What levels of graduate schools can various combinations of GPAs and GREs get you into

I'm presuming that you are referring to PhD admissions in the U.S.?  I should note that GPA and GRE are relatively low on the admissions criteria as far as I am aware.  There are other (more important) factors involved, such as research/teaching experience, statement of purpose, and especially letters of recommendation.
GPA can only help up until a certain point (usually around 3.3-3.7).  Once you are above this threshold, you are better focusing on other aspects of your application.  Especially since PhD programs are all about research and publications, focus on getting as much of that as you can, since this is also how you can get quality letters of recommendation.  I have heard of people with GPA's of 3.1-3.3 getting into top programs (even MIT) because they had research experience or publications.
Also, GRE is one of the least relevant parts of your application (less so than GPA), since it mainly serves as a filter.  Once your score is above a certain threshold, same with GPA, your time is better spent stressing over other parts of the application.  Some schools have stated they do not consider GRE (even before COVID), and because of COVID, while some will still consider GRE, the list of schools that won't require GRE is likely to grow.
HYPSM: your mileage will vary here.  At least in my field (Computer Science), Stanford and MIT are definitely at the top.  However, for Harvard, Princeton, Yale, etc. mileage may vary more, since there are state school programs like Illinois, GA Tech, that are ranked higher.  So it isn't necessarily the best comparison, to compare programs like "good state schools" between "HYPSM"


The main goal, from my experience, is the facetime with many different people. Skype is nice, but it's primarily intended for conversations with very few people. A visit allows students to to talk to many professors and students face-to-face in a short timespan, get to know the place, interact with students in a lab, and get a sense for what the place is like, something which is impossible over the 'net.

Also, this gives the university a good chance to see what the student is like. It's easy to look good on paper and can put on a clean shirt (pants optional) for a skype interview. It's a lot harder to keep up a fake act in front of dozens of faculty and students over a one-or-two day period.


Is three citations per paragraph excessive for undergraduate research paper?

If you are asking whether it is a general "best practice" for a research paper at any level to have three citations per paragraph: no, it is not.  In any level research paper, you should cite as often (equivalently, as little) as necessary in order to inform the reader of relevant prior work.  If seven papers are relevant to what you are saying in a given sentence, you should cite those seven papers.  If in a paragraph you are not saying anything that makes reference to or would be aided by making reference to prior literature, then there should be no citations in the paragraph.  You never insert citations to meet numerical requirements.

However, this is an assignment for a course, so the best practice is whatever your instructor told you.

  The way that she phrased it left uncertainty whether this was for every paragraph, or only for the quoted ones, so the context of whether similar works have this level of quotation in them is the only standard I have to go by.

No, you can ask your instructor which of the above is what she wants.  I encourage you to do so.


Is there a way to edit author name after publication for trans people (at least online)?

I know of one theorist who did the following:

She edited her preprints to use her correct name. In the new preprints she adds a header with the reference to the published version (in the APA style, which is common in her field and also only uses initials of first names).
Posted them to the relevant preprint service (PsyArXiv, in her case). PsyArXiv has fields for two DOIs: a "preprint DOI" and a "peer-reviewed publication DOI". The latter points to the older published version.
She now encourages other researchers to cite her using those preprints and their associated preprint-DOI.


Is it acceptable to write reports in the IEEE standard paper format?

As an EE student, I used to submit reports in IEEE format (if none was specified by the instructor). So yes, it's perfectly acceptable in my experience.

However, some professors prefer more whitespace so they can write comments while grading student reports. I therefore switched to the Springer Lecture Notes in Computer Science format, which has much larger margins.


Do PhD students really publish so committee doesn't have to thoroughly read dissertation?

Some thoughts on this:

It certainly helps the committee if (parts of) the thesis were
already assessed before - along the lines of "If somebody else already said that
this is good then it can't be that bad after all".
It also helps the student to convince the committee that this is
mature enough for graduation (same argument as above).
Some universities allow cumulative theses i.e. introduction + 3*
pdfs of first authorship papers + discussion. (* the number depends
on the field). This is mainly as writing a thesis with several hundred pages is something you will never need again even if you continue in science. Most fields just publish in short journal article nowadays and writing 200 pages about a content that can be covered in 5 pages is not a skill you need (and nobody wants to read these 200 pages (including your committee)) - sounds mean but it is like this.


Should accomplishments be included in a CV? If so, how?

Actually, I wouldn't worry too much about "categories" on you CV. Create new ones as needed. But yes, you should include such things - especially if they have been recognized by others. The bullets you give seem reasonable for inclusion. Perhaps the ones most related to your work should be higher up the list as should the more significant ones.

You can say only a little or a lot, depending on the significance, of course. Some that you just mention might open discussions in any interviews.

In general, if you think it is something good you have done, then list it. No one will know otherwise.


Can I understand the rejection reason of an article by reading the reviewers' comments?

You can't really tell, unless it's explicit in the referee reports you receive. A referee could well give suggestions for improvements even if they advise rejecting the paper - they don't assume that just because the paper wouldn't appear in this journal it won't appear anywhere. It also doesn't matter whether all the referees recommended rejection - it is the editors that make the call, and that is what stands.


In Sweden, can a supervisor ask his PhD student to provide a private future work list of his thesis?

A supervisor who asks you to write a detailed "future work" document might be trying to cheat you as you appear to worry about, but it's unlikely.

What's much more likely is that they're interested in the scope for future projects both for students, and for postdocs.  If your supervisor can get a grant based on work you've done during your PhD, and there's funding for a postdoc on that, it could well be to your benefit - you should interview well on the topic at least.

Without the backing of your supervisor (either in their lab, or moving on with a reference from them) you're unlikely to have the chance to work on this material anyway, and your dead ends may prove to be good projects for new students with a different skill set.

Finally viewing anything in academia as a simple transaction is rarely helpful model.


Choosing the title of a paper: are provocative titles better?

It might be viewed as incivil to refer to someone else's work as "obsolete", whether or not one could defend such a claim. An editor or referee might object to the title, too, and, perhaps even be subliminally biased against your result because of a too-aggressive title.

That is, "provocative" in the sense of more-vividly-descriptive, without too-direct negativism about prior work, might be a very good thing. But I think if "provocative" too much means "antagonistic", the net would be counterproductive and regrettable.

Asserting that you've made progress is already a bit aggressive, suggesting, as is inevitable, that previous work is being superceded (even if still relevant as some sort of historical/dialectic record). My own taste is that winners can afford to be generous.

Edit: in light of edits to the question... I'd still encourage a sort of "innocent" -seeming, or almost-apologetic seeming, self-description. My point would be that people who understand the situation will see the implications of even a very-modest statement. Descriptiveness is good, yes, but perhaps not "judgemental" phrases.


How would I reference a Linux man page in Harvard style?

This is my try, based on citation principles, Open University's guide to citing software in Harvard format, and Mendeley's guide to core Harvard style.

In general, since the "man bash" page is a particular page, you may want to have the in-text citation specify that as the page/section. That will solve problems if you also want to reference the same manual about something else. Then you have just the more generic reference in the references section.

If this is the only manual citation:
In text: Free Software Foundation (2018)

In references: Free Software Foundation (2018) 'Bash manual page', Linux (Version X) [Computer program]. Available at [URL to get this version of Linux]. Copy of manual text available at http://man7.org/linux/man-pages/man1/bash.1.html (accessed DATE).

If referencing multiple parts of manual:

In text: Free Software Foundation (2018, bash manual page)

In references: Free Software Foundation (2018) Linux (Version X) [Computer program]. Available at [URL to get this version of Linux]. Copy of manual text available at https://www.kernel.org/doc/man-pages/ (accessed DATE).

Does the Free Software Foundation itself host a version of the manual online? That would be the ideal reference for the text. I realize that this response is kind of clunky, but it helps readers find what they need without having to download (your version of) Linux.


Ethics - Asking someone to work for free

In academia, it is not common to ask people to work for free. It is also not common to ask people to work, full stop.  What is quite common, though, is to see people seeking work in academia. This include people looking for funding to help them developing their research ideas, and people looking for opportunities to join someone else's research projects.

You came to the professor seeking an opportunity to work with him. The professor did not offer to fund you, but instead offered you an opportunity to work without compensation for a period of time. You can take this opportunity or leave it. If you take it, the funding may or may not come in 3-4 months. You are free to quit this arrangement at any time, before or after the initially agreed period.

The professor did not want you to do his work. You wanted to do some work with him and he offered it. You also wanted some money and he did not offer it. You make the story look like you were deceived or forced into unfair relations - no you were not.

There is no insult in offering someone to work without payment. In some countries such an offer is illegal, and in some universities it is not permitted to work voluntary. This is done in order to comply with employment laws in a particular country. However, you seem to imply that this is somehow unethical or not normal in a weird way - no it is not.

BSc and MSc students often work on their own projects which contribute, sometimes significantly, to projects run by employed academics. Obviously, BSc and MSc students are not compensated financially (on the contrary, they sometimes have to pay tuition fee), but they use the feedback they receive in order to learn new skills. PhD students in some countries get a stipend, while in others they have to pay tuition out of pocket.

You have just completed your master, and have not yet got a PhD. From what I see, the opportunity to work on a project, receive a feedback and learn from it, with a chance of future employment, is not an unfair offer. Whether it is good enough for you to take it, you have to decide yourself.


It is not ethical to remove you as co-author from a resubmission, if you contributed to the first submission and your contribution is still relevant in the resubmission. In that case, there seems to be a portion of the text in the resubmission that is a revised version of text that you wrote, so your contribution is indeed still relevant to the resubmission.
Do not agree to being removed from the author list. Don't let yourself be pressured to agree by an impending deadline. In most cases it is no problem to get an extension, even up to multiple weeks, on manuscript resubmission deadlines. Moreover, it should have been the lead author's responsibility to plan everything so that the deadline can be met.
If the importance of individual contributions has changed by the revision, it may indeed be appropriate to change the author order. That has to be agreed upon by all authors. The editor might also want to have approval from all authors for that change.
Start collecting evidence to support your claims. In the text from the first submission, mark which portions of the text or data have been contributed by whom. Collect earlier drafts and emails or other communication that further evidence these contributions. If you have the revised version, mark which portions in that are based on contributions you made earlier.
If the lead author does not resubmit to the same journal with you as co-author, try to keep an eye on other journals in the same area. They may just try to go to another journal with the revised version, where the editor will not be aware that the manuscript may still contain contributions of someone who's not listed as an author. If you see a publication with text based on your earlier contributions, but not listing you as an author, contact the editor with a complaint, and provide the evidence you collected.


PhD Student/Candidate distinction - European/French universities

In North America, usually PhD candidate is also called ABD (all but dissertation), so, are PhD students who has passed all PhD requirements but defending/submitting their final thesis. The distinction between a candidate and an ABD is not very clear, some say candidate may imply that one is still working on their dissertation while most candidates who quit may call themselves as ABD. I would not concern myself with the distinction between candidate and ABD on my CV as providing dates (e.g., expected finish time) can clarify it.
Now, in answer to your question, I would say if you can call yourself an ABD (nothing left but defending your final thesis) then you can call yourself a PhD candidate, else, you might count as PhD student.


Do professors have to cite references in their Powerpoints? And what if data is manipulated to make PPT more "current"?

The situation you are describing is not very pleasant. I try to cover most aspects in order of appearance.

First of all, everyone citing work must reference it (including images). It is not just helpful for you as a learner to find the original material, but also a legal liability.
A ppt creation date or author is not a helpful information source. The date of the most recent change and most recent author might be helpful, but maybe the ppt style (corporate design) was created long time ago by the named autho. I just checked one of my very recent ppts which was created 2011 by a person I don't know - and I created every slide in it by myself and it was updated very recently.
If the slides do not reflect the current textbook you are recommended to use it might be on purpose (which would allow you to ask why this is the case) or just lazyness of your teacher - which is just frustrating since you can not force them to update their slides. It the later is the case, try to compare the content of slides and textbook and try to figure out which information is true (or more relevant) - sometimes slides are only an excerpt of a textbook to reduce complexity. This allows you to make the best out of a bad situation.
If there are really made-up facts in the slides, this would be a matter of academic misconduct. You should be very sure about it and if you are, report it to a person responsible for academic misconduct. Every insttution should have one.
The fact that you recieved a "disciplinary memo" is disturbing. At my institution we are glad if students bring up issues with lecture materials and we try to improve constantly. If this is a generally accepted behaviour a your institution, I would consider finding a better place to study. If it's only one teacher, I would recommend to swallow it and move forward, you did your best to improve the situation and if they don't want to improve, you can not force them to do so.


Choosing full time vs part time on a PhD application, is one necessarily better than the other for increasing chances of admission?

Or does part time indicate that I would have other commitments and so would not be seen as a whole hearted student (and hence full time means that I would be a whole hearted student)?

Yes, this is my understanding of how it would be interpreted.  It would definitely not mean working as a TA or RA.

Unless you have a job you'd like to keep, or other comparable responsibilities outside of studying, I'd recommend checking only the full-time box.  I don't think expressing an openness to part-time study would help get admitted to a math PhD program, while it might look odd or worrisome.

In particular, in the math PhD programs I've studied or taught in, there have been essentially no part-time students.  (It might have been a theoretical option, but I can't think of any actual part-time students.)  For programs like this, the application might ask about it, but the expectation would be that everyone is a full-time student.

I think this is standard in U.S. math PhD programs, but some programs may run differently, so I can't say this advice is necessarily universal.  (The biggest variance would be that some applied math programs may be more open to having part-time students.)


In addition to the OpenJournalSystems (OJS) software, I'm aware of the following free and open source solutions that you might want to consider. They are similar to OJS in terms of functionality, but, perhaps, simpler:

DPubS (Digital Publishing System);
EPrints.

While I would strongly prefer open source software, just for completeness, below I will mention some commercial hosted solutions:

Atypon's Literatum;
bepress' Digital Commons.

Finally, a few words on alternative solutions that you consider. In my opinion, the CMS solution is feasible, but, you will likely to lose some features found in specialized open source solutions, such as DPubS or EPrints, for example, document workflow, flexible user rights management and more. I would be very cautious about and, actually, don't recommend the handmade MySQL/PHP system (or any other handmade solution, for that matter) due to various reasons, including, but not limited to, significant efforts required for creation and maintenance of such system.


Balancing between finishing past projects and working on current ones

This is a very broad questions, so I’ll try to chirp in with some of the “tricks” I use to get things done.

Find ways to keep track. It can be very easy to feel that you have so many things going that you feel overwhelmed by remembering them or else. There are a number of hardware or software tools to do that. I have a list of ongoing stuff that I keep in the last pages of my notebook, which works pretty well.

If something needs to be done, which takes little time, just do it right now. More importantly, the critical amount of time depends on the life of the project: the more advanced the project is, the more you need to finish. This prioritizes finishing older projects.
For example, if I have a current project with a task that requires half a day of work, I'll try to find a time to do it later. If I have a one day task for a project that's almost done (such as revising a manuscript after reviewer comments), I'll just treat it as high priority to do ASAP.

When working on a project with others, be clear to assign someone to monitoring progress (and reminding everyone of their contributions). On some projects, you need to take the back seat, and just let someone more concerned about the outcome drive the project.

If some project isn't seeing any progress, try to break it up into smaller work units. Like: I'll write a detailed outline, then circulate it to colleagues or co-authors, then use feedback to write the paper (instead of trying to write the paper in one big piece).

Finally, some advice I have received as a young parent, and that is very applicable to academic life: academic life is a long-term game, you're in it for 40+ years. You being very productive right now, then extenuated for 6 months isn't a net positive. You are a better researcher when you are rested and (relatively) stress-free, so avoiding exhaustion and stress is actually your #1 priority!


Undergrad research in Computational biology

wet lab like actual experiments are getting more experience

It is a common misconception that biology almost always happens in a wet lab. Indeed, some things can only be done in a wet lab, but computational biology is actually one of the greatest examples that counters this misconception, due to its flexibility.

If you want to spend more time behind a pipette instead of a keyboard, you should be able to ask your research advisor for projects or classes that get you more involved in that direction, for example PCR and gene sequencing. However, if you believe that computational biology is "less experience" than wet lab biology, it is important to understand the benefits that dry computational biology brings to general biological sciences.

Take Mendel's cross-pollinating peas exercise. If done in the real world, it would take several weeks to generate a single generation of peas (and hope that nothing bad happens that causes them to die). With the power of computational biology and some programming, you can perform dozens or even hundreds of generations' worth of experiments in a single day.

The power of computational biology comes from the fact that it can be done either cooperatively or independently of a wet lab. If you only want to do data analysis, you can do that. If you want to apply some real-world wet lab culturing with image-based analysis of PCR scans, you can do that.

As a computational biology student, you should be able to determine as much or as little wet biology or computer science that you want to do. My thesis was entirely done without ever seeing a biological organism, as I only used neural networks to simulate generational development.


How to cite a reference in another reference?

You should cite and read the older article that shows the finding. Referencing articles through somebody else's publication should be avoided at all costs. the reason is simple. When you reference a fact through somebody else's work you are also unwittingly citing their interpretation of the original work. There are examples of misconceptions that have been born and carried through many publications because the original have been misinterpreted or misrepresented by a citing author and from which other have sourced the information.

If no other options exist then citing the work as, for exampe " X (yyyy) cited by/in Y (yyyy)" or "(X, yyyy, cited in Y, yyyy)".


Is it possible for a cs undergrad like me to apply for a cs grad program and study computational biology?

I suggest that you make contact with the admissions of the target faculty, as well as make contact with academics whose research interests match the field you are interested in.  Have a look at the academic's profile pages as well as looking at papers that they may have published.

As JeffE said in his comment - why not?  You have computational background and a clear interest.


Should I get my chair a card/small going away gift although she has never been there for me?

I understand your frustration but let me explain a supervisor’s point of view. It is your research, your examination, not mine and you are probably doing fine! I would break in only if I would detect problems.

My university, officially gives me 10 hours for supervising a master thesis student. I have 5 master thesis students under my supervision, I teach, I have piles of examination work, I have students approaching me with all kinds of request (assisting in finding internships). The other part is my own PhD research, publishing and reviewing. All part-time. I also have a regular and demanding job outside the university.

Your supervisor is just extremely busy. I agree with you that your supervisor should follow-up promises or not raise expectations. I suspect her intentions are well meant but reallity and work pressure catch up with her.

My advise would be to have an open conversation with her to share your disappointment. But also be open for getting feedback because everybody has blind spots. The ideal supervisor doesn’t exist, the ideal student neither. If it still doesn’t work out between the two of you, you could consider changing supervisors.

Good luck with your thesis. I am convinced you will be graduated in a few months ;-)


A range of statistics can be useful in providing a quick snapshot of your research productivity. Common statistics include: number of refereed journal publications; number of publications that meet a criteria such as you being first author or the journal being above a certain impact factor or on a discipline specific list of quality journals; h-index; total amount of grant funding; etc. These would supplement a complete list of your publications.

With regards to h-index, make sure you make clear what citation database you are using.

I know that some people on this site object to the bureaucratic reductionism that can result from using measures like h-indices, impact factors and the like. Nonetheless, just because they are imperfect, does not prevent them from being useful. Such measures should not replace actually reading your work to assess its quality, but they can be useful in getting a rough handle on the impact and status of your research.

In terms of anecdotes, I have read several promotion applications that have successfully incorporated a range of such summary statistics to make the case for promotion. h-index, total grant funding, total publications, average teaching scores are all evidence, albeit imperfect that decision makers who are often outside your area will use to decide how to allocate resources like jobs, promotions, etc.


Should I pursue physics or computer science?

We cannot tell you what to do with your life, that's for you to decide.
However, note that there are mixed degrees and many programs for either Physics or Computer Science will require you to choose a minor subject, which then would be easy picking for you. I'd recommend to start either with a mixed variant or with one as the major and the other as the minor. If your university has both as fully fledged degrees, it should be easy to switch if you notice during your studies you like the minor more.
In addition, in most Physics degrees you get some basic programming exposure as well. It is typically not thaaat hard to switch and do the master in the other topic. I know quite a few Physicists that now work as software engineers. The other way around seems a bit more rare, but also possible (there is less automatic exposure however).
If you are really ambitious you can also try to study both, given that there is some overlap, that can arguably be easier than say computer science and History.
German examples for mixed degrees (from a quick-search, you would need to check what TUM specifically has to offer in that fashion):

https://www.zbh.uni-hamburg.de/studium/informationen-fuer-schueler/was-ist-physinf.html
https://www.merkur.de/leben/karriere/neuer-bachelor-kombiniert-informatik-mathe-und-physik-zr-12539261.html


Academic Interview: What is your Greatest Weakness?

I would answer it as recommended.  The best strategy is probably to admit a real weakness that is relevant to the work (which shows honesty and the ability to be self-critical), but focus on how you are working to improve.  There's nothing really academia-specific about this.

Your examples seem largely fine to me, except "I have trouble managing my work-life balance" is too vague and could be interpreted as a very serious issue.  So I would avoid that or make it more specific.

I wouldn't spend too much time preparing for this question. Its reputation as a common interview question is greater than the reality. I've never been asked it (at interviews in and out of academia).

It's a poor interview question, really, because it's unlikely to lead to genuine insight on the candidate. Good interviewers don't ask it. Your main task is just to avoid a big mistake. Don't say your biggest weakness is plagiarism or stabbing colleagues in the back, and you'll be fine.


How to Approach Students with Different Expectations on Coding Lab Sessions as a TA

I often get asked, "Why am I taking this course?"

There are some courses that are required regardless of major. Similar questions could be asked of mathematics faculty. However, it turns out that not only math majors are obligated to attend calculus courses.

I come from a institution that is similarly organized, namely, the first year is the same for all engineering students, which afterwards chose their respective major. This common year contains introductory courses: math, physics, computer science and electronics.

The school's curriculum is as it is, it can be good, it can be made better, but neither you or the students are in a position to influence it, let alone change it. So, stop thinking badly about you or your course, there is nothing wrong with either (at least nothing deducible from the question).

My advice to you is to stick to a medium curriculum, i.e. one that upholds the criterium of the course but is of reasonable difficulty for the average student,  and, if required by your TA agreement, make yourself available for (again reasonable) office hours, where struggling students can find help. And by help, I don't mean that you solve the problems for them, but to help them understand the material.

Students that are on a more advanced level can be motivated with additional assignments, projects or literature, while those "dissatisfied" need to provide the bare minimum effort for passing the course or fail. The same as with any other course.

The same approach is applied to cheating. The fact that someone doesn't want to attend a compulsory course does not entitle them to cheat and such behavior should be reported to the proper authorities.

In short: Don't give in to guilt or sympathy, you have a course to TA and nothing to be sorry about. Uphold the institution standards in teaching, grading, helping and maintaining discipline.


When and how should you talk to a professor if you think you deserve a different grade?

Does anyone have recomendations on how many marks to ask

Yes, one: do not, absolutely, ask for a specific amount of marks. Explain your interpretation, but leave to the professor to decide whether you deserve more marks or not and, in case, how many.


Assistant professor: is it bad if I attend a class in a discipline close to mine but not exactly mine?

There's nothing bad about this; it's pretty common, especially for advanced graduate courses.  You don't have to be secretive about it.  But here are a few things to consider.

First, time.  As a new assistant professor you are going to be busier than you ever imagined.  Are you sure this is the best use of three hours a week?  Keep in mind that taking this class isn't something that "counts" towards tenure, so the only career benefit for you would be if it helps improve your research productivity.  Of course, if it's just something generally interesting to you that will make your life happier, that's a consideration too - but think about whether you can afford it.

Most people do this by "sitting in on" a class - you'd plan to attend the lectures, but normally you wouldn't turn in homework or take exams like a real student would, since that would create extra work for the instructor.

In all cases you should ask the course instructor for permission, by email or in person.  "Hi, I'm Lupocci, I'm a new assistant professor in department X.  I was wondering if it would be all right if I were to sit in on your course ABC 321.  I have been meaning to learn more about this topic and this seems like a great opportunity to do it."  Make sure there is available space and that you won't displace actual students.

You should ask the instructor how they would like you to participate in the class.  Should you ask questions, participate in class discussions or activities, etc?  Sit in the front or the back?  There's a possibility for your presence to be distracting to the students, so you want to minimize that.

Some institutions might require you to formally register for the course as an auditing student, so check your regulations.  Tuition would usually be waived, but you still might have to pay lab fees or something.  At other places this sort of thing is done "off the books" as a professional courtesy between faculty.  At still others, rules require you to register, but everyone ignores the rules and just does it off the books.  So you might also ask your department chair or a senior colleague what the norms are.

Finally, as you take the class, be mindful that you don't interfere with the learning of the students.  It might be tempting to ask lots of questions in class, bring up connections to things you are interested in, etc, but this may tend to derail the class, especially if the questions are too advanced to be useful to the students.  This might also have the effect of intimidating students who worry that their questions are not as smart as yours.  So you may have to stifle yourself in class.  You could discuss things with the instructor outside of class, but try not to take up too much of their time either (see second paragraph).


How do you build a healthy and productive relationship with your supervisor?

I would say that one of the largest things that a student/post-doc can do to foster a relationship with their advisor/mentor is establishing expectations early. This can be in the form of goals, research statements, or mutually agreed upon research plans. One of my former universities had a research statement form that students and mentors were asked to fill out. It specified what the goals of the partnership would be, what types of funding would be provided, what publications (with authorship order) were foreseen, etc. The partnerships that actually took the time to fill out the form had a much lower "failure" rate in their relationship.

In my experience, many of the issues that arise between mentor and student center around differing expectations. Expectations about timeline, work load, authorship, copyright, publication rate, etc.

Now, of course, this is easier said than done. As a student, it can be hard to tell an advisor that you want to discuss "expectations." Some advisors would feel affronted by being asked to establish goals and plans. One thing that I have seen students do in this case is present their advisor with personal goals that the student wants to establish for themselves. This communicates several things to the mentor:

A willingness to be forward thinking and take responsibility for one's own work. It shows a "communication starts with me" approach to the relationship.
An actual structure for the mentor to build upon. It is much easier to advise a student that can build a basic framework for the metrics of the partnership.
A willingness to ask for feedback as a means of improving.

I will add an sort of post script to my answer: Some mentors are anything but. Vetting an advisor can be very important for ensuring that your relationship with you mentor is positive. Part of having a good relationship with your advisor is selecting a good advisor in the first place. (Which is much easier said than done). Not every mentor is in academia because they love students. That is a reality that does need to realized here. Some professors are in academia because they are too combative to survive in the "real" world. Attempting to foster open communication with a potential advisor can act as a litmus test in this regard.


Is it possible to find an unpaid and "half-time" postdoc?

I know that some institutions can offer the "associated member" status to a researcher who is not on their payroll. The researcher needs to be recommended by a senior professor from the institution, who typically presents a project with this researcher to justify the request. However I've seen it used only with somebody after they had been a postdoc in the institution.

Obviously one needs at least to prepare a research project with a member of the institution, so I think the best way would be to contact the academics in your network who could be interested in a project with you. I'd suggest to propose to work with them for free on a grant proposal, since this would be interesting for both the PI and for the institution. If you find a suitable EU call, you could even try to involve a partner in Spain which would hire you if the grant is successful.


What is "research-based intervention program"?

It sounds as though s/he is unconvinced of the validity of your conclusions, and is attempting to tell you so without actually saying it! If this is so, then addressing this comment means providing more information on why your solution to the problem should be prefered over other potential solutions.

Note that I am not familiar with the term in this context--research-based intervention usually refers to targeted interventions/actions in education or medicine.


What to do if cited papers are not freely available while reviewing a manuscript?

Reviewing a manuscript does not mean you have to know or have read all the literature cited. In some cases, however, you can be unsure of a statement or a method used and need to consult the original source.

You have multiple options here:

1-Try to access the article on the web. The OA button can help you here, but there's many other way, some less legal.

2- Contact the authors of the article you want to obtain and ask for a PDF copy. Academians used to send each others postcard to access articles! A demand by email is most often met by a yes.

3- In your reviewer report, write something along these lines:

  The authors cite Smith et al 2005 in line 105 to support this statement. I have no access to this article and I can't confirm that this statement is correct.

There's probably some other possible actions here. Unless the article you want to access is from the journal for which you are reviewing, I wouldn't bother to contact the editor.


Web of Science has a lag of potentially several months before a given paper from an indexed journal is uploaded. There is (I believe) nothing at all you can do about this - it's simply a matter of their workflow taking time due to the level of manual involvement needed. I would normally say that you could reasonably expect it to be up after about three months - but I wouldn't in the least be surprised if it takes longer, especially if it was up as some kind of "advance publication" and its official publication date is later than October.

Howver, I've never heard of anyone asking for proof a specific paper is indexed - the decision to index covers the journal, not individual papers, so it's normal to talk about "a paper published in an ISI-indexed journal" in this context. I would point them to the entry for this title in Journal Citation Reports or similar, to confirm that it is included, which implicitly states your paper will be indexed as part of it.


Is it a good idea to ask the person who one has applied to for a postdoc position about the status of that application

More of a necessity than a good idea.

  What should be the "reasonable" time period after the deadline of the application to enquire about the position.

I'd say this depends on:

(As OP has suggested) The amount of time that has passed since the deadline.
The amount of time before employment is set to begin.
The information published beforehand about the application procedure.
Whether it's the academics or the administrative staff whom you intend to ask
The number of expected applicants for the same position

but if you have not been instructed to await a reply in X time, it's perfectly reasonable to write and ask after, say, min(1 week + 1 week * round_up(log_8(number of applicants)), 0.25 * time between application submission and work start).

That's a very rough rule of thumb, and perhaps not super usable. Another way to put it is that you should write after having allowed a generous amount of time for your application to be processed, but no later than you need to make serious decisions based on the reply. It's not improper to say that you need to know because, say, you have to decide whether to move to another country or not, enroll your children in school for the next year etc.


I slept with my advisor's daughter and she is blackmailing me now. What can I do?

First off, you haven’t committed a crime (assuming she was above the age of consent) and you haven’t engaged in academic misconduct (since there is only an indirect academic relationship between you). However, the fact that she is threatening/blackmailing you is very concerning. The fact that she is your advisor’s daughter makes things more complicated, but being threatened or blackmailed by a sexual partner would be deeply concerning in any circumstance.

I do not know the exact nature of the threats or blackmail, but I would not engage in a relationship with someone who is threatening or blackmailing me. Only you know the exact situation, but your choice of words rings alarm bells. My primary concern in your situation would be worrying about whether she will make worse threats — e.g., false rape accusations. That would be much worse than a spat with your advisor.

If I were in your situation, I would try to record my conversations with her so that I have some evidence to protect myself if she does carry out her threats. Save text messages and get a voice recorder app on your phone. (Check the laws on recording conversations in your state first.) The only thing other than “he said, she said” you have to defend yourself is such evidence.

Maybe I'm misreading the situation from your question, but your choice of words "threatening" and "blackmail" is concerning. And there is no harm in trying to protect yourself from possible future accusations. Hope for the best, plan for the worst.

This is not a complete answer, but I think you should worry about being threatened/blackmailed before you worry about dealing with your advisor.

In terms of dealing with your advisor, two (conflicting) points: Generally, honesty is the best policy (as Buffy's answer emphasizes), but she is an adult and her father has no automatic "right" to know about her sex life, and there is a good chance both of you would prefer him not to know (as Nicole's answer suggests).

In terms of dealing with her: It sounds like you are still on speaking terms with her and you should absolutely try to talk things through with her. Treat her with respect and acknowledge her feelings. (See Geoffrey’s answer.)


In physics, a lot of “letter” journals or sections of journals limit the contribution to a few pages.  The better known example is Physical Review Letters where the current limit is 3750 words, or about 5 pages depending on figures etc.  (The one recent exception is the initial paper on gravitational wave detection, which was allow to go well beyond the normal page limit).  PRL is currently ranked top physics journal
by Google and its Clavirate impact factor score is also one of the highest for a physics journal.  People read it precisely because it’s to the point and usually timely.


How should I approach the scholarship committee for reconsideration if they have rejected my application?

Give Yourself another Chance

You can conduct your second try during the next scholarship application cycle - and the time frame of a cycle varies between scholarship providers. Some scholarship providers have an all-year round application cycle, which means you can re-apply for a scholarship as soon as you hear of your unsuccessful application. On the other hand, the time period of other scholarship providers' application cycles is more limited, only allowing you to make a second application a year later.

Write an Appeal Letter

While it is recommended that the next application cycle would be the time you attempt your second try, it also wouldn't hurt to submit an appeal letter to the scholarship provider directly.

In your letter, reiterate that you are trying to apply for the scholarship a second time (even you got a scholarship with another institute but you prefer this one). Make them aware that you are not one to give up after a failed attempt, and are more eager than ever to receive the scholarship in question. Apart from your determination to reach your goals, this will also speak volumes about your courageous, indefatigable spirit.

All in all, it is important to allow your humility and sincerity to shine through in your letter, or in your interview if you are given a second chance. And if, in the end, you do not secure the scholarship of your dreams, don't be disheartened - work towards your career goal anyway. You can always do well in university and clinch a college scholarship, one that comes with no bond and essential financial support. There are many paths towards your end-goal and you should never put out the fire of your hope.


Statistics could be artificially increased, but also the advertisements of the serious computer scientist could be faked (if they are on the website of the conference). Almost all of the scamming conferences use real, "famous" scientists that are supposedly chairing sessions and giving lectures, even though they themselves don't know anything about it.

If you really think it's a scam you could withdraw, however I don't think they will actually remove your abstract from the website.

I personally think the best way to avoid scams or second tier conferences is to just talk to colleagues / mentors / professors in your field, as you might also end up at conferences that seem interesting but are actually not completely about your field.


START v2 (Softconf): what markup is allowed in reviews?

I emailed Softconf's support and Rich Gerber replied with the following:

The review is always considered a plain text entity, but to display it we insert a bit of markup where we believe markup is warranted.   But *this* will add emphasis, and you can also use bold tags like this.   There is also implied ordered lists, by numbers starting lines.  You can also insert HTML super and subscripts.  That's about it.

That is:

*emphasis*
bold
* bulleted list item
1. numbered list item
xsuperscript
xsubscript


Switching between active and passive voice

"I realize..."

Active.

"arguments being made..."

Passive.

My point here is that it's normal to switch.  It's probably a good idea to favour one or the other, but I imagine you would have a lot of difficulty using only the active voice or only the passive voice throughout a paper.  Don't worry about it too much.


Usually conferences that are overly generic are a scam because anyone's work can fit in this category. Which field of engineering is this conference on? All engineering? This would hardly be an interesting conference to attend for engineers, because it would be very unlikely that someone else publishes in their specific field, on their topic or problem. There are conferences on sub-sub fields of engineering of more than a week in duration and this journal will cover any and all innovations in engineering in 2 days?

A good first start is to ask your supervisor or other professors in your field of study. Since your supervisor's name has to be on the paper alongside yours, they should guide you in this regard.

As a second filter, you should try and publish in a journal or conference that you cited often, or that published on work related to yours, as typically your own work would be a good fit there.

As a third filter, try and find papers that are published at this conference and see if they are any good, and if they all have the same style / formatting. I cant seem to find a template for this conference on their website, which is another red flag. Why would they allow everyone to just post in whatever format they choose?

Something odd, there is a gallery link to a generic gallery website (why would they have this unless it is a general catch all for a bunch of conferences), and none of the photos have any significant number of people in it. In the photos no one is smiling.

Finally, if your paper is accepted in 1 day or in a week, or in two weeks you know no academic or researcher looked at it. A good conference provides peer review feedback, typically of 3 reviewers, sometimes more. A response in a single day, guaranteed fake conference.

Random idea: Maybe we should have rubbish fake papers to submit to conferences before we submit our original work to test if it is a fake conference.


Is computer science worth double majoring in for an aspiring Data Scientist?

If becoming a Data Scientist is your only ambition, I doubt you require to complete an entire major on computer science.

In a computer science major you will learn a lot more ranging from programming languages, semantics of both software and hardware design, data structure, computer architecture and organization, signal processing, AI among many others. Most of which is not even directly connected to data science. In fact a standard computer science graduation course that I've been through (both my undergraduate and graduate) did not have any element of data science in it -- no data mining, machine learning or inferential statistics. Well, most of these subjects are included as part of the current generation syllabus. But the main point is that you would learn a whole lot more than what is needed to become a data scientist if you were to take a computer science major.

Computational statistics encompasses a major part of data science, one that a computer science major would cover is lesser proportions. I suppose you would cover a considerable portion of data science just by following your current major. I've resorted to online courses and practising the skills myself to learn data science. I find this more helpful. Also, bear in mind that not all successful data scientists are computer scientists.


How to respond to peer review - a step by step guide to my first response?

Variations are possible, but I have found that the following seems to be a fairly typically form of a response to reviewers:

Begin with a letter to the handling editor and reviewers, in which you thank the reviewers for their useful feedback (even if it wasn't) and say you believe you've addressed all comments.  If you've made any really major changes, a sentence or two here is a good to address them.
Quote the reviews as sent and address each comment inline, either saying how you've done what they wanted or explaining why you haven't.  I always organize by reviewer and address in the order of their comments (rather than the structure of the paper) because the goal is to clearly show that you have addressed all comments.

I recommend adopting a polite and semi-formal style.  You can be a bit more informal than the paper, but I still don't use contractions.

Do not get argumentative with the reviewers, and do not blow off their criticisms.  Even an apparently crazy criticism should be treated politely, and as a matter of confusion rather than as a personal attack.


How to set up an efficient watch on publications in planetary science?

There are different ways of keeping up to date that come to my mind:

Using your favourite article indexing database listing articles in your field (e.g. Scopus for life/biological sciences or Web of Science). Most databases allow you to set up 'Search Alerts', when results of a certain search string change. This can be done either via E-mail or RSS feed. Usually you can customize how often you get notified about such changes (daily/weekly summaries)
Some citation management programs automatically notify you of recommended and related articles depending on your own collection of articles. For me, this often not only includes the newest research but also older classics and other highly related articles that might not necessarily be very recent.
Thirdly, you can follow your peers on twitter and be notified of their most recent works that way. With the advantage of being able to start off discussions.


Doing research/travel between postdocs (pure mathematics, Europe)

I was unaffiliated for a little over a year between postdocs.  I attended two conferences in that time and didn't list any affiliation.  I also made two research visits, for one of which I received some funding from my host's research grant, and being unaffiliated (or 'an independent researcher', as my host put it) was no obstacle.

This might depend somewhat on country and research area, of course.  And I didn't need a visa for either of the research visits, but I'd be quite surprised if not having an affiliation right now would be an obstacle to getting one (again a little depending on the visa-issuing country).


Receiving Degree Late due to late payment of tuition

I would put the date shown on your physical (paper) diploma or on your official transcript. If there’s any question about your eligibility or truthfulness, they are what you would show to immigration services.

That said, most universities won’t give you your final transcript or diploma until after all bills are paid. So in your case, the diploma might show 2006 when it arrives but they won’t actually give you the diploma or transcript to prove it until you pay the bill off.


How do I ask the author of a book in English if I can translate it into my native language?

In most cases books are published through a publisher and certain copyright laws apply that may be shared between the publisher and the author. Exactly where the right to decide on translations lie may vary. You therefore need to contact both the author and the publisher to look into what might apply and to what extent they are interested in such translation.  My suspicion is that it will not be as easy as just getting permission to translate. When a book (or any publication) is translated, there will be a need to get a translation that properly represents the original content. A publisher may not be content with "anybody" translating the work, they may request some form of review etc. So, the bottom line is that you need to contact publisher and author to see what is possible and under what conditions. It is possible they accept translation into a different language for different reasons but they will most likely want to retain some form of copyright.


Editor not responding. Should I withdraw my submission?

Check if you are using the correct email address and try to verify that it is not outdated. You can also try emailing some other contacts to communicate your issue.

If you are not receiving any responses from the editor for extended periods of time, you are justified in withdrawing your paper. Just make sure that you clearly communicate your decision to withdraw, either through their online system or through email (or both).


How much programming experience is needed before contacting a college professor for research/internship?

There isn't any general rule about the level of programming required to work as a research assistant in computer science. There are many different subfields in computer science, and in many of them, doing research does not involve any programming at all. At the other extreme, some research projects might only be suitable for students with highly specialized knowledge in a particular kind of programming.

Even the same professor might have multiple projects, some of which require prior programming experience and some of which don't.

I am a researcher in the field of computer networks, and I work with high school students in the summer. I don't require any prior programming experience. Some of my students have prior experience, and some don't, but none of them have experience in the specifics of my research area, anyway. In general, for students with no research experience, I am looking for general qualities - learns quickly, responsible, punctual, good at taking feedback, good at writing notes and documenting their work - rather than any specific kind of technical expertise.

(P.S. I do not hire high school research students who contact me by themselves - I work with students who apply through a high school summer research program organized by my university. I encourage you to look for opportunities like that.)


At least at the universities in Paris where I took courses, there is a strong distinction between the first and second master year. In the first year you still take general courses in a variety of topics, whereas in the second year you really specialise. Someone explained to me that this is a remnant of how it was a while ago: first 4 years of undergraduate (which is now 3 years of bachelor, then the first year of the master), then 4 years of graduate (second year of master and 3 years of PhD).

I know that some of my friends in physics had something which could be called a research position at the master 2 level, i.e. they were integrated in the research group, doing some type of research, whilst not yet being PhD students.

So no, it should not be a second master degree, it should mean that you are in the second year of your master.


The answer depends on whether the result in any given trial depends on the previous sequence of trials.  For example, is this a state machine for which the output and next state is a combination of the present inputs + the current state or is it purely combinatorial, where the output is always dependent only on the input?

If each trial is independent, there's no harm in sorting it any way you like, especially if it clarifies the relationship between input and output.  But if there's a sequential relationship, no, you cannot sort the data.


What are the incentives for universities to recruit athletic student

There is likely more than one correct answer to this, but here are a few answers that vary and may be true in multiple environments.

Student athletes

If we are talking about athletic students who are going to be "student athletes" (i.e. play on the universities intercolligiate sports teams) then the incentive is to win those tournaments. Depending on sport, winning an NCAA tournaments can be a very valuable endeavor. Additionally, as noted in the answers to this question, noted in the comments above there is a publicity value to having a notable sports team.

Athletic Non-Student Athletes

Involvement in extra-curriculars with attendant good grades shows that students aren't just getting by in high school, or dedicating all of their time towards studying, and therefore are more likely to succeed. In these cases, members of the student body, people in the band and on the yearbook committee get more or less the same boost.
A different type of student participates in sports, and by seeking out those students, you can improve the chances of a well rounded student body. People who are sports minded are often different kinds of competetive from your "type A" valedictorian-type students, where team values are rewarded. Also, Charles Murray has noted that sports participation is more highly correlated with lower SES, although not perfectly. Relatedly, there are many who grow up in a very poor environment, who pursue sports because they feel, wrongly, that it is their only ticket out. They have shown significant capacity to learn, but not enough capacity to play on the college team, and seeking those students provides them an opportunity the otherwise might not have.
For some universities athletecism is part of their mission. For example the U.S. military academies require participation in intra-mural sports for all students, for somewhat obvious reasons. One can imagine that other schools might have primary training objectives that require physical fitness.
Some schools make an athletic student body a part of their sales "pitch." Places the University of Colorado play up the active nature of the campus and the student body, and consequently they want to ensure at least a modicum of that. On the other hand, if a student body is organically athletic, then recruiting students who are interested in that sort of activity is part of the "goodness of fit" that selection entails, and schools want to ensure that their offers are accepted, so they will tend to opt towards students that are like their current students, to increase the probability that the students they admit come.
Finally, the advantages of fitness for intellectual activity are well documented. Admissions may simply be trying to do what they can to skew in favor of this additional criterion for admissions that increases the probability of success at school. It is probably a less reliable proxy variable, but since all schools are chasing pretty much the same graduates they could be using a "Moneyball-esque" strategy.

All of this is based primarily on my own experience and conjecture. I doubt highly that any of these factors weigh heavily at any school, and certainly not all of them at any school. I doubt, further, that many schools actively recruit athletic students on principle, any more than they recruit people from a language club or the choir, but these are at least some reasons they might want to.


What happens to surplus referee reports?

From my experience, things happen differently. Comments do highlight it correctly.

Initially, N reviews are solicited by the editor. If they disagree (or, I have to assume, some reviewers miss their deadlines), more reviews are solicited. I've been reviewer #5 few times.

Typical values for N are:

2, with third as a tie-break – a typical grant application review scheme;
3, with 4 or even 5 as a tie-break - seen more often with journal papers.


In the USA, do college courses deeply differ from high school courses?

First of all, the US has no university system.  It has somewhere around 1500 community colleges offering 2 year degrees and 3500 colleges and universities offering 4-year degrees, all of which run with more independence than an ordinary French university.  (Keep in mind the federal government has established only a tiny handful of universities; public universities are nearly all set up by the individual states.)
Second, you should understand that there is no high-school leaving exam like the bac.  Basically anyone who is willing to sit in the classroom and do a minimal amount of work can get a high school diploma.  Harvard is incredibly selective and it's about as hard to be admitted to Harvard as it is to be admitted to the ENS.  The top 100 or 200 of US universities are all selective, and the average student would not be admitted.  However, most universities and all community colleges will allow anyone with a high school diploma to attend.  (My university officially has admission requirements based on high school grades, but high school grades have been inflated to such an extent that these requirements are almost meaningless, and the admissions office routinely gives waivers to these requirements anyway.)  About 85% of Americans earn a high school diploma and can attend community college.  (Another several percent obtain a GED.)  Only about 45% of French take and pass the baccalaureate general and can attend university.
At a community college, you should expect that many students do not actually know what you might think they should have learned from high school, and a significant number of students will have trouble with upper elementary material such as adding fractions.  There will even be a few students who are functionally illiterate.


Conceptual graphs in a business subject PhD thesis

Whether the graphs add value seems to depend on the content of the thesis. If you don't perceive what those graphs would look like, then either none are called for, or you haven't recognized opportunities to use them. In the latter case, having someone with graphing experience read and reflect on the thesis could provide you with solid proposals.


You might cite both by saying "Idea X, originally developed in [1] and extended in [2], shows that ..."


Apply for PhD before finishing my Master's degree

It's not a big deal for you not to have publications—remember, many of your peers also will not have published anything, either!

Moreover, it's important to note that in the US, most of the applicants for graduate school do so in the fall of their fourth year of studies—which would, contentwise, typically line up with the third year (or sometimes even second year!) of study in a German program. So, in many ways, you're already much more experienced than your counterparts.

If you're interested in doing this, I would recommend that you just go ahead and apply. The worst that can possibly happen is that you're not accepted, in which case you find another means of achieving your goals.


How to cite my own report that hasn't been published?

If you create a profile on researchgate you can upload your work and it gives you a citation. It also gives you your own personal dio code so that you can cross reference your work with other sites. This is what I have used. Here is the web site: www.researchgate.net

Additionally you can also create a google scholar profile sync your work from researchgate and it automatically gives you a citation.


recommendations for increasing the visibility and ranking of a faculty?

As ff254 correctly mentions, you are asking two different questions. "Climbing the rankings" is sort of a science of its own, and making your research be more visible to the outside is only a very minor part of it. I am not an expert on ranking optimization (I am happy to say that university rankings are not particularly relevant where I work), but if you really want to noticeably improve the ranking of your faculty, serious money and management commitment will be required (and better consulting than is available in an Internet forum).

Now, assuming that you are really more interested in making your faculty internationally more well-known. I sort of disagree with Simmy that ResearchGate is a good vehicle to achieve this goal. At least in my community, ResearchGate is not considered a "serious" source at all. Nobody goes to ResearchGate to discover new researchers (and the technical Q&A forum there is a joke). People go to conferences to meet up and coming as well as established researchers. That is, if you as a new faculty want to improve your international visibility, you should:

Produce excellent research. This should be obvious, but having a bunch of mediocre papers listed in Scopus or DBLP will not make you stand out. One top paper will.
Go to as many reasonable conferences as you can. Skip on the spam ones (no interesting people will be there and publishing there will not help you in any way), but even smaller conferences usually have a lot of interesting professors in attendance. Definitely go to whatever the big conference in your field is, even if you do not have a paper to present.
Socialise. Don't be the person that just works all day in a silent corner of the conference room. Your task at the conference is not to write the next paper, but to get in touch with other researchers.
Have a nice-looking web page. Publish all your papers as preprints there. Plus points if you do  nice write-ups of your published or ongoing research in a recurring blog.
(In some communities) have a Twitter account, and follow the big wigs and engage in discussions if appropriate.


How to initiate an application of a research attachment fellowship directly with the potential advisor?

If they expect you to get in touch with faculty first, and they widely accept students from beyond CalTech, then they're expecting you to reach out - no undergraduate has a particularly robust academic network beyond their institution (beyond a few edge cases).

Generally speaking, the best way to do this, in my view, is to email the professor, give them a brief introduction about yourself, your research interests, that you're applying for the SURF program, and that you'd like to work in their lab. Link this to the work they do.

I'd consider doing this for several professors, unless there's just one whose work matches your own. Worst case, they'll ignore it, but professors often at least read these, especially if they're from institutions they recognize, have concrete information, and are in coherent English.

For the record, this is how I got my first undergraduate research position, and ended up with a wonderful colleague I work with to this day.


Where can I find statistics about papers (length, writers, etc.)

Scopus can provide you with a statistical analysis of publications that it has recorded that match a query. It's behind a paywall I think, but your organization might have a login.

Using it is pretty straightforward;

If you want more information on the query format;

Then;

It can give you results over time or various filters etc.


Are there any journals or conferences that take into account the availability of the source code when selecting the papers to publish?

I can confirm the answer given by amlrg in comments. I have recently published a paper in Computer Physics Communications and the referees pay significant attention to the code. There was no requirement, however, to upload the code as Supplementary Material with the paper — the referees were happy to consider our public github repository. It was probably the first time in my practice when referees have actually bother themselves to reproduce the results claimed. We had a number of comments regarding the clarity of the run files in the code (but not in the rest of it), and even a suggestion on design.


Letters of Recommendation - Duration Etiquette

It would be normal to have some letters of recommendation from professors at your undergraduate institution.  In my experience, faculty often write such letters for students a few years after they've graduated and will typically keep old letters of recommendation on file as a starting point for an updated letter.

However, it is also important to have positive letters of recommendation from your current advisor and possibly others at your current institution.  If you don't get such recommendation letters, then this could be taken as a sign that you've done badly at your current institution.


Is it cheating if I develop some part of my MSc. thesis in a hackathon in a team?

I believe it would be fine and acceptable as long as in your thesis writing you name who helped you and how they helped you.

I doubt anyone will think less of your thesis for having people help you. As long as it is still clear that you did a lot of work yourself... this team isn't completely doing your project and thesis for you!

You could ask your thesis advisor to be certain.

Many PhD students hire research assistants to help them code software engineering projects.


Should glossary links be used as much as possible?

Actually, I question the value of hyperlinks at all. You are assuming that the reader will be using a specific technology to read, rather than just a printout.

It is really enough, in my opinion, to refer to the glossary at the first use of a term and forgo it thereafter. If the reader is aware that there is a glossary, they can go there in any case if they are puzzled.

The links will interrupt the flow of reading in any case. There is value in making the work beautiful, not just informative.


How do I get rid of google scholar recommendations

Two possibilities:
1.) Open Google Scholar, open the left-hand menu and click on Alerts. You will then see a list of all alerts you receive. Click on "CANCEL" in each row.
2.) If you wish to cancel a specific alert: At the bottom of each alert e-mail, there is a link called "CANCEL ALERT". Click on it and confirm that you wish to cancel it.


Advice for a math PhD student who is also interested in a part of EE/CS

I think you are correct in your estimate that doing ML work that requires only basic knowledge of mathematics probably won't get you hired, promoted, or tenured in a mathematics department.

The best I can say is this: If you publish enough in your pure math area for hiring, promotion, or tenure, then doing additional ML work can be a plus.  Interdisciplinary work and public outreach could be emphasized at your future institution.

The other possibility would be getting a job in industry related to ML, and giving up on your pure math career.  A Ph.D. in math, even in an unrelated field, may be useful for getting hired at such a place.


Why do many instructors avoid giving personal introductions?

I am not sure whether this is in any way related to the age of the instructor, but the primary reason that most people I know don't do a "this is me and my vast experience and research results" style introduction is that it is all too easy to come across as bragging. Even if you have the best intentions and just want to explain your background to the students, so that they can judge your qualifications for themselves, it may sound to them like you are really just showing off.

Most students assume that the instructor knows what he's talking about, until they have solid evidence to the contrary. There is really no reason to explicitly talk about your experience beforehand.

That being said, if you feel like a short introduction of yourself will add to the course, go ahead. In the grand scheme of things, I am sure whether you talk for 5 minutes about yourself in the beginning of a course is the tiniest of issues. What I would avoid is what one industrial lecturer in my alma mater did. This guy spent 5 - 10 minutes of the beginning of every lecture talking about himself and his company (and was ridiculed a fair bit for this by the students :) ).


Is it ever appropriate to ask a professor to be a business advisor?

Due to the mentioned ethical aspects you should avoid any financial relationship with professors of which you are still taking courses.

On the other hand, it is happening quite often that a professor is supporting a start up and compensation can be either money, company ownership, or sometimes just personal satisfaction.


Who is eligible to apply for instructor or assistant professor positions?

No, you are not wasting your time.  For assistant professorships at colleges with little or no research component, you should feel free to apply in your last year of a PhD program.

  I do realize that someone that has already had an instructing position, or "assistant professor" position previously, or experience as a postdoc, would look better than a fresh PhD.

In my experience that is not necessarily the case.  In my PhD program, probably more graduates go on to this type of job than any other career trajectory.  Many of our graduates do get tenure track jobs straight out of graduate school.  Getting such jobs later after doing a temporary position is still possible, but it seems to me that the chance goes down.  Even top twenty liberal arts colleges still hire many assistant professors straight out of grad school.  Obviously they could select candidates with postdoctoral / visiting faculty experience.  They often choose not to.  I would go so far as to say that in many teaching jobs, postdoctoral experience could be viewed as a bit of a mismatch.

(An old friend of mine has written an article about the pleasures of being a visiting faculty member.  To a certain degree it contradicts what I said above.  But I think he is more looking on the bright side of taking multiple visiting positions than suggesting that they are necessary.)

Three more comments:

You should know that an "instructor" position is typically very different from an "assistant professor" position.  Suffice it to say that if you want an assistant professor position, you probably do not want an instructor position.  In many math departments, there are recently hired instructors with PhDs teaching alongside of instructors without PhDs who have had the job for a longer period of time.  This is not saying good things about the current job market.  In my opinion, having a PhD makes you overqualified (and certainly, underpaid) for most instructorships, but of course it's up to you to decide on what's worth your while.
Rather than further academic training, what you want to have in order to get these jobs are a strong teaching record and excellent teaching abilities in an interview / model classroom situation.  Many PhD programs nowadays provide opportunities for their students to display these credentials.  If you are looking for a primarily teaching job post-PhD, I hope you have been doing everything in your power to acquire these credentials during your graduate career: in many cases, this provides the best opportunity to do so.  (If you are not sure where you want to go on the teaching/research perspective, I hope that you have erred on the side of acquiring more of these credentials than you will necessarily need.)
When it comes to individual departments, Nate Eldredge made a good suggestion: you can look through CVs of recent (and less recent) hires to see what their credentials are.  However, a small department may have a small sample size.  Nowadays many (most?) people on the academic job market apply to on the order of a hundred jobs; necessarily this includes many jobs for whom the goodness of fit is unknown to them.  Not applying to jobs because you are worried that you might not be competitive does not seem like a good strategy when so many other strong candidates are applying for everything in sight.  You don't have to stuff envelopes anymore (like I did when I was applying for jobs less than ten years ago!), so the differential amount of work in applying to some positions that you fear might be a stretch but don't know is small.  When in doubt, apply.  I say this as someone who reads through hundreds of applications a year.  If we're not interested, then we're not interested, but it's no problem.


Do scientists using user facilities (such as Advanced Light Sources) have to travel frequently?

I did my PhD in experimental nuclear structure physics, in a similar situation to the one you've described here. Within a month of starting my PhD, I was sent to the IFIN-HH lab in Romania for a week or so, to help a collaborator with their experiment. A few months later, I traveled to the experiment which provided my PhD data at Argonne National Laboratory in the US. This level of travel kept up for the 3.5 years of my PhD, to Germany, Italy, Switzerland, France and Romania, all on multiple occasions, although it tail off a bit towards the end when I was writing up my thesis. I have to admit, the travelling did get a little tiring, but I generally enjoyed the experience.

So not only are you attending your own experiment(s), but also those of collaborators from both your own institute and others. I was ok with this as I wasn't in a long-term relationship (well, I eventually was for a while, but with a PhD student on the same course), and didn't have children, so had few commitments which required my regular presence.

Really what a person looking at this level of travel needs to decide is if they actually want to travel this much, and if their commitments can handle them not being at home for days or weeks at a time, on a regular basis. (Admittedly, this is much more thought than I put into it at the time!)


Probably no burned bridges. Like everyone else (especially now) they are busy and just focused on the essential things they need to do to keep everything else together. In normal times you might have gotten a few more replies, but not from everyone. They just say to themselves "oh well" and move on to the next crisis.

I suspect that even those who haven't replied hope you succeed. When one does, we all do.


Asking for recommendation letters for postdoc positions in mathematics

Things have changed since I was about to finish a PhD a long time ago, but the fact that you are unknown outside your university would have been common then, perhaps even now.

What you suggest seems to me to have two downsides. First, you are putting all your eggs into one basket (the conjecture) and second, you are entering into a time consuming process where others will need to verify your work. But beyond that, those others don't really know much about you beyond this one thing.

I would suggest, instead, that you depend on your advisor for a very strong letter and on others (professors and such) with whom you have interacted and who can speak now to your general mathematical ability and future potential. That can all be done quickly and can get you into what may be just the first round of applications.

But don't abandon your stated idea here to reach out to those others who have seen your work and might also help with an application if the more common approach seems not to be working as well as you hope.

You can get started early and if it doesn't work out, then the longer term solution may start to fall into place for the next round.


With regards to replying to emails, are my expectations too high from Group leaders?

As I have come to do again and again lately, I completely agree with @Buffy. You need to calm down and take it easy.

You have no idea what might be the reason for them delaying a response, it could due to:

delays with the paperwork to the rest of the faculty,
delays with interview all candidates,
delays due to other urgent matters such as grant/paper deadlines,
or simply some sort of personal emergency

2 weeks is not an insultingly long time, so you have no basis on which you can demand an answer. These are busy people we are talking about.

On a different note, it wouldn't prevent me from applying to somewhere else. Everyone who has ever applied to a position, or hired a person, knows the dynamics of this "game". Apply to other places if the wait stresses you, and you can always say that you had a more favorable position when you turn down a position. As long as you haven't played foul (i.e. lying, withholding important information etc) nobody should get upset.


Is it necessary to apply spaced repetition when reading research papers?

If you want to remember something long term, spaced repetition is a good way to remember it.
I interact with hundreds of papers per year.  Trying to remember them all is futile.  You should prioritize.


Contacting Potential PhD Supervisor: Including grades

I'm a little confused -- you're contacting faculty when you have not yet applied to or been accepted into the program?  What is your purpose in contacting them?  In my experience, at the very beginning stage before you apply, you might contact a faculty member to talk about their interests and what you'd like to work on, to see if you'd be a good fit, what the research possibilities might be, and so on.  Including all your background information at this point would be inappropriate, in my opinion.


affiliation if I change departments within university

Of course it’s also possible to have

  Zero the Hero, Department of Nothing and Institute of Heroes, Gong University

or else you can have your “old” address on the byline with a footnote to your new address:

  Zero the Hero*, Department of Nothing, Gong University

(* now at Institute of Heroes, Gong University )

The latter (and variations on this) is the model used for sabbaticals or for people who have moved since the work was completed: the researcher will acknowledge the host institution but will have a footnote to the current or the permanent address.


Should I ask for a recommendation letter from a professor who I know from an industry training program?

You mentioned in a comment that you already have two referees, one of whom you have published a paper with. I imagine this person will give you a very strong reference, and that the details of your other referees may not matter so much.

You also say that the professor you worked with is in the field you are interested in, which means they are well placed to talk about your ability and potential in that field, therefore using them as a third reference is a good idea.

You can find advice about emailing them to request a reference here.


Publishing again acknowledging the original publication of oneself

That means that IJACSA will not try to stop you from publishing your work elsewhere.  (They'd have little reason to do so, as they are not profiting from it.)  It is common for open-access journals to let the author retain the publication rights.

However, no reputable journal will publish an article that has already appeared somewhere else.

You could "publish" it on your web page, or on arXiv, or as part of a book (though again, a reputable book publisher will probably balk if the content is just recopied).

Note: IJACSA is published by The Science and Information Organization, which is on Beall's List of Predatory Open-Access Publishers.  Its website makes the journal look very dubious, especially the ridiculously broad scope and the promise to complete peer review within 15 days.  I wouldn't publish there (or would I?).


Hiding M1 grades or first year of master grades

Yes, 'hiding' any grades you are asked to supply to support an application is an ethical violation.

It seems like missing M1 grades are going to be a pretty obvious omission, and their dubious absence is likely to hurt you much more than their unappealing presence.

There are several existing answers here covering how to deal with and explain sub-par grades, or whether anything needs to be done at all.

How does the admissions process work for Ph.D. programs in the US, particularly for weak or borderline students?

How do I make a bad semester not look bad during my scholarship application?

How much will a poor first semester affect my grad school chances?

Should I explain a single bad grade in my personal statement?

Thoughts on Student with Bad Grades in Easy Courses and Better Grades in hard courses


Because of the way our systems work, at the top end of the distribution in fame, you will find people who are not only very good, but who also strongly desire to be famous and are very skilled self-promoters.  The market is simply too large for people to rise to the very top without that being the case.  And that means they are more likely to be abusers as well.

Sufficient abuse, academic or otherwise, can destroy any person.

Abuse can also help the abuser, by allowing them to effectively exploit other people... and that in turn might help those who survive (or who also learn to profit from the strategies of abuse), because they have a famous supervisor.

So: abuse can be profitable to the abusers and their chosen disciples, but it's a bad deal for the rest of the human beings they interact with and should be resisted at every turn.


BSc and further career in Academia on different subject

You might check in advance the application requirements for the MSc and/or PhD in Statistics or Applied Mathematics. By doing so, you will have a better overview on the technical competences you have to show to receive admission to the program.

In addition, you can show your interest by taking part or leading extracurricular activities with strong technical components (e.g., programming clubs, competitive programming, and so on.). Admission boards not only take into account your degree but the sum of your experience and potential.


What are the pros and cons of pursuing a professorship without a post-doc?

If I have a decent number of journal publications as per my area of
  research, is pursuing a post-doc after PhD worth it before searching
  for a professorship?

In many disciplines it is practically necessary to have done one or more post-docs in order to amass the research record needed to obtain a tenure track position at a research university.

In my discipline (applied mathematics) it is also common for a new PhD to use a mixed teaching/research post-doc or a primarily teaching visiting assistant professor position as a way to get teaching experience.

In my experience, many students apply for both post-docs and tenure track positions.  Reasons not to apply for a more desirable tenure track position are if you don't have any realistic chance of getting the position or if you feel that you want to gain more experience through a post-doc before starting on a tenure track position (starting in a tenure track position when you aren't adequately prepared could result in your failing to get tenure.)

Depending on your discipline, applying for a tenure track position immediately after the PhD may be extremely unlikely to get you the job.  On the other hand, if applying for a position (using a generic CV, cover letter, and research and teaching statements) takes less then a minute, then why not?

  Do faculty search committees give more preference to candidates with a
  post-doc over those who just finished their PhD, even though the
  number and quality of journal publications are comparable?

The search committee will be looking at post-docs who had as many publications as you during their PhD and then continued to produce at that rate or faster over a couple of years as a post-doc.  In my experience, someone who took longer after the PhD to amass the same number of publications and citations would be at a relative disadvantage.

  Does the opportunity to work with a well know professor significantly
  boost the chances of getting a faculty position?

In my opinion, yes.


Why would manuscript status change from "awaiting reviewer decisions" to "evaluation requests sent to reviewers"?

This happens frequently if e.g.

some reviewers agree to review, but don't submit their reports by the deadline (or tell the editor that they won't be able to complete the review after all.) Then the editor tries to find additional reviewers. Or,
the reviewers' reports come in and they are conflicting, so the editor wants more reviews to help him/her make a decision.


Why does a degree take several years to complete?

Specifically for a U.S. bachelor's degree, four years is a learning requirement, not a duration requirement.  By that I mean that institutions are constrained, by accreditation, tradition, and sometimes by law or regulation, to require learning (work) that can be competed in four years by a student working at "full load."   Where I taught, there was a legal requirement that specified the number of credit hours needed for a degree.

Some, perhaps many, students take longer—often much longer—than four years, but they complete the same number of credit-hours as the student who finishes in 3-1/2 years.  Some degrees, e.g. architecture, are five-year programs.  Similar reasoning applies to masters' programs.

Note that, in the absence of such a learning requirement, a university could just hand out degrees.  We call those "diploma mills."

So, the answer with respect to undergraduate education in the U.S. and often elsewhere, is that the amount of learning (work) is established by tradition and often embodied in law or regulation.  Someone who can complete that work in fewer than four years is free to do so; someone who takes longer is similarly free to do so.

Doctoral programs are different; the work is set out, at least in general, and can often be completed in about three years, but the student is time-limited to seven or ten years to be sure actual progress is being made.


Is it acceptable to submit papers anonymously to Computer Science conferences that don't ask for anonymity?

This is not a good idea. You just have to read every Call for Papers carefully and submit according to the instructions. That being said, I'm surprised that your program chair didn't ask you to resubmit with proper blinding instead of outright rejecting your paper. Submission errors happen, and authors are frequently given the opportunity to resubmit as long as the content isn't changed. The latter fact might be a little hard if the self-references weren't originally blinded, but I would think that most program chairs would have worked with you on this.


You should check the conference's policy on rebuttals.
In general, you can add results in the rebuttal, but they may or may not be ignored. A rebuttal should be equivalent to a minor revision, not a major revision. That said, there is not much harm in trying as an author to promise more in the rebuttal.

The problem is that rebuttals sometimes promise amazing improvements to the paper, but there is no way for the conference program committee to evaluate the promised improvements before making an accept/reject decision. So the general policy is that authors should ensure that the original submission is up to scratch and not rely on the rebuttal to make major improvements. Reviewers are instructed to evaluate the submitted paper on its own merits.

In your case, the reviewer has explicitly asked for something -- that is a clear license to provide it. If space allows, you can include that in the rebuttal and promise to add that to the final version of the paper.


What can I do, for I cannot read documents on screen for long times, but my required readings are too heavy?

e-ink

As also suggested in comments, a quality e-ink reader as (for example) the better Kindle models will provide a paper-like experience for your eyes at a limited weight.

PDFs are not the optimal form for that (ebook formats allow re-flowing to have screen-sized full pages at a font size tha't best for your eyes), but it will certainly work; reading hundreds of pages on that is more like reading a book than a screen.


Should we trust a journal article that does not cite any previous work?

I think it depends what you mean by "trust".

A modern academic paper which references no other paper is unusual and possibly fishy, but at least in my field (mathematics) there is nothing inherently faulty about the practice: perhaps you really are answering a question that you thought up yourself and for which the answer does not require you to use or cause you to refer to any published result.  (There must be some examples of this: anyone?)

If you're being asked to evaluate a paper then, sure, read it much more carefully if there are no citations.  That's not a good sign.  If you know the field well enough to know specific papers that the paper you're reading should have cited, then you should evaluate the paper negatively for not citing them.  If the paper has been published in a reputable journal you might consider writing to the editors to suggest missed citations.

On the other hand, a lack of references (or in-line citations) does not cause a paper to cease to exist.  If you want to cite the paper then you still can, and if you do use the material in the paper then you must cite it, as usual.


What do I do if I feel there are many things which need to be learnt to do my research?

so have others experienced this?

Basically every smart person feels like that when starting their studies. The majority of the people for which this is not true are usually not the second coming of Terence Tao or Dr. Sheldon Cooper, but simply affected by the Dunning-Kruger Effect. You are not supposed to know everything, and in fact you never will. You already have a head start on your colleagues, who have simply not yet discovered (or wilfully ignore) that they do not fully comprehend many of the seminal papers in your or related fields. You, at least, can work on this in order to produce better research.

  what is the best way of getting around this?

There is no getting around this. To paraphrase the title of your question, many things are to be learned. That's part of doing a PhD. The trick is to learn what you will really need for your research, and to not get lost in the things that are interesting but ultimately not relevant to you. This requires some experience. Hopefully, your advisor or a postdoc will put you on track of what to focus on for now.

As funny as the advice mentioned by @dgraziotin above sounds - in practice, what you really need to develop is a good mental filter to select the 15 or so papers from a 30k papers field that are really relevant to to you.


Are researchers permitted to mislead subjects about the purpose of a trial?

Standard 8: Research and Publication of the "Ethical Principles of Psychologists and Code of Conduct" of the American Psychological Association pertains. Specifically:

  8.07 Deception in Research

  (a) Psychologists do not conduct a study involving deception unless they have determined that the use of
  deceptive techniques is justified by the study's significant
  prospective scientific, educational or applied value and that
  effective nondeceptive alternative procedures are not feasible.

  (b) Psychologists do not deceive prospective participants about
  research that is reasonably expected to cause physical pain or severe
  emotional distress.

  (c) Psychologists explain any deception that is an integral feature of
  the design and conduct of an experiment to participants as early as is
  feasible, preferably at the conclusion of their participation, but no
  later than at the conclusion of the data collection, and permit
  participants to withdraw their data. (See also Standard 8.08,
  Debriefing.)

Whether or not a planned study satisfies these requirements is for the Institutional Review Board to decide, which must review every proposed study before it starts.


manuscript, excluding author names and affiliations

As Alice mentioned in the comments, the editor requests you to send an anonymized manuscript for the review process. The review is most probably double-blind, i.e. you do not get to know the reviewers' identity and neither do they know yours.

Be careful to adjust any language in your manuscript accordingly (e.g. "... as we showed in our earlier research [1]" -> "as has been shown in earlier research [1]").

For answers on why double-blind peer review is beneficial, see here.

TL;DR This is normal, do as the editor says.