be helpful.

As always, you should talk with your advisor/professor to ensure if this is exactly what they have in mind, or if there is some specific template or example for your field/subject/use that you should follow.


Student wants to show everybody how much he knows

If the student is just overexcited and more advanced than others, then the  question linked above by ff524 has an excellent answer. However, that does not seem to be the case. By all appearances, the student talks to talk, and drops references to superior knowledge - real or imagined - to show it off. I've studied with plenty of students whose knowledge exceeded even advanced classes they were forced to take, and - in my experience - the common reaction of a true talent is boredom or eventually failing to show up, not jumping on stage. The closest case similar to yours failed his qualifying.

Hence, I think your problem is one of learning to assert yourself in a challenging situation. Here are some suggestions for what you might want to try:

Be an authority figure, not a friend. When I was a squad leader at the army, I was an unkissed geek-kid; my soldiers included a drug dealer, coal miners, and someone 10 years older, divorced, 2 children. I've found that, absent natural charisma which I don't have, acting somewhat reserved and distant, while always having an open ear for feedback, was the best way to get through this. When later TAing, I resisted the urge to fraternize and acted similarly, which worked very well for me (in both cases, I was top rated among my peers.)
Create a system of taking questions, and stick to it. This might be simple ideas such as one day taking questions front to back, the next left to right, etc. which - as students tend to gravitate towards seats in a particular part of a classroom - means your problem student will only get to lead a discussion every now and then.
Be professional, but honest about your frustration. If the student interrupts others, or you, first follow the advice of the linked question. I expect it to fail though as your student isn't interested in talking after class when no one witnesses their awesomeness. If it fails, tell them "I'm sorry, there are many questions others have, too, and I need to address theirs as well.(meet me after)" If you can't shut them up, keep eye contact, and say, more seriously but calmly, "I really have to move on. Please allow others to talk", etc.
Seek advice from your professor, as needed. If the person becomes disruptive and unresponsive to your hints mentioned in 3., discuss with your professor, and ask if you can kick them out of a TA session when that happens. Express your concern about preparing the other students properly.
Assume good intentions, and talk with your student. This should probably be point 0. Ask the student if you can talk after your session. Be a bit flattering - interested student, knows much - then point out that others don't, and you really need to focus on them, and their more basic questions, while handling his in 1-on-1s, as necessary. This might clarify if they are acting in good faith and just get overexcited, or not.
Mention that TA sessions are optional, and that no one already having the knowledge taught is judged for not showing up. One of my TAs, stuck in a basic linear algebra II class with a 4-time math Olympics participant (b/s/g/g) who had gone through the entire Bourbaki already did this, and it was the last time the student was seen. If it works as in this case, you might also get a chuckle out of the other students who probably understand what you mean.

There is an additional informal way to address this as well. The next time you catch them being wrong in their aggressive ways, talk them into a corner. If they change topic, say so - "That's interesting, but let's not change topic. I'm really curious to understand what you meant when you said (X - the wrong statement)." Be calm, friendly and insistent, and keep this up until an error is admitted, or they shut up. As their interruption is only to show them in a gleaming light, it might help greatly in making it stop. I would only use this as a last resort though.


Where Can I Get Certified Copies of Documents for Master's Applications in the United States

Option (1) is probably easiest.
It's normal in the US to send official transcripts directly from one educational institution to another. The way you do this is typically to go to your school's website and search "official transcript". You may need to pay a fee or may only need a fee to send more than some number.
Since schools are used to sending these to other US schools I'm sure they are also prepared to send them to Germany. They'll come directly from the university with some sort of seal.
When I was applying for grad school this step at least was still entirely by physical mail; there may be digital options now too.


Can Journals settle all legal processes related to accepted papers before publication on behalf of authors?

This isn't usually done. The authors are assumed to have gotten the permissions themselves. However your question is whether the journal "can". In that case, I'd say the answer is yes. They can, they just don't usually do it. Just about the only possible exception is if the author is a famous researcher and the journal is willing to go to great lengths to publish the manuscript.


What are the disadvantages of opening the source of your own science tools

Some disadvantages could be:

People may expect you to maintain the code. If you don't maintain it, the code may be rendered useless at some point.
You might feel forced to document the code. This is actually an advantage, but many people would not realise that ;)
You might have to work on cleaning up the code. Exactly the same point as above applies, if you ever want to re-use your code this is actually an advantage.
If people start using your code (this is not impossible), they could e-mail you and start asking questions. This takes your time. On the other hand, it also provides you the opportunity to be co-author (so hey! don't document, so people are forced to ask your help ;-)

More points are raised in the very similar question that was asked at Programmers.SE less than a month ago:

Why don't research papers that mention custom software release the source code?


How do I handle academic references for US PhD program, when I have been out of academia for a (very) long time?

In contacting your old professors you might start by reminding them of what courses you took with them and what grades you earned in those courses. It would also be appropriate to supply a copy of your full academic transcript.

I frequently get requests like this from students that I haven't seen in 10 years or more.  I comment on the students transcript and grades in my courses and whatever I can remember about the student.  This isn't ideal, but it's better than nothing.

Another common strategy for students who've been working in industry for a long time is to begin graduate study by taking a few courses on a part-time basis at a local university.  It's much less of a commitment by the department to allow you to take a course or two than it would be to admit you as a full-time student and provide you with financial support.  If you do well in those courses then you can ask the instructors for academic references.


Plagiarism is using the words or ideas of another without proper credit.  So, if you don't give credit, you're plagiarizing.  If you do give credit, you're not.  It is really that simple.

In your particular case, there may be something else at work.  If your professor taught merge sort, and the assignment is to demonstrate that you know how to do it, then you might be in trouble for copying another's code even if you give proper credit; it's not plagiarism, but it still might not be allowed.   As Mad Jack has said in the comments, ask your professor.


Is it self-plagiarism to repurpose a government report into a journal article?

Can I use the same texts/paragraphs from the report to write journal articles? In other words, does it consider plagiarism to do that? I am the author of both, the report and the research papers. Does the final report for a project consider a published work?

The short answer to your questions are it depends. The long answer is likely yes, you can probably publish both with some caveats.

In principle, there is nothing wrong with using a project report as the basis for a journal article. Speaking from experience, I have co-authored several completion reports that were used as the basis for manuscripts. For example, the Great Lakes Fisheries Commission Sea Lamprey Control Broad publishes completion reports on their webpage, but still encourages the investigators to publish the work in peer reviewed journal articles. However, there are some important considerations:

Make sure your funding agency is okay with you publishing their report. On a more positive note, some funding agencies will encourage you to publish.
Is your completion report public and is it citable? You may or may not need to cite your previous work. Mentioning the completion report in your cover letter would also help address this problem with the journal.
The completion report likely will not be formatted correctly or written in a style suitable for a journal. Likely your methods section will be okay and possibly the results section. Most likely, the introduction and discussion will need to be adapted to fit the journal's style and tone.


Whether to mention contributions on Stack exchange in Statement of purpose (SOP) for MS/Phd application in US?

My rough answer would be that you need to convey to your reader:

What SE is.  Many people think of it as a place to cut and paste answers without thinking too hard, but the community side isn't as well known
How to indicate your interest/passion.  The reputation number is fairly meaningless to an outsider.  Possibly a statement like 'contributed daily for 5 years' has more weight.

Personally I'd view it as a plus but not a massive benefit.  It would be more remarkable at undergrad entry to show engagement in the subject, but at masters/PhD level I'd assume you're already engaged.  It does show interest in teaching which could be positive (eg if you're likely to be a TA at some point).

I'd weigh carefully what you convey by this statement against the space needed to convey it: it may be there's a more impactful way to use the space.

[Disclaimer: I come from a UK perspective.  Other countries may be different]


Will Potential Publishers View an MA Dissertation as Plagiarized?

It depends on what you're trying to publish. If you're publishing your MA dissertation as your MA dissertation, then there's no problem. This implies your MA dissertation has never been published before, and the fact that it's available already is unimportant. Preprints are a thing, but publishers happily publish the papers that follow preprints.

However if you are publishing chunks of your MA dissertation as part of some future work - for example, if you took a chapter from your MA dissertation because it works great as an introduction to the next thing you did, and you are trying to publish this next thing - then you are self-plagiarizing. This would be taking something that's already been published and publishing it again, and would not be acceptable.


Is it well-received to thank the assignment author at the end of a course?

Yes, I think it would be fine. Everybody likes to know their work is appreciated. Teaching assistants are often not appreciated enough  by their students (and sometimes not enough by their professors!).

Just a short concise form of thanks would be enough:

  Thanks for those exercises you set for course xyz. They were really interesting, and I enjoyed solving them. I hope you liked creating them as much as I appreciated their contents.

Something along those lines perhaps. If you make it too long it might sound obsequious or sycophantic.


A professor accidentally sent me a copy of my letter of recommendation for grad school. What should I do?

You still need that hardware letter so I guess some uncomfortable situation may have to happen. Yet, I think some awkwardness can be avoided by focusing on the application. I'd suggest e-mailing him and tell him that it appears a wrong attachment was sent to you, and invite him to double check if the hardware approval letter was uploaded to the school application portal, follow by a polite ask for the actual approval document. End with a statement saying that you'll delete his previous e-mail and the attachment, and thank him for his help.

If you have not read it, then delete it. That'd be the best scenario. If you have read part of it by accident, notice that you have done nothing wrong. You simply waived the right to read it; you did not signed a contract to never read it. Yet, don't try to read all of it even it's not your fault, it isn't meant to be for you to read, and knowing the contents may affect you, even you think you can be completely objective.


Do German universities have "ethics boards"?

There is the notion of Ethikkommission (searching for it you will find many hits).

However, this is in my understanding mainly concerned with ethical questions related to research activities, in the sense of question whether a particular research activity is legitimate or if there are ethical or moral concerns against it (rather than academic conduct or misconduct).  To interact with it  is quiet widespread and routine in the life sciences, I think.  In other disciplines it is by and large a non-subject.
For the second quote you link to it could be relevant.

As far as other subjects go  I am not sure if there is a uniform naming or legal regulations, but typically universities will have things like:

Datenschutzbeauftragte or a Datenschutzkommission for issues related to handling of personal data and alike.
Gleichstellungsbeauftragte or a Kommission fûr Chancengleicheit  for questions related to equal opportunities and discrimination.
Behindertenbeauftragte for concerns of persons with special needs.
Kommission zur Untersuchung von Vorwürfen wissenschaftlichen Fehlverhaltens for investigations of scientific misconduct.

Instead of a Kommission it could also be an Ausschuss, or some other variation.

At a university level such committees are often attached to the Senat, but they can exist on lower levels, too.


A PhD is a research degree; it’s a piece of paper that says “this person is a competent researcher”. If you want to go into a field where being a researcher is important (e.g. corporate R&D), then it’s worth your time to get one. If you’re not, it probably isn’t.


Capitalising terms like “machine learning” and “natural language processing”

This question is probably more apt for English Language & Usage SE.

But no, don't capitalize them. They are not proper nouns. Do capitalize "Machine Learning" if it's the name of a journal, or if it is otherwise part of the name of some entity (e.g. the International Conference on Machine Learning), but do not capitalize it when you refer to machine learning as a field.


Central dot as decimal point in top journal

This notation was more common historically, particularly in the British empire. My guess would be that the Lancet, being an old journal founded in England in 1823, is sticking with it because of tradition rather than a really good reason.


When citing in MLA, do you need to cite the same source twice?

The URL in a reference should lead the reader directly to the material you have used and cited.  Unless example.com has only those two items, you should cite each one.


What does it mean when a school asks for a missing GRE score that I submitted?

We can't really answer whether the school you sent is specifically considering you, but there are three main things that could cause them to ask for the score (regardless of how/why they said they don't have it). The key is to understand that graduate admissions (at least in the US) is a compound process involving the department and the graduate school.

In order of least encouraging to most encouraging (for your prospects):

The graduate school may have either a policy that they only pass on complete records and viewed yours as incomplete or the graduate school wants complete records for all applicants for book-keeping.
The department did not have the data and wants it before it begins evaluating applications at all. Good side = this would mean the department is looking at it. Bad side = some departments in some fields use a cut-off based on GRE scores to lop off the most unlikely candidates (obviously with exceptions mutatis mutandis)
The department and/or graduate school is making selections and needs to complete files before sending out offers. Slightly less positively maybe they need this as a tie-breaker to figure out the last candidate.

Obviously three would be great, but often the reasons for these queries are much more mundane.


What kind of help can I request from a terminally ill professor?

Edit: note that my original answer below addresses OP’s original version of the question, which has now been edited.

To address the current version of the question: yes, it is okay to ask for help, but your motivation should be wanting to get help, not artificially creating feelings of “being appreciated”. If you want to let someone know they are appreciated, just tell them that that’s the case. And if you don’t know what questions you should ask, to me that is a sign that there isn’t really anything that you particularly need help with, so the best thing to do is to not ask any questions.

Finally, the fact that you know the professor is ill shouldn’t change anything about the nature of the questions you should ask him. Just ask what you want to know, whether it’s an easy or difficult question to answer. I am confident that if the professor finds the question too burdensome to answer given his illness, he will either not respond or will simply tell you that he is unable to help.

My original answer:

Maybe I’m misunderstanding your intent, but the way your question is phrased (particularly your statement “my main goal here is to make the professor feel appreciated” and the slightly absurd list of hypothetical questions you are thinking of asking the professor) I get the impression that you’re thinking of inventing a fake request for help, that is, a question whose answer doesn’t actually interest you very much, out of the belief that the professor will feel “appreciated” when receiving the question.

If this interpretation is correct, my strong advice would be: no, it’s not okay, so don’t do it. The reason is that this would be dishonest (and somewhat transparently so, for some of the questions you proposed - not to mention that you’re publicly posting your plan here using your real name...). I can’t claim to know what it feels like to be terminally ill, but as a general rule people don’t appreciate other people being dishonest with them, so I think your question could end up having quite a different effect than what you intend.

Here’s an alternative suggestion however: if you want the professor to feel appreciated, why not simply tell him that you appreciate him (assuming that’s correct)? And certainly I think it’s okay to offer to help him in any way you can — again, assuming the offer is genuine and you intend to follow up in case he takes you up on it. It’s also okay to ask him a question if you genuinely want to know the answer, but you should be asking it because you want to know the answer. Please don’t invent questions solely for the purpose of making someone feel appreciated; I find that idea patronizing, offensive, and highly misguided, despite the fact that the intentions behind it are good.


What is the purpose of peer-review in journals?

It's a method to inform journal editors about the soundness of any arguments, their originality, and the correctness of any data used in the submitted work. This enables them to keep a good standard of published work (and helps the authors to improve their manuscript to achieve the required standard).

Thus, it serves as a quality control mechanism. Without it, editors would have to review on their own (which is still some form of peer-review, though not anonymized). This was standard in Einstein's days, but is completely impractical today for three reasons.

The sheer amount of submitted manuscript has grown substantially.
The scientific community is much more diverse with less overlap of personal areas of expertise, such that no single editor can judge more than a fraction of the manuscript they receive.
Allowing reviewers to stay anonymous avoids biases and provides a fairer process.

So, the editors' expertise must now be to find expert reviewers and to interpret their reviews appropriately (rather than being experts themselves as 100 years ago).

Admittedly, the mechanism does not work 100%, i.e. sometimes good work is rejected and sometimes poor work is accepted (depending also on the community and journal), but their appears to be no viable alternative.