Do any legitimate conferences charge per publication?

In computer science some legit conferences charge per accepted publication. In my experience, legit but small conferences perform this practice, perhaps to better cover the organization costs. Bigger conferences are often sponsored by big partners, e.g., Google, Microsoft, Facebook, Cisco, .., so they do not need to look for money elsewhere.

Generally speaking, conference registration pages are not very clear on this issue. Let's observe the registration page of the three biggest and most respected software engineering conferences, that are ICSE, FSE, and ESEM (there might be another better example for the third place here).

ICSE 2015 registration page:

  As specified in the acceptance letter, each accepted paper must be “covered” by one registration in the name of one of the authors.

FSE 2014 registration page:

  our paper submission and acceptance implies that one of the paper's authors should register the paper using non-student registration, i.e., either as non-member or ACM/SIGSOFT (Student) member, and present the paper at FSE 2014.

ESEM 2014 registration page:

  Conference registration is compulsory for at least one author of accepted papers and posters.

In my opinion, all three pages might imply that the conferences require a per publication fee. But,

I have just asked an author who was accepted twice for ICSE, and he was not required to pay twice the registration costs. (confirmed by @Psychonaut)
@Psychonaut can confirm that FSE does also not require multiple registrations.
I have asked some ESEM authors and organizers, and ESEM does not charge twice if a single author presents two papers.

Smaller conferences tend instead to ask for a per publication fee in case of multiple accepted papers and one author is presenting them.

An example is PROFES, which is a small yet respected and established venue.

  Each paper published in the conference proceedings (full/short/poster paper) requires at least one early registration to the main conference as regular attendee.

I happened to be there with two papers (one full, one short), and I had to pay twice.

I have seen some variations, e.g., one full registration for the first accepted paper, one discounted "student" registration for subsequent accepted papers.

To further clarify, if you have two accepted articles which are co-authored by Author A and Author B, either only Author A or Author B register twice (and present both papers), or both Author A and Author B register once each and present one paper each. In the second case, it might be just a matter of speaking with the organizers to still let one author present both papers.


It depends on the type of publication, I would say.

It would not be typical for journal or conference publications to have prefaces since dead trees are at a premium and long prefaces are not useful technical material.

It is common for journal and conference publications to have a short "Acknowledgements" note at the end of the paper (just before the bibliography), or linked as a footnote from the title. This note is typically for acknowledging funding sources of the authors, as well as people who contributed informally to the paper (but are not co-authors). Sometimes I like to thank (even anonymous) reviewers if their feedback was useful. However, these notes are concise: they are not prefaces where you would discuss, for example, the invaluable contribution of your cat or somesuch.

For books, monographs, etc., prefaces are fair game. But do consider what you put in there. It is often the first thing a reader will read.


Is it OK to add citations from low impact factor journals?

Of course, you should cite any relevant work.

You can't ignore work just because it is in a journal that someone believes to be lesser. That doesn't mean the work is bad.

As long you do a thorough literature review and avoid predatory journals, there should be no negative impact on your paper.


Why do professors want to make sure that their notes written on the blackboard will not be published?

The scribblings a professor writes on the board during a lecture represent the lowest-quality type of content that that professor will ever present in public: handwritten, hastily created under time pressure and at a time of high cognitive load, messy, unchecked, and prone to error. On the other hand, professors, like any other professionals, will much prefer to be judged by the highest-quality content that they produce, e.g., their research papers, which are carefully crafted over a long period of focus and concentration, digitally typeset, polished repeatedly, and double- and triple-checked for accuracy. So, to the extent that a professor gets to control which of the content they produced gets publicly released, they will almost never voluntarily consent to the release of the low-quality content.

An analogy that occurs to me is that of a movie actor: for precisely the same reason as I described above, actors prefer for the public to form its opinion of them through their movies, and not through a paparazzi photo of them taken while they were out shopping for groceries, wearing disheveled clothes, no make-up, a sloppy hairdo etc. So, if you don't want to be like a paparazzi, you will respect the wishes of your professor and not publicly post photos of their blackboard writings.

Edit: I feel a need to clarify my remark about "lowest-quality type of content" and "hastily created [...] messy, unchecked, and prone to error". It seems that some people are reading this as a description of some kind of unprofessional professor who comes to class unprepared, delivers a poor quality lecture, then out of insecurity and fear of having their poor lecturing skills exposed publicly, refuses to allow pictures of their blackboard posted online. That is not quite what I meant (or at least is only one possible scenario covered by my answer). I was talking much more generally about any professor, whether excellent or poor, who comes to class, well-prepared or not, and delivers a lecture, which may be an excellent one, and then, for completely legitimate and rational reasons and not out of any insecurity, guilt, or shame, objects to having pictures of their blackboard posted online.

Why would they object if their lecture is so good? Some have asked. The logic behind this is that the blackboard scribblings, even of an excellent and well-prepared professor, will still be a type of content that was created during a very short amount of time (the time of the lecture), while the professor is busy doing several other things at the same time (talking to the class, figuring out the details of the math or whatever it is they are writing on the board, consulting their notes, keeping track of time, etc.), is under the psychological pressure of being watched by a large group of people (many people find this a stressful situation), and has no time or cognitive resources available to detect or correct small errors that may be introduced inadvertently, no matter how carefully prepared one is. So, in a purely relative comparison between this content and other kinds of content that the same professor creates (e.g., research papers, which as I've said are thoughtfully prepared over many months), blackboard scribblings are relatively speaking a low quality content. It is simply an unfair competition: two different kinds of content, two different quality standards, and for the reasons I explained, many professors quite reasonably prefer to have only one of the two types be posted publicly online.

Finally, note that all of this is not at all at odds with the fact that the blackboard writing can still be good or even excellent in the context of the lecture in which it is performed.


“Percent” in chart title and on axis – redundant?

Percentage (parts per hundred) and, more broadly, abbreviations like ppm (parts per million) or ppb (parts per billion) do not describe any quantity, they are just multipliers for dimensionless quantities.

In a graph, instead, you should accurately describe the quantity being represented. In the example given in your question, a more appropriate title would probably be: "Fraction of the widgets that are blue".

In the SI brochure, §5.3.7, the document that defines the International System of Units, it is stated that

  In mathematical expressions, the internationally recognized symbol % (percent) may be used with the SI to represent the number 0.01. Thus, it can be used to express the values of dimensionless quantities.

and, furthermore,

  Phrases such as "percentage by mass", "percentage by volume", or "percentage by amount of substance" should not be used; the extra information on the quantity should instead be conveyed in the name and symbol for the quantity.

The percent symbol can, instead, appear in the tick labels.


During an application/interview should an applicant justify leaving a current faculty position (pre-tenure)?

It's not uncommon for people to move because of two-body issues, and if you're not comfortable disclosing the specific reasons, one possibility is to mention (at interview time) that you have non-academic constraints that force your departure from a place that you like.

Having said that, you're not going to get an interview call unless you're a superstar and everyone wants you OR you have some positive argument for why you're interested in a particular university. So in your cover letter you'll at least need to provide some positive reasons.


How to overcome my resistance to lecturing?

I don't enjoy lecturing either and yet my student reviews ask for more lectures even if I prefer discussion. What I've done for some classes is prepare a portfolio of 15 minute mini-lectures that are on one specific point, targeted, succint, and within the attention span (maybe) of 18 year olds.

You might also want to create a similar grab bag of canned material so that when a particular topic arises, you can easily lecture on it.

Otherwise, the only other way is to practice. I've realized my own aversion to lecturing is something I need to work more on, so I deliberately designed a large lecture course that was 100% lecturing, rather than the smaller seminar courses that I prefer.


Do professors tailor recommendations to universities?

Professors often write just a single general letter about the student and send that everwhere.

Advantage: don't feel shy about applying as many places as you want.


If there is a gap in your knowledge, and there is a course being offered that is a good fit for you, you could either enroll in the course or audit the course.  One course per semester maximum, please, so that it is clear where your priorities are.

One PhD is enough.  Math and computer science are close enough.

Yes, your self-confidence will grow as you build up a publication record.

Congrats on getting the job!


Guidelines to follow if my adviser suggests that I work on dead-end projects

This is a difficult issue to deal with. You are correct in stating that (in some disciplines) this can be a significant problem, but as a graduate student, it may be hard for you to argue your case that the project will lead to a dead end.

I see two possible solutions:

If you have a good relationship with your advisor, speak with him about your concerns. He may admit that he's not sure where the project will lead, but he will likely be willing to give you the background as to why he's interested in the project, and where it will lead you. These types of projects are also good opportunities to ask your advisor to introduce you to collaborators with whom you can complete the project, as he's only tangentially interested.
If your advisor likely won't listen to you, then put in the month or three to do the necessary background research to prove your case. Look up the references, research previous findings, contact others who have worked in the field. One of two things will happen: (1) you will change your mind, or (2) you'll build a strong case to present to your advisor as to why this research is not worth yours or his time. If at that point he still wants you to work on the project, then either he has political motivations or he's just being unreasonable, both of which are indicative of larger problems which you should deal with.


Open university and admissions into a US Masters

Some of this may be superfluous but the US system is very different from anything in UK or EU. In the first place there is no national system at all. Even within a single state, policies can differ widely, though the official state university system (so called public colleges, but not the same idea as UK public colleges) will usually share a set of policies within that state. But many schools, including some very highly rated ones (Stanford, Harvard, Yale, etc. i.e "Private colleges") aren't part of any system. Some "flagship" schools within a state may also have more rigorous admissions than the rest of the state system (UCBerkeley, UMichigan, etc.)

While Open University in general is highly regarded, each college (or system of colleges) will have its own admissions policies. These can even differ by discipline, so Chemistry might be different from Mathematics. Some admissions systems are more personalized, depending on interviews, and some have various requirements on grade averages, required courses, and other things.

The only real way to know if X is acceptable at a US university is to ask that institution or to apply formally. If your situation is non standard you might get asked for additional information. If an educational program is very popular and also highly regarded the unusual cases might be easier to simply reject as there are enough very highly qualified applicants who are easy to judge.

In general, however, a Masters degree application won't face extremely rigorous requirements. This may be different from European experience. It would be a different story for doctoral study, of course.

With all that said, I would guess that if you meet a particular school's requirements for prerequisite courses, roughly what an undergraduate would be expected to have in that discipline, and your grades were good, and you represent yourself well in the application, then I doubt that having studied at Open U would be an issue - most places. But the only way to know is to ask the institution in question and expect to get different answers from different institutions.

BTW, students in the US think of this "system" as perfectly normal.


Can I include under-review content in my PhD Thesis?

I am sure this may vary but this is standard procedure for our theses since they are based on papers. A student will typically have about four papers/manuscripts in their thesis ranging from published through all stages of revision in a journal to not yet submitted manuscripts.

You will need to check with your local guidelines what is expected from a thesis to figure out the details but it would seem difficult to demand all published papers unless the period to complete a PhD is open ended.


What is typically expected of a conference session chair?

Perhaps things are different in electrical engineering, but in math, the chair:

introduces the speaker, sometimes just saying their name and the title of their talk, sometimes a lengthier introduction ("[speaker] is professor at XYZ University and works on blablabla");
says "thank you" out loud and starts clapping at the end;
asks if there are questions or comments from the audience;
[optional] if the questions are taking too much time, the chair will say something like "we can discuss this more during the break" and go onto the next step;
once the questions are over, says "let's thank [speaker] again" and starts clapping;
announces the time of the next talk ("in 10 minutes", "after the break at 10:30"...). Rinse and repeat.

Sometimes the chair will go as far as warning the speaker if the time limit approaches or has passed. An extra task that sometimes pops up is when the organizers want to make an announcement before/after the talk; then the chair will say "[organizer] has an important announcement, please listen". This is pretty much it.

A handy trick is to get the schedule with speakers' names and talks' titles ahead of time. Then you can practice pronouncing speakers' names, and there's no awkward silence while you say "The second speaker this afternoon is [speaker], who will talk about... uh... squints to read the title on the board [title]".

It's also more or less expected for the chair to prepare at least one question about the talk, even a very simple one. This way, if no other member of the audience has any question, then the chair can say "I actually have a question, [insert question]" after the pause that occurs after "any questions?", saving the speaker a bit of embarrassment.


Do all accepted students in top-tier engineering programs get invited to interview before getting admitted?

Not all graduate programs in the US have (official) interviews at all.  In particular, except for Caltech, I'm not aware of any US computer science graduate programs that regularly interviews applicants before making admissions decisions.

There are a couple of sporadic exceptions, which are almost always handled by phone or skype:

Departments sometimes interview non-domestic students to check for English fluency, especially if their TOEFL (or equivalent) scores are missing or borderline but the application is otherwise strong.
Some individual faculty arrange informal interviews with prospective students before deciding whether to offer funding.

Outside computer science, some US engineering departments do regularly invite PhD students for on-campus interviews before admission, but I think this is more the exception than the rule.  In particular, as far as I know, none of the engineering departments at my university (which is highly ranked in most engineering disciplines) do this.


what should i do if professors don't reply my mail for graduate admission?

In the US, admissions are normally handled at the department level, so there's no reason you shouldn't apply, even if a potential advisor hasn't answered your email.

However, you may also want to consider the possibility that the advisor in question either didn't get it (it was sent to a spam folder, for instance), or overlooked it (it happens).


When choosing the institute as a Phd candidate, what aspects should be considered? (In Germany)

Of course, as you said, your academic interests are important. And your advisor is also important: there is (in all places I know) no academic training "how to supervise" whatsoever - there are extremly bad advisors and very good ones. If you know something about the prospective advisors, take this into account.
Of course, some advisors are good for some students and bad for others. As you want to go to industry, it could be nice not to have one of the "industry is evil"-type of advisors (if they are common or not is field-dependent).

Having a good advisors is really important, especially in Germany the situation is really hierarchical and if your advisor is mean to you, you cannot efficiently complain about them.

Otherwise, pick a place where you can imagine to live in. And, it goes without saying, if you have a partner (and/or kids, or family you have to take care of) take their opinions absolutely into account! Having a good PhD position but a bad private life happens unfortunately very often to academics.


Is there any guideline or consensus about reviewer's scores from ACM?

There is no such thing as “scoring an article according to ACM”.

I have seen scoring systems that rate papers on a scale from 0 to 3, from 0 to 10, from -5 to 5, from 0 to 6, from 1 to 7, ....  Scoring rules vary significantly from one conference to the next, sometimes even from one iteration to the next of the same conference.  These rules are decided by the program committee chair, sometimes but not always in consultation with the other members of the program committee and/or the conference steering committee.

Moreover, even when conferences use the same numerical scale, the meanings of the numbers change from one conference to the next.  For example, on a scale from 1 to 10, a score of 7 might mean "weak accept" (leaving 8–10 for "accept", "strong accept", and "best paper"), or it might mean "strong accept" (leaving 8-10 for "plenary session", "best paper", and "Turing award").

The publisher (in this case ACM) plays absolutely no role in the design of these scales.


Rejecting Postdoc Extension for Other Grant Management Opportunities

Or am I obliged to extend the contract so that the project does not get stuck in the middle?

Let's start with the easy question -- you are not obliged to extend the contract. A post-doc is inherently a time-limited position; both your funding agency and your university are (or should be) well aware that you could leave at any time. Your case is even more clear cut, in that the university deliberately structured your contract in such a way that they could cut you loose at any time. This flexibility cuts both ways.

I feel the guilt because I had the experience of having to take over other postgraduate student's work because they left.

This shouldn't induce guilt; rather, you have created a new project that can be used to give a new opportunity to someone else. Sure, this might not happen and the work might be instead forced onto an already-overworked student, but that is not your concern.

Should I let my supervisor know that I would like to move on to a different career path

Well, there are competing norms here. One (mostly in business) is that you should never express any thoughts about leaving until you have accepted another job. Another (mostly in universities) is that you should give as much notice as possible so that your advisor can make plans. Which of these you opt for will depend on your supervisor's personality. You should also check your contract to see what the provisions for leaving are -- renewing your contract for six months might not mean that you have to stay for the full six months.

I also stumbled on a few job openings for research grant management elsewhere, which I am interested in applying.

The way you have written this makes it sound like you have only the vaguest idea about what this career path entails. If this is the case, I would caution you against becoming unemployed too soon; your job search may take some time. I'm not sure which position you are referring to, but "contract administrator" positions are usually bookkeeping positions that are not a natural fit for an academic, while "program manager" positions are generally rather competitive and might not be something you would be certain to easily get hired for directly after a post-doc.


Is there a need for corrigendum in this case?

You don't specify your field, but in engineering and physics typos in formulae are fairly common (I daresay that papers without typos are the exception rather than the rule), and, no, there's really no need to write a corrigendum, especially if the formula is well known (everyone will understand that it's a typo).

Of course, in the above I assumed that what you derived in the rest of the paper was derived with the right formula.


Interviewing for a PhD with intent to reject the offer if admitted elsewhere

Having spent many years on the other side, I can assure you that what you are doing is completely ethical. Interviewing at multiple locations is simply part of the process. As a department, we spend considerable resources, both time and money, trying to recruit the best students that we can to our graduate program. We are fully aware that most if not all will receive other offers at top universities. And we know from experience that about half of the students we bring in will ultimately turn us down. It's a calculated risk that we are happy to take in order to recruit a top-notch cohort of students.


What should I do when my work has been published by my supervisor without my knowledge?

There is probably little you can do formally or legally. Not citing your thesis was a lapse, but getting that changed is not likely to happen. You can, of course, point people directly to your thesis.

I don't see any ethical issues with the publication itself. The work was, in some sense, unfinished. It is natural to want to finish it and you weren't there to help. But you should have been cited. But the ethical lapse was in failure to cite, not the publication itself, assuming that it was an extension.

But you might also be able to obtain a letter from your old supervisor explaining that the publication in question incorporated prior work of yours. That might be enough for your current purposes.

However, you might also be able to publish your thesis unchanged with original dates attached. It would be a late publication but if you can convince a journal to publish it, you could establish priority on at least some of the ideas. Your university will verify that the work was done prior to the new publication's date. If you change/update it, however, you lose the advantage of priority.

But try to work first with your old supervisor.

Another option is to extend not only your own old work but the publication itself. Then it is new work. You can cite your old thesis and the newer publication in this work. Ultimately that is what you want to be able to do, of course.


Conference claims they have indexed proceedings and publisher denies it

There are quite a lot of predatory journals, and some of them organize conferences. Some of these organize conferences with information that is outright false, in order to get money from academic in exchange of "academic credit" i.e. publications. Stay very away from these organizations, as most reputable academic institution would see worse having a publication in these places than no publications at all.

Can Springer do something about it? I assume their lawyers are on it, but its the same for any institution that is based on scamming. Its hard to get rid of them because they are playing outside the law already.


Does "scut work" contribution to a paper as a math undergrad carry weight in grad school application?

writing dozens of lines of code using Mathematica and helping my professor computing things

That sounds like normal undergraduate research to me.  It's probably not a menial contribution.  Very few people can write a dozen lines of Mathematica code.
If you do a good job, this could be a big help to your graduate school applications and even later career.


What to do when visa is in administrative processing and PhD program is starting?

The US state department says that wait times for administrative processing are usually less than 60 days, and they don't allow complaints or inquiries before those 60 days have passed.

July 17th sounds really late for PhD admission. You should have applied for a visa when you were admitted, probably back in April, or May at the latest, especially if you are in a country likely to have more scrutiny of visas.

You can talk to your department and inform them of the delay and ask how they would like to to proceed, but this seems like it falls under the category of "your fault" and there isn't anything your university can or should do to expedite the process. If your visa was denied for some incorrect reason (like they didn't believe you were admitted as a student), then the university would be of more help.


On the possibility and legality of bulk downloading papers from IEEE Xplore

No, it's not allowed.
IEEE Xplore terms of use (emphasis mine):

Authorized users are not permitted to:

Allow anyone other than an authorized user to use or access IEEE Xplore;
Display or otherwise make any information from IEEE Xplore available to anyone other than an authorized user;
Transmit electronically, via email or any other file transfer protocols, any portion of IEEE Xplore;
Download or attempt to download an entire issue or issues of a publication contained in IEEE Xplore;
Create a searchable archive of any portion of IEEE Xplore;
Use robots or intelligent agents to access, search, and/or systematically download any portion of IEEE Xplore;
Use any portion of IEEE Xplore for document delivery, fee-for-service use, or bulk reproduction or commercial distribution of materials in any form;
Alter or modify any portion of IEEE Xplore;
Delete or remove in any form or format, including on a printed article, any copyright information or notice contained in IEEE Xplore;
Reproduce or redistribute any portion of IEEE Xplore.


How to ensure my papers are indexed by Google Scholar

Besides the already mentioned options arXiv and Zenodo, you can also check if your have a local institutional repository and whether it is indexed by Google Scholar. Additionally, you can search in OpenDOAR (DOAR = Directory of Open Access Repositories) for repositories based upon subject area, content type, repository type, ...


The reference list only indicates the page numbers of the whole article within the book or journal etc in which it is contained. The citation indicates the page(s) within the article to which you are referring.

See https://www.library.cornell.edu/research/citation/mla


To what extent do Easychair Scores Affect Acceptance/Rejection in Theoretical Computer Science Conferences?

I've served on the program committees of several major theoretical computer science conferences, most recently SODA 2017.

  What percent of papers are usually accepted automatically, i.e. only with basis on the automatic ranking system of easychair?

Negligible.

For every submission, the assigned reviewers are asked to come to an agreement whether to accept or reject.  Each submission is assigned a shephard to guide the discussion and summarize it for the authors.  For the very few (≤5) submissions that receive only strong-accept scores, this discussion is usually perfunctory ("This appears to be a clear accept; any objections?" "Nope."), but not always.  The discussion is based on the content of the reviews, not just the scores (which may have come from subreviewers, who can't calibrate against other submissions).

For most conferences, the number of papers with supportive reviews is larger than the number of papers that can be accepted.  Especially later in the decision process, PC members are often asked to rank remaining papers, including papers that they were not assigned to review.  That instigates a higher-level discussion about this paper versus that one, or this AREA versus that one, which is rarely reported back to the authors (because the other submissions are none of their business).

In short: A paper with strong reviews can still be rejected because a majority of the other PC members preferred something else.

  Which score a paper should receive to be a clear accept? (assuming the paper has no flaws, and that no program committee member will claim to have found a flaw.)

There is no such score.

I have seen submissions with scores of (2,2,1) rejected after discussion.  Typically for such papers, PC members are encouraged to reduce their scores to reflect the discussion, but that does not always happen.  I don't remember if I've ever seen a (2,2,2) submission being rejected after discussion, but that doesn't mean it can't happen.

  My paper got a score of (2,1,1), that is to say, one strong accept and two weak accepts. The reviewers confidence were not disclosed but from the reviews I could see that they were either 4 (high) or 5 (expert). Would such a score guarantee the paper to be on the safe side?

Definitely not.  Most papers with those scores are accepted, but definitely not all.  Certainly I've had several conference rejections with similar scores.

More broadly: There is no "safe side".


How to enter a completely new research area as a 3rd-year Ph.D. candidate?

I hope you find the following beneficial.

Firstly, you need to gain some familiarity with the new area and gain
confidence on the general problems in the area. Survey papers,
classic materials (e.g textbook chapters), youtube videos etc at this stage. Say 1 week.
E.g, say a hypothetic paper is titled: "Statistical Modeling of Natural Disasters: A survey". However don't
be too distracted by reading too much general papers as PhD is highly
focused. Also, yotube videos should not distract and take too much
time!
Secondly, get a little deeper e.g say a hypothetic paper is titled "Survey of probabilistic modeling of
hurricanes and floods", "Birth and Death Processes for natural disaster
modeling" etc. Say this takes another week: Here you look for
something interesting to have an idea of potential technical papers.
Thirdly, you should already have a wide and narrow scope now, so you
could pick say 2 journal papers. One classic reference (relevant, rich, clearly expressed, highly influential and perhaps well cited) say 2005
and one recent paper, say 2017-2018.
Fourthly, briefly look and get an idea of the basic concepts in the
first reference (2005) to get familiar with the technical basics, basic relationships and
professional technical terms. Then, I suggest you re-write the second
(2017-2018) journal paper with your own hands etc. to keep yourself
"on it" systematically. During this process, you could get some
things and not get others. It is still fine at this stage. Also, at this stage it has been implicitly assumed that you have basic ideas of the statistical knowledge and tools to understand these materials.
Fifthly, you could summarize your handwritten note into a personal
tutorial, note the open areas, assumptions, problem solved, intuitive
questions etc. for future extension etc.. (It has also been assumed here that you are comfortable with the research tool e.g simulation approach etc.) Then begin to think about how to implement these (practicable and realistic) ideas, formulate a problem and hypothesis etc.

I hope others may continue from here. However, I hope this will get one on his feet, then everything coming after that may be more flexible. Note that I have not included survey paper writing as it may take more time.

Disclaimer: Thus is a suggestion and may not work explicitly for everyone at everytime


How much knowledge is expected of an MPhil applicant as compared to a PhD student, a postdoc or a research assistant?

How much is expected of background knowledge for an MPhil applicant?

This depends a lot on the domain and the institution, and MPhil doesn't exist in every country. So it's impossible to answer this question precisely, but I think one can broadly define the differences in terms of how operational the person is expected to be at producing research:

A postdoc is a professional researcher hired on a temporary basis. For all intents and purposes they must be able to carry out their research work on their own (i.e. produce research), under the direction of a PI.
A PhD student is training to become a researcher, and this training includes producing research. They are not expected to be autonomous in the production of research, their PhD advisor is here to train them. However they are supposed to have acquired the background knowledge and to be able to complete their knowledge in their specialized field on their own.
An MPhil student is at the initial stage of research training. They are expected to require more supervision and are not necessarily required to publish papers.
A research assistant is simply somebody hired to assist in research. They are not expected to produce research by themselves and might have a very limited knowledge of the research questions. For instance a software developer can be hired as research assistant in a physics project where they provide a service according to their skills. In general this is not a training position.


Is Facebook a necessary tool for a student?

Is there any explicit advantage I would get by joining the course's Facebook page

If you want to interact with your classmates on Facebook before starting the course, then joining the page would enable this.

  or equivalently, is there any disadvantage of not joining?

If you don't feel a need to do the above, then no. There is no reason to expect this to be any kind of handicap. You will have plenty of chances to interact with your classmates face to face, when the course starts.

Facebook is a useful marketing tool for universities, which is why they invited you to join the page. If you personally don't want to interact with others on Facebook (for very understandable reasons), then there is no need to join the page.


How to do a flawless and natural presentation?

A natural presentation comes from practice, and lots of it.

From practice comes confidence. Excellent speakers rarely have more than a few words bullet pointed on their slides. This means that the audience's attention is focused on the speaker. The speaker then tells the audience what the speaker wants them to hear, or directs the audience's attention to an image displayed on the screen.

Aside from not splitting the audience's attention between speaker and loads of text on-screen, having few words on your slides means that you are not tempted yourself to read your presentation to the audience. Such recitation is only suitable if you are analysing the text itself closely.

Further to that last point, having only single or few key words on your slides forces you to know your subject and what to say on each point. You don't have the slides to fall back upon, allowing you to lazily read them to your audience.

Which brings me back to practice. One way of getting familiar with what you want to say on each point is to write down a few detailed notes for yourself. When you practice your talk, you can refer to these detailed notes. Next time through, distil your notes down to only a few key words. Next time through - or when you are confident - your notes should be only the key words on the screen for the audience, and are therefore redundant. No notes, fluent delivery.


Reusing someone else's code in my own publication

You are doing the right thing as long as you clearly cite your sources. In other words, as long as you say that your code is based on someone else's code, and as long as you clearly cite what that "someone else's code" is and where a reader can find it, you are ok.

The fact that the basis for your work is open source does not require you to share your code as well (though that would clearly be in the spirit of open source software). Open source software generally just means that if you give someone else an executable of your implementation using an open source package, that you also need to give them the source code of your implementation. (The details vary based on the license in question, but that's the idea.) As long as you write the code only for yourself, there is no need or requirement to share it with others.


Reviewer wants me to do x - Should I admit I don't have the resources to do so although I think it's a good idea?

When I have been faced with a situation like this in the past, the course of action that my co-authors and I found best was to get in touch with the handling editor to negotiate.

Editors are the ones who will generally make the call, and if doing the experiments will pose an high burden in the time-frame available, it's worth having a discussion before starting them.  Sometimes a reviewer has pointed out a real flaw and more experiments really are required in order to deal with it.  Other times, a reviewer is just giving "wouldn't it be nice if..." homework.  It sounds like you think it's more the latter, but the editor may disagree.  I would recommend starting with an explanation of why you think your current experiments are sufficient for a significant publication and why the new experiments should be pushed into future work instead.  The discussion with the editor is likely to end up in one of three places:

The editor agrees that the experiments aren't necessary, and you can talk about them as a direction for future work.
The editor decides your paper will be rejected, since you can't do the experiments.
The editor agrees to a "middle ground" where certain critical studies are done (it may surprise you which ones), perhaps with an extension on time to allow you time to do them, and the paper moves forward.

Talking with an editor is taking an additional risk, since your paper might get rejected quickly, but I would recommend a "fail-fast" strategy over putting in lots of time and effort that turns out to be futile because you were working on something that wouldn't be enough to satisfy the editor in any case.


Is it ethical to submit a research proposal to multiple funding agencies?

Ask your program manager(s). NSF for example specifically asks you to list any simultaneous submission on the cover page.


Do graduate schools care about published solutions of contest problems in Mathematical magazines?

Sure, that would certainly be viewed favorably.  How favorably would depend on the rest of the application and the institution (though I can't think of any situation in which it would play a decisive role), but if the question is having done it whether to list it, then the answer is a clear yes.

If on the other hand you haven't done the problem-solving yet but are wondering whether you should engage in this activity for the value it has in your future grad school application: I don't recommend that, but I can think of plenty worse ways to spend your time.


The answer to your question is yes: there are research-only career pathways for mathematicians. One way of achieving this is to secure a job in a research-only institution, e.g. Max-Planck Institute in Germany, Academy of Sciences in Russia and other post-Soviet countries, or one of many government research labs / institutes in the USA.

Looking for a research-only career in a University can be much more challenging, if at all possible. This would usually imply buying off your teaching duties from a sequence of successful grants, and supervising many PhD students (which also involves a fair amount of teaching).

I can also recommend this article.


What can I do to maximize my chances of getting into a CS PhD program if I switched to a CS major during my junior year?

The first two years of undergrad in the US are mostly general education classes anyway, so I wouldn't worry about it. It is common to switch majors.

You seem like you are in great standings. You've taken a fair number of CS classes, received good grades, and will have two good letters. On top of that you'll have research experience and plan to take a few graduate courses.

From the little info you've provided, you seem like you are well on track!


Can I present myself as a postdoc at a given institution if I have a supervisor, but no official appointment there?

You may present yourself as a postdoc at X if, and only if, you have an official appointment at X, the kind that comes with an official title, effective start date (and usually an end date), and is documented in some kind of official document of the institution X - a contract, appointment letter, etc, signed by some official person. Otherwise it is simply not true that you “are a postdoc at X”, so obviously you shouldn’t say that you are.

If you have such an appointment (it sounds like you don’t), it would then be appropriate to list it in your CV. The best practice in that case would be to write your official title rather than “postdoc”, although if you want to clarify that the position is a kind of postdoctoral position, it would be reasonable to add this in square brackets or as a footnote.

Note that some official appointments are unpaid, so whether you are paid or not is not the main point.

Finally, everything I said above also addresses the question of whether it’s appropriate to represent X as an institutional affiliation in your papers (if you don’t have an official appointment, it isn’t; the institution hasn’t given you an appointment, which means they have not endorsed you as someone they are willing to have their name associated with on scientific publications).


Abandoning vs. further pursuing a rejected paper?

However, given that I ultimately aim for an academic career, I think it might be worth some efforts to get something published.

This alone makes me thing that it may be worth the effort - attempting to enter an academic career becomes vastly easier with some publications under your belt. Don't be discouraged by negative reviews - more than one of my papers has gotten reviews back that are essentially "This paper is bad, and the authors should feel bad" that end up seeing publication.

I would continue to pursue your paper for at least another round or two of submissions, but given it's not strictly speaking what you're interested in, if it becomes a burden either in your classwork or in publishing something you are interested in doing (I had a paper become just such a problem) return it to the shelf.


Final paper submission while NOT attending the conference

Mohammad, your co-author can attend the conference on your behalf, as he/she is also the part of that paper. However, it's better to contact the convenor/organizer of that conference. It depends upon their policies whether they allow it or not.


Is obtaining Multiple PhDs in two different and barely related disciplines detrimental to the career?

I think you're planning too far ahead, and are definitely overthinking this.  Most people find a PhD a pretty grueling process, generally well beyond expectations.  My feeling from having gone through it myself, and knowing many others who have, is that the odds are very high that you'll have no interest in going through it a second time.

Get a PhD in the field you actually want to work in.  Finishing a PhD is hard; finishing a PhD in a field you're not very interested in is even harder.  Put your energy into doing one field well, rather than spreading your energy out and doing two fields at a lesser level.

But to disregard that and answer your question, I think people without PhDs would probably be impressed, while people with PhDs would think it very strange, and not necessarily good.  But I suspect there would be pretty wide variance in opinions, depending on surrounding circumstances.

Edit: I should add that Master's Degrees make a pretty good supplement to PhDs.  So if you finish this MA in Education and then move to a different field that you can plausibly supplement with Education, that would be normal and probably pretty effective.  But again, plan to do your PhD in a field you're interested in.


How long should I wait for the receipt acknowledgement?

Most journals work with electronic submission systems but some still work with manual handling. Regardless, both systems require a person to handle the manuscript once it arrives. Since the past week has been the Christmas holiday for many and persons working with journals such as editors are usually not employed to work with the journal but do it aside their regular job, it is not strange that not much will happen during the holiday season.

I am sure you will receive notice of your submission sometime in the next couple of weeks into the new year, once the persons responsible will have a chance to have a look.

As a side note, as an editor, I can see that the number of submissions is slightly increasing before summer (holidays) and Christmas/New Years (holiday season). Authors, naturally, want to get their works away before taking time off, unfortunately, editors and reviewers, naturally reluctant to take on reviews during the holidays, do the same so the increased flux of manuscripts creates something of a traffic jam at these times. From this perspective, submitting a manuscript away from these times of the year will likely result in, at least slightly, faster response and turn-over times.


Journal publication and acceptance to competitive conferences

I'll give you my own opinion, as something of an interdisciplinary scientist in a nearby field (I work in mathematical epidemiology) with publications in both places (the conference paper frankly by accident):

First, your impression is indeed correct. CS and related fields very heavily weight conference presentations and proceedings papers in ways the life sciences really don't.

In my mind, there's two things you should be considering:

The opportunity to double-dip a bit. We had a question about this recently, but I think it applies to you as well. If your project has "Life science spin-offs" and "Computational science spin-offs", you can submit to both places. For example, I have a project that will end up living in both applied math journals and clinical journals. There's no reason you can't do both.
This part is purely my opinion. When in doubt, I'd go for journal publications, for a few reasons. I've found most CS and technical people recognize that outside their field, its papers or nothing, better than the other way around. Journal papers are also more likely to get on the radar of people you want seeing your work, get indexed in PubMed (LNCS for example is not indexed in PubMed) etc. Those departments will also probably recognize your technical chops either via talking to you, the technical bent of your publications, or a few conference presentations.

I sympathize with your problem - it's sadly familiar. Generally, I'd try to figure out which audience you want to sell yourself to more, and do as they do.


I want to pursue topics from different fields (pure math,CS) as a researcher. Which one to choose for my PhD?

Generally speaking PhD studies are all about specialization. One dives very deeply into a narrow field. This is especially true of math and can also be true of CS, depending on subfield.

There can be exceptions and some synthetic work is possible, but it depends a great deal on your advisor and what he or she is comfortable with. If you can find an advisor at the intersection you should be able to pursue a joint approach.

After the PhD you are much freer to pursue your own goals not constricted by the concerns of your advisor. I would suggest, pretty strongly, that you explore your wishes with a doctoral supervisor and take their advice. If the advice is to pursue the one field for now, it isn't a decision you need to live with for all time. But the advice will likely be good advice.

Doing a second doctorate will probably be superfluous. You will have deep research experience from the first. If it is in math, much of what you learned will have some application to thinking about some of what is important in CS.

Doing two doctorates simultaneously seems masochistic to me, especially as you will have two advisors each with different, possibly conflicting, expectations and each putting constraints on your time.

Think specialize now. Think widening interests for the future. It will better match the expectations of those around you and make life easier.

But you will also need ways to not get bored, given your description of the problem. It might even be that while focusing deeply on one of the fields you can 'play about' in the other for a short periods just as a stress reducer as needed.


When should an author retract their paper as a result of misinterpreted results?

Outside of ethical issues, I'd argue that the only time that retraction of a paper is warranted,  is when there is a methodological error that is so great that it completely invalidates all or almost all of the paper's key results. For example, if a paper is supposed to observe phenomena A, B, C, and D, I wouldn't retract the paper if the experiment that was supposed to measure D was done incorrectly, but the results of A, B, and C remain unchanged. A correction or erratum should suffice in such cases. However, if a paper was trying to derive X, Y, and Z, but faulty assumption Q invalidates all of the derived results, then that paper should be retracted.


What is the purpose of an undergraduate viva for a dissertation?

There is no single purpose of the viva, but broadly speaking it tests a student's ability to act like a researcher. It is not easy to define what does "being a researcher" mean, but the list of skills required definitely includes such things as: understanding the importance of the problem and its place in a wide picture of researchchoice of appropriate method to solve the problem ability to find a sound, elegant and technically accurate solution ability to communicate the solution for different audiences Many undergraduate assessments only test skill 3 from the list and (partly) skill 2. When students prepare a coursework or sit an exam, they always communicate their results in a certain style, typically in writing, and written for the single reader: the lecturer running the module.

Unlike a typical assessment, the format of viva allows three-way communication between the student, the text of thesis, and the readers / examiners. The opportunity to ask student a question about the text changes the game completely for all parties. For the student, the task is not only to write and present a text with the solution, but also to understand the solution, the questions which may be marginally connected with the topic of the text — a «big picture». For examiners, the goal is not only to check the formal correctness of the arguments, but also to make sure the student can freely use these arguments, and apply them to problems within the big picture.

Answering your specific question: it does not matter, what does the supervisor know. In viva, you, as a researcher, present the thesis. Your skill to be solely responsible for the text you produced is what is tested, not the text per se.  It is you, who should focus the examiners on the important parts of your thesis. Through the way how you present the research, you should be able to create a right context, and to attract the attention to the strongest parts of your thesis. Success in this part will invite comfortable questions; failure will result in a number of random questions distributed all over your thesis, which you'll have to answer. If you feel really uncomfortable talking about (some) part of your thesis, you possibly should ask yourself, why this topic is still a part of your thesis in the first place.


Negotiating for a higher hourly rate for RA position?

I think that under the circumstances you could just state your requirements. It doesn't seem like he is offering you very much professionally so you should ask for what you want to make it attractive.

Of course, he may not be able to offer what you want, or may be unwilling to do so. But you are giving up your current position to do this and the rewards seem a bit nebulous.

Other considerations might apply, of course. Is he a superstar that can/will advance your career otherwise? Is his position on co-authorship firm?

Think about the whole package.


Is being a poor writer a serious impediment as a researcher?

Yes, you need to be able to write to be successful in academia, as in many things.
But it is a skill that can be learned. You can take courses and you can practice. And, as with most learning, practice with feedback is the path. It isn't a short path, necessarily, but it is one that you can follow.
Actually, there are courses in both creative writing and technical writing.
You need to write with both precision and clarity and sometimes those are in opposition. But practice (with feedback) helps.


What do I do if my supervisor insists that the classical CLT is false and wants me to write that in my paper?

(1) Would you say that my supervisor is scientifically incompetent?

If he says the CLT as stated and proved in textbooks is false, he is obviously wrong. "Scientifically incompetent" sounds like a very sweeping statement that I would avoid endorsing given the information currently available. He could simply be misunderstanding something in the language of the paper, or his knowledge of rigorous math could have an embarrassing gap (wouldn't be the first time), or it could be a failure of communication between you where you have a subtle misunderstanding of his position.

In any case, textbook CLT is correct, no question about it.

  (2) How should I handle such a situation?

An honest intellectual dialogue with him to clarify the issue would be ideal, if he is the kind of person who can have such a dialogue when he is in the wrong and not back himself into an emotional corner and become upset and unable to reason. If you think that's risky, try to find another professor you trust and can consult about the issue, and if they agree with you, ask them to participate in a discussion with the advisor to make him understand your point. And try approaching any discussions with an open mind, in case it's you who are in error about what his position is exactly.

Finally, it's possible that your advisor really is scientifically incompetent, so if you are unable to make him come around to your view and conclude that he is intellectually unsuited to be your advisor, you should probably switch advisors. In any case, under no circumstance should you concede to his demand to deny the truth of a standard formulation of CLT in your paper. Good luck!


How can I manage the time of my research project under uncertainty?

Unfortunately, this sort of uncertainty is just part and parcel of the life of a researcher. I've been doing research for 15 years now, I run my own research group and this is still a problem for me.

With this in mind, my first piece of advice is not to feel alone in this. The uncertainty is not because of your inexperience. We never know how long research will take because, by definition, we don't know the answer yet, thats what makes it research.
Keep a notebook (real or computational) for each project/idea category and write your thoughts in them.
Celebrate any concrete progress however small.


Arxiv substantial text overlap after breaking up paper

While arXiv does not publish the exact details of their implementation, in their help section on overlap detection, they have to following notes that may be useful for you:

  Submitters can preempt the addition of a text overlap admin note by marking any known overlaps in advance in the "Comments" header (as long as the earlier appearance of the text has a coauthor in common): for example, "this article draws heavily from arXiv:x, arXiv:y," or "this article supersedes arXiv:z."

and

  A submitter who believes that an admin note indicating text overlap has been incorrectly applied to their article should contact arXiv moderation with a detailed explanation or justification.

In short: if you have sections that are intended to be in common between B and C, point them out in the comments, then flag for attention from a moderator.


Should I challenge the GRE requirement for a doctoral program in education (in the U.S.)?

I think the answer to your question is this:

How much do you value getting into graduate school versus how much do you value feeling like you are making a point?

If you value feeling like you are making a point, by all means, pursue the Soft Activism. My guess is that it will come across to the department like a complaint that you didn't do well enough on the test and are going rogue to make your point.

If you value getting into graduate school, then engage in "begrudging acceptance" that this is how you get into that particular graduate school. Like it or not, there's often a line of people willing to take your place, suffer the test, and smile. Moreover, if there's money on the line in the forms of scholarships or fellowships, consider the time/money you put into the test an investment. Study, practice, and prepare until you get a score you can submit in the hopes of getting in. You don't have to actively like the idea, you just need to accept this is the means to acceptance in graduate school.

For middle ground possibilities, I actually think the "hardline activism" approach is softer and less whiney than your "soft activism", because true or false it makes it seem like you've had a principled stand against the GRE since the beginning. Depending on the contours of the education program that might bode well for you. Some education programs might agree that the testing is bunk; my colleagues in education don't like standardized tests.

You can of course just submit the scores you have, but if you think they are inadequate for acceptance, that seems unwise.

After you're in, then write all the principled essays you want against it and try to change the system.


Managing relationships with uninvolved supervisors

The main problem from your side that I see here, is that you published the article without even telling her in advance. (Which might be based on you seeing her so rarely.)

Had you asked in advance, and maybe told her that this is how things work at your home university, she would probably have given her consent. That way she might feel backstabbed.

So the immediate action for you should be an appology from your side, telling her, like you told us, that this is what you thought you were supposed to do. (But don't make it a pure explanation, but make it an honest appology, the phrase "I am sorry" should appear at least once.)

I never had a publication without my advisor during my PhD, and (since we did alphabetical order) he was first author of all the papers. But than again, I met him on a weekly basis, so he was far more involved. I assume that by now, things have gone wrong for too long to change without you havily interfering (by requesting more frequent meetings and more involvment from her side). However, if you want this, I would tell her in a seperate discussion.

Thus, from this short description, I see the main flaws in your relationship on her side, but the main need for a concrete appology on yours.


Is it OK to add extra paragraph to a paper during the proof stage?

In general no. There may be some circumstance when it can be necessary but the proofing stage is too late for any substantial changes. The manuscript should be published in the form it has been accepted and it is an authors responsibility to provide a final version of the manuscript which ideally should not require any changes once type-set and provided in the form of a proof. Changes that are acceptable are changes that do not in any way change the science of the paper.

If  any major changes are done to the paper at proofing, the editor will likely decide whether or not these are permissible. What would happen if anyone tries to push substantial changes altering the core science of the paper probably varies, but in the worst case the paper might have to undergo new review.


When should I tell a collaborator about a mistake in their work?

On the other hand, if I leave it until the talk, it means that I have to bring it up in front of the rest of the research group, and he has no time to prepare a response.

Not necessarily.  You have the option of bringing it up with your collaborator privately, after the talk.  In general, a talk is not the ideal time to figure out whether the work presented is correct: that makes things stressful for the presenter, and unless the group is small and well-chosen, likely there will be some people there who are not invested enough / do not have enough background to want or be able to follow such a discussion.

If you talk to your collaborator afterwards, then this is less awkward in case you are mistaken or there is some kind of misunderstanding.  (In my experience, a lot of perceived mistakes in other people's work turns out to be some kind of misunderstanding.)  If you are right, you can still offer him help to fix the problem, in a way which might not work in the context of a talk.  In particular, in order to recognize and correct the error your collaborator will likely have to stop and think for more than a minute or two, which is the one thing that is almost impossible in a talk.

Maybe you feel bad having a talk in your research group that you strongly suspect is wrong.  Well, certainly if it turns out to be wrong that information will be conveyed to the group: your collaborator can send out new slides, a new paper, and so forth.  Moreover, just because the results are flawed doesn't necessarily mean the talk itself isn't worthwhile: it still may be.

It could be that you feel strongly that the material is so flawed that it is not worth subjecting your research group to a talk about it.  That's a tough situation.  Fortunately you've collaborated with your collaborator, so you may have some insight into how he would behave if he learned a few days before his talk that you think his results are seriously flawed.  If you've given this kind of negative feedback to him before and he's reacted well, I would risk it and let him know ASAP what you think is wrong.  If he agrees, maybe offer him the opportunity to reschedule.

For what it's worth, here's one data point: if someone that I worked with found what they thought was a flaw in my work, I would like them to tell me immediately. I would much rather cancel a talk then give a talk that I later found out was wrong, and if given a few days' notice I would probably just switch to something else.


Thesis project outside of advisor's expertise

Step 1:

Figure out if your professor is actually not capable of advising this project, or if you are just not communicating well. For instance, oftentimes when I hear that advisors are giving inconsistent advice, it just happens that the student often misunderstands what the advisor is trying to say (or the advisor is just throwing out ideas in a brainstorming style, which almost by definition means that some of those ideas will be conflicting - that does not necessarily mean that he does not know what he is talking about). For instance:

  it's a machine learning project, and while the first critical thing is training data, he told me to focus on finding features.

Focusing on the features first does not seem entirely crazy to me. Of course you'll need to find good training data for supervised learning at some point, but identifying the potential features is indeed usually a very early step in the process, afaik.

  sometimes he want it to be unsupervised, and when I mention training data he switched to supervised system.

It's a research project, he probably does not have a 100% clear vision of what exactly you need to do to make it work (nor should he). Maybe he is just throwing out ideas, and you are taking his words too seriously?

Critically question whether he or you are not understanding the project correctly. If this is the "main project he gets funding from", chances are that actually you are not understanding correctly.

Step 2:

If you decide that he actually cannot advise the project, and you can't do it alone, you can either get help or get out.

Getting help may include finding a co-advisor, but this may be difficult for various reasons (one being that most faculty are not overly interested in joining in ongoing, troubled projects of other professors for the dubious honor of being a co-advisor). Usually, it is easier to get the help of other persons in your lab more senior than you (postdocs, or even older PhD students), who have the necessary skills, and collaborate with them on your project. For this to work, you need to figure out what is "in it" for your collaborator (joined papers? something useful for their own dissertation / projects?).

If you are unable to get help, I see no other way than to get out, that is, change your project.


Asking a professor whether my application has been accepted or not

When a department decides to accept someone, they try to tell them as promptly as they reasonably can (sometimes they need to get administrative approval or the like), so delay indicates that a final decision has not been made.  If you haven't heard anything, you can assume you have not been accepted yet.  It's theoretically possible that the acceptance e-mail got caught in a spam filter, but that's probably not likely enough to be worth worrying about.

If you reach the point where large numbers of people have heard acceptances and rejections, but you have heard nothing, then it's worth asking about your status, just to make sure there wasn't a communication difficulty.  It's also worthwhile if you are facing an upcoming deadline and hope for an answer before that point.

However, if just a few students have received acceptances so far, then your best option is to wait and see what happens.  Asking for a status update will likely just lead to a response along the lines of "Sorry, we haven't made a final decision yet.  We'll let you know when we do."  (And asking more than once is likely to annoy the committee.  It's better to save your request in case it matters more later.)


What is the difference (if any) between a postdoctoral fellow and a postdoctoral intern?

Sometimes there is none, depending on the field or college.

In the UK, there can sometimes be a distinction. There are certain postdoctoral researcher positions that are positions in a PI's group where one works under a professor or more permanent faculty. A fellowship in the UK system means one has research independence and is allowed to pursue her own research program freely. Sometimes postdoc interns can also do this but it depends on the field, program, and position.


How do you organize your academic papers?

I highly recommend a software to manage this like Endnote, Zotero, or Mendeley. The last two are free if your library is small enough (depends on the size of the PDFs). That will make things much easier by cleaning up the metadata and helping you use search tools to find the right papers.

In each of these software, you can also sort the papers around. The key is that within these software, you can put a paper into multiple folders/categories/groups/whatever else they call it. I use this liberally. Note that the software will keep the reference as one reference with multiple links, and so if you do things like annotate or add notes to the file they will be visible at all locations where you can find the paper.

Before doing anything make sure the metadata is all correct. You can always last resort with using the search bar if it is.
First put each paper into a field. So I would make a folder like breast cancer, and then have a subcategory like metastasis if I have a bunch of papers specifically on that subtopic. Finding odd papers reduces to remembering what subtopic it's from, and finding that subtopic folder within the right topic.
If a paper works in multiple different places, I put it in each place.
Then add the papers to project folders. I make a master folder for each project, and subfolders for different parts of the project, put the appropriate references. The software can now automatically generate a file with all of the references for the paper which helps with citing.

Using this method, you can always dive down into a folder/subfolder that makes sense, either by project or by field, then sort by title/author/year/etc (and easily switch between these), or use the search in the subfolder, and always quickly find what you need.

But... you will need to take a day or two to set this up. That's a long and tedious task, but definitely worth it. Then I usually just do a minor fix up for new additions every few months to keep it tidy.


Is it OK to start a PhD with a side project still running from your master's?

Let me answer in two parts:

With the right advisor, projects undertaken on your own initiative will be valued rather than seen as a problem.
You definitely need to talk to your advisor now to make sure you're with the right advisor.

Expanding on this a bit... one of the hardest things for many people to learn in a Ph.D. program is how to organize and initiate their own research portfolio.  You show signs of doing this right from the start, so as long as you are willing to accept feedback and guidance, this is potentially a really good thing.

Whether it is a good fit for your advisor, however, depends on what your advisor's needs are at their current stage in their career.  Some professors really need their students to be focusing on particular problems that the professor currently wants or needs to tackle.  Others are able to give their students more freedom to wander intellectually.  This is partly based on career stage (pre-tenure professors are likely to demand more focus), and partly on personality (a control freak or an empire-builder will not be mellowed by tenure; a highly confident professor may give much free rein even before tenure).

So: talk with your advisor about your desires and plans.  If your advisor is receptive to the idea, great: now you can sort out how to balance things and make sure you aren't neglecting any responsibilities or making strategic mistakes.  If your advisor is not receptive, you need a different advisor.


Is it the number or quality of internships that is more important for Graduate School admission into Computer Science?

The short answer is a lack of internships is not a problem.

The long answer has two cases:

MSCS programs in the United States are profit makers for
universities.  It is much easier to get into an MSCS program at a
top university than the PhD program at the same university.
Research experience is a plus, but I don't think industry experience
matters.  Grades and recommendations from professors are most
important.
CS PhD programs in the United States almost exclusively admit
students that they are willing to fund, so they are much harder to
get into.  In addition to strong grades and letters of
recommendation, schools want to see that you are capable of working
independently at research.  The best way to do this, as Leon palafox
answered, is to have research experience, including a thesis and/or
publications.  Next best is to have completed projects not required
for any class.  That shows you are capable of doing a project
without its being broken down into lots of steps with intermediate
deadlines.  I'd say Summer of Code-like experience is at least as
valuable as an industry internship.  It shows passion and the
ability to work independently.  Incorporate that into your essay,
and get a letter of recommendation from someone on the project (or
from a professor at your institute if one is nominally supervising
your work for internship or independent study credit).

I am not knowledgeable about admission into programs outside of the United States.


How to "become familiar with the literature", inter alia to find appropriate method to publish independent research?

Maybe look for review journals on the topic. In my area there are several such journals. Researchers often do a "state of the topic" paper on something they are working on. You can scan a few 100 review topic titles. Should take you three or four hours. Then find three or four articles that you can zero in on. You should be able to "surface" read these articles in a couple days. Your university librarian should be able to help you find appropriate review journals. Once you have those papers you can also read the citations they tell you are most important.


Is it acceptable to extend results from an arXiv paper that has not appeared in a journal?

I understand your logic, but I do not think that many people treat papers on arXiv in that way.  Papers on arXiv are public unlike the papers you reviewed or the work you just heard by personal communication.  As such, extending the results in a paper on arXiv is a perfectly acceptable practice as long as the second paper cites the paper on arXiv properly.


Accused of cheating, without anyone witnessing it?

You admit that you knew that phones were not allowed in the testing room (being realistic, that they were not allowed on your person/in-plain-sight) during the exam. Yet the fact of the matter is that you had your phone out in-plain-sight, in the testing room, during the exam.

The short answer here is that there's isn't much you can do -- it's your word against the TA's, and unfortunately the evidence is not in your favor. I believe that you're being honest -- but I'm a random individual on the internet. And even if your professor/instructor/department believes that you're being honest, they can still fault you for having your phone out, period.

So the only advice I have: be honest, acknowledge that you made a poor decision but deny that you were actively cheating, buy a cheap $10 watch, and accept that there isn't much you can do here. Best-case scenario is that you get a stern warning; I can't tell you if that's likely or not. There's a variety of worst-case scenarios -- I'm sure you know that though.

As for the individual questions at the end of your post:

What are my options here? Be honest with your department. Study up on your school's honor code violation policy and be aware of the possible proceedings, as well as your rights as a student.
How are they possibly going to accuse me of cheating when it never happened? You had your phone out during an exam when you knew you shouldn't. That alone might be their motivation. As to "how" -- again, read the honor code violation policy to see what official actions they would have to take.
I've been thinking of witnesses... This may be helpful in an official proceeding, but only if these women can explicitly testify that you weren't cheating. Which, unfortunately, is unlikely if they were focused on their exams. In any event, I wouldn't bring this up in the meeting with your department.
The other thing that worries me is that I usually answer questions very nicely and sometimes word for word. Could go either way. You're not that different from a lot of students most likely -- but they could also cite this as evidence that you were reading the slides on your phone. Unfortunately, not much you can do about that now.

Mistakes happen. If this is your first run-in with the school's honor code, odds of it destroying your future are slim -- I'm not sure I've heard of someone being suspended or worse on a first offense. But make sure you learn from this experience -- that's about all you can do now.


How do you discover new papers as a mid-career academic?

CS/AI perspective

I get to them by

a. reviewing (you get stuff outside your field every once in a while)

b. Collaboration with colleagues outside my field (can be really fun but can take a while as you get used to each other’s discipline and its idiosyncrasies).

c. Going to seminars, listening to talks in conferences outside my field.


When a professor takes an affiliate appointment in another department, do they get an increase in salary?

I have never heard of a joint appointment in a second department being tied to a salary increase. It’s possible that in some rare situations such an increase will be negotiated as part of the deal for a professor to take on a joint appointment, but generically, the answer to the title question is “no”.

On the other hand, the answer to “or is it simply more responsibility for no incremental salary, kind of like service work?” is also “no”. Being a joint appointee does not involve “more responsibility”, rather it’s more accurate to describe it as a shift in responsibilities. Professors without a joint appointment already have a full time job, so they cannot increase their responsibilities (at least in a formal sense, and to a large extent also in a practical sense). If a professor takes on a joint appointment in another department, it’s likely because the professor simply likes the idea of being involved in the other department because their interests are aligned with that move, in the sense that the professor wants to have collaborations with other people in that department, wants to advise students in that department, wants to teach courses offered by that department, or similar things. But they had a full time job before the change in appointments, and they have a full time job after the change in appointments, so the total amount of work they are expected to do overall does not change.


Is it normal for a Ph.D. student to spend stipend money on research related items?

While in principle everything that you use in your research should be paid for by those funding your research, in practice it's not unusual to buy oneself small supplies at the "minor office supply" level for sake of expedience, or because they're outside of the main line of one's research.

For example, a student might want a $10 piece of electronics today that would take several weeks to acquire through normal channels, and then might decide it's not worth it to them to get reimbursed.  You might also buy something for yourself if you want to be the owner: for example, I bought my own laptop late in graduate school, rather than using a school laptop, because I wanted it to be my own personal machine that I could take with me when I finished.

What you have written, however, sounds like a much more problematic situation: it appears that you're effectively being asked to lie to your professor's funder, by misrepresenting how their money is being spent.  If it's a significant amount of money, then you could be abetting in a felony-level crime.  As such, if it is a significant amount of money, I would strongly advise you to not buy the equipment yourself.  Instead, I think you should tell your advisor that you need the equipment, but if they don't get it, you'll just have to do your best without.

If your advisor doesn't buy the equipment, you shouldn't badmouth your advisor to the funder. Just do your best, and if they ask you why you don't have the equipment you need, you can tell them the honest truth: you've asked your advisor for it and are hoping you'll get it.


Does students asking questions in class improve the learning outcome of the entire class?

In a group class setting, educators, mistakenly, think that if one person responds, subsequently the rest of the class shares the same understanding. Most instructors would agree this is not the case.

Questions on relevant topics help to engage all the students. Often times I use the student's question as a connecting point to ask one of mine. Other times I involve other students by asking questions such as “Good, now can someone provide another example? Who else has an opinion? Who disagrees?”

If the question is off-topic then it is the educator's responsibility to bring the class back to the discussion by asking one of their own questions.

At this time, I am unaware of any research related to this.

Note: I will append any links to this post if I come across relevant studies.


Strategies to remember papers that you read

The advice I was given by my supervisor is to write about a paragraph on each of the four following points for each paper you read (note, this is from a very CS perspective):

What's the context for the paper, in other words, what is the issue that the paper's trying to tackle, and what's the prior work in the area, or the work that the paper's trying to build off. For word published as parts of bigger projects, what's the overall aim of the project, and how does the paper fit in.
What's the key contribution of the paper, i.e. what is the central idea, or improvement that the paper presents over the state of the art. I (personally) find this one of the more important sections (especially in terms of remembering papers later), as this is where you need to really hone in on what the code idea behind the paper is, without all the extraneous implementation detail/proofs/arguments.
Criticisms of the work, no research is perfect! I'm personally terrible at looking back at papers I've read with rose tinted glasses, leading to a little bit of imposter syndrome. Having a list of criticisms of the paper can help to dull that, as well as providing a good counterbalance to the "key contribution" section.
Any other thoughts. As the purposes of the four points is to help remember the paper later, it's also important to make a note of what you personally thought while reading the paper. Really liked a sidenote they made? Make a note of it. Found an corner case you don't think they cover properly? Make a note of it - you could turn it into research later!

I usually find that I take about 10 minutes writing notes on each paper, along with about the amount of text that I've written for this answer. Your mileage as to how much you want to say about each paper may vary however.


How should a mathematics major choose between doing a Masters or PhD?

I'm not in mathematics so take my answer for what it is.
The fact that you were turned down by 6 PhD programs suggests that your applications probably weren't too strong. Maybe you had bad grades, bad test scores, bad recommendations, etc. Or you simply overestimated your application strength and applied to schools beyond your reach (i.e. top 15 schools).

Whatever it is, you need to overcome these shortcomings in your credentials. A Masters degree could be a great way to prove that you are grad school material, especially if you can demonstrate that you fit in academia by publishing article(s). This could be a jumping point to a decent PhD program. Generally, graduate programs would rather accept successful masters students over successful bachelors students, simply because good masters students already know the system and how to make it work.


Citing someone directly with additional information in footnote

My preference would be to avoid the footnote altogether, as I find them distracting. Keep the quote verbatim, give the source, and then explain the terminology in the next sentence of your text:

  Smith claims that "the best breakfast is a soft boiled ovum" [Smith87]. (Smith's "ovum" refers to what our paper calls an "egg.")

Another option, if you don't really care about  showing  Smith's exact words to the reader, is to make the change in the quote itself, indicating the change with brackets.

  Smith claims that "the best breakfast is a soft boiled [egg]" [Smith87].


To which point is a paper considered as a "student contribution"?

In my experience, such declarations are typically defined in terms of authorship.  Thus, you will see, for example, a prize to be awarded for papers with a student first author, or for papers with only students as authors.

I would therefore generally interpret "solely written by" as meaning "all co-authors are."

If you want to be certain, however, it should not be any problem to request clarification from the organizers.


As an instructor can I use previous work history as examples?

Yes, students always like “real” examples. You seem to have “anonymized” it sufficiently.

Those examples that start “You have 3 widgets produced by a widget company...” are SO boring, using relevant material is always good.

Could you re-write it as a case study if that is relevant.


What can I do, if I don't like the proposed research subject by my potential supervisor?

A successful project profits from both supervisor and candidate being interested in the same question. If you really dislike the topic, you should try to convince the supervisor to accept a different question. He will then, if he is amenable, try to convince you of a variation of his, you will amend it, etc. until - hopefully - convergence.

However, you may find that the supervisor is simply not interested in your direction. This can happen, even if he likes you. That's fine, and then you either have to find somebody closer to your question of interest or compromise.

That being said, it seems that you are talking about an MA Sc degree. This is considerably shorter than a PhD, so, depending on the details of the situation, it may be easier for you to find a compromise.

If topic really matters for you, however, you need to think hard whether you want to go into a field which you have qualms in.

I am not sure about what the ethical consideration of a "theoretical topic" as opposed to a practical one could possibly be; be is as it may, I would avoid bringing this up, as it may insinuate that you cast doubts about the ethics of your prospective supervisor.


Avoiding the appearance of name dropping in fellowship applications

The term "name dropping" represents an excessive use of auxiliary authoritative figures, with no justification or substantive basis, to promote one's image.

This means that if you say that you worked closely with Figure X, and you haven't, you are name dropping. But if you did work closely with Figure X, it is not name dropping to mention him/her. That is, a name dropper is an imposter, while someone who lists relevant names with sufficient justification is not a name dropper.

Hence, the advice you got from your colleagues regarding "a panel that hates name dropping will kill your application" is probably misguided and false.


Possible internship topics for a second year undergraduate student interested in astrophysics

Yay, astrophysics! That's my field, too. ^_^

I would focus less on what topics you could work on and more who you could work with.

For a research position, I'd suggest asking your physics and/or astronomy faculty if they have any research you can assist them with. This is a fantastic place to start, and it's where the vast majority of astrophysics people get their first research experience. In my experience, these positions are usually paid, but I know of situations where undergrads informally volunteer (and work fewer hours) in order to get the experience and extra advising. If your institution doesn't have any options, see if there's a college or university nearby that does.

You can also volunteer with your college or university at astronomy and physics outreach events. You can also see if there's an observatory or astronomical association near where you live, and see if you can't get involved there. You may find some paid part-time positions through the connections you make there.

For an internship, you can look for astrophysics-like businesses near you and see if they have any openings. There aren't many businesses that specialize in astrophysics, but there are many aerospace businesses. If you're open to looking at any of these, you may find luck.


What are the best practices for teaching second-language students in classes that have moved online mid-semester due to COVID-19?

how can professors teach their online classes in a way that is easily accessible for students whose first language is not English?

Teaching online does not change the students' brains.  Use all the pedagogical techniques you would use in a lecture or discussion class that was not online.  They will still work.

One thing that can be easier online:  you can record your lectures.  This can be done for in-person classes, but typically online teaching software makes it easy.  Lecture recording allows English language learners to listen repeatedly, at their own pace.  Just keep in mind that some students need privacy to practice speaking.


Publishing working paper before submission to peer-reviewed journal

The 'Guide for Authors' states the following:

  [...] Submission of an article implies that the work described has not been published previously (except in the form of an abstract, a published lecture or academic thesis, see 'Multiple, redundant or concurrent publication' for more information) [...]

  [...] Please note that preprints can be shared anywhere at any time, in line with Elsevier's sharing policy. Sharing your preprints e.g. on a preprint server will not count as prior publication (see 'Multiple, redundant or concurrent publication' for more information). [...]

Source

Additionally, the page 'Multiple, redundant or concurrent publication' states:

  [...] Multiple, redundant or concurrent publication: An author should not in general publish manuscripts describing essentially the same research in more than one journal or primary publication. Elsevier does not view the following uses of a work as prior publication: publication in the form of an abstract; publication as an academic thesis; publication as an electronic preprint. [...]

Source

To answer your question, you should clearly define what the WP-series really is. Is it just a collection of pre-prints or is it a primary publication? That's how you will get the answer you need.

In case of doubt, contact the Editor in advance.


This is completely up to the job. Maybe they will accept a Masters degree + work experience. Or maybe they won't.
Example:

The ideal candidate will have post-graduate qualifications (PhD, or MSc plus relevant experience) in molecular biology, molecular genetics, bioinformatics, epigenomics or a related discipline. A few years of practical experience working in epigenetic analyses would be preferred too.


Why can't friends or family members write recommendation letters for graduate admissions?

Because they cannot be objective.
Because they do not have firsthand knowledge of your academic abilities.
Because they do not have the background necessary to compare you to other graduate school applicants.

Also see Kisses of Death in the Graduate School Application Process, page 2, "Harmful letters of recommendation," subsection "Inappropriate sources," and Protocol for writing a recommendation letter for someone you only know on a personal basis.


Should I appeal the F grade I received in my programming class?

Mistakes happen.  If the prof couldn't grade your work because of some system problem -- regardless of whose fault the problem was -- it could have easily been resolved at the time with a simple email from the prof to you.  You could have resolved the issue, and he could have deducted an appropriate amount for the glitch.

In the meantime, I assume that because you're using a version control system for managing the project, that absolutely everything is time stamped.

I think you'd be in line if you send one more polite email, once again apologizing for screwing up privilege on his access, and asking him to please reconsider the grade, given that all the submissions are time stamped, and that you wish he would have notified you of the problem when it arose, and not surprised you with an F.

If that doesn't work, you might politely approach the department chair.

It goes without saying that I offer this advise assuming that I know the whole story, and that there are no undiscovered surprises such as academic dishonesty anywhere in the mix.


Is it possible to do PhD in pure mathematics after engineering

Sure, it is "possible".

I really question your stated rationale for it, though (couldn't get a job in engineering, thus staying in school and moving to a field that usually has harder time with job placement).  I think you would be better served beating the bushes and getting a job.


Preparing for the GRE Mathematics Subject Exam?

I am a student at a "Top 10" applied math program in the US. For us it was not the case that we needed top scores of the math gre for admission/fellowships (thought this was not the case for my pure math cohorts). So maybe this will help with the stress of the exam.

To answer, since you say that you are the weakest on vector calculus, I would spend the most time reviewing this materiel. Calculus makes up a majority of the questions and from my experience these questions were either you knew the "trick" or you were going to lose a lot of time doing it from the fundamentals.

Since you say that you are going to take it twice, here is my biggest advice. Try your best to remember the questions from the first exam. Especially if you don't know how to answer them. I also took the exam twice and ended up getting a couple of questions that were identical. So when you are done I would try to write down as many questions as you can remember to learn how to do for the next one.


Ask an expert in your field that you have never met to write a reference letter?

If you feel that A is sufficiently familiar with your work and your expertise and can comment upon those responsibly, then it is not inappropriate to ask him for a reference letter.

Your perception of your relationship maybe, however, different from his. And if that is the case he will probably politely turn you down (he is too busy, he does not feel comfortable doing it, etc.) in which case don't take it personally and don't hold it against him, and certainly don't force the matter. Having a weak letter at times is worse than not having one at all.

If the request was made to a complete stranger, it is possible that person may develop a bad impression due to this request out of the blue. But since you have been in correspondence with A, the worst that can happen really is that he would say 'no'.

To put in a personal perspective:

I have had an experience where an expert in the field, who has read some of my papers, and who has invited me for seminars (and hence whom I have personally met), turn down a request for a reference letter because he feel he is not in a position to write me an extremely strong letter.
I have had also an experience where an expert in the field agreed to write me a reference letter based on having read some of my papers and having conversed with some of my co-authors. We only had e-mail and Skype discussions after he agreed to write the letter and want to find out more about me and my interests.