In letters of recommendation, how are the different percentiles of ability perceived by the admissions committee?

Great question. It is one of the most ridiculous of all the forms we have to fill out when recommending people. Despite the illusion of being a quantitative measure, in reality it is qualitative and subjective. I imagine most people (certainly in my case) do not do what you have done and actually calculated where the student fell in terms of actual percentage. So if you do the honest thing, and say 25%, you may indeed be putting your student at a disadvantage. I have heard some professors say "oh, anything not top 5% or 10% is code for mediocre student." I'm not defending that view, but it definitely exists and is another symptom of how ridiculous the form is. As the comment by Bryan Krause states, people tend to rate higher, so your student will gain little from your honesty. Top 25% might even be perceived as a red flag. I also agree that admissions committees look at other measures (including the text of the letter) for a better indication of the student's promise.


Putting the cart before the horse: to state a claim without proof then prove it later or use a worse method?

(I have turned my comments into an answer).

Whether or not to discuss statistical assumptions depends largely on the nature of your work. Many authors of statistical textbooks and manuals discuss assumptions in great depth. They also highlight the importance of reporting the results of assumptions testing in your manuscripts. In my experience, this is very rarely done for several reasons. For example, results are often the same regardless of assumptions (this is not always the case), if you are reporting statistically significant results and effect sizes then perhaps the need to discuss assumptions is less important, word limits often restrict the ability to discussion assumptions, and it is often very rare these days to find discussion of statistical assumptions. Note that these points relate to applied journals and papers. If the paper is statistical in nature, or you have non-significant results and need to highlight that your statistics were appropriate, then perhaps discussion of assumptions is warranted. I very rarely run across discussion of assumptions for statistics ranging from t-tests to survival analyses and latent growth modelling etc. In statistics papers though its often important to highlight what assumptions are needed and such.

I have published in the pre-eminent journals on pain and you certainly do not need to discuss assumptions in them most of the time. If you review recent papers you will see that these assumptions are very rarely discussed. A simple "we did regression" and "here are results of regression" will suffice (with more elaboration, of course!).


Is an Additional degree required to qualify myself for post doc/industry position outside my area of expertise?

Is it reasonable (your original question), yes. Is it necessary to get the job you want, probably not!

"Requirements" for a job are often just loose guidelines, and in some cases are used to scare unqualified, untalented, or under-confident people away from applying. Good employers will usually loosen these requirements (or sometimes even outright ignore all of them) for the right candidate. Someone with a B.S. in computer science and a Ph.D. in math is exactly the type of person who could potentially qualify for a position that asks for a Ph.D. in CS. Requiring a Ph.D. in CS might be used to scare away all the coding ninjas who might otherwise apply. It is all about the story you are able to tell in your resume and interviews. Make the skills you have learned while completing your math Ph.D. appear as transferable as possible. Talk to math grads who are now in industry and peck their brains. Your degree is lucrative if you know how to sell it. I wouldn't recommend getting a second Ph.D just to go out into industry. At the very least apply to a bunch of jobs and see if you get some interviews before you go off and spend 4-6 more years in school.

I know of several people who have Ph.Ds in math and applied math without a B.S. in CS who went into industry. Many of the jobs they took said Ph.D. in CS required. Some companies just want really smart mathy people in these positions.


How does one use a paper that's not written in a language that he can read?

There is no general answer to your general question. It depends on a paper.

Do you have to cite it? We know that a2+b2=c2 and we don't cite Pythagoras manuscript on it. We don't cite the basic results we use.

Do you have to read it first? You probably don't read Disquisitiones Arithmeticae in Latin to quote some of Gauss results, and you don't read Théorie des mécanismes connus sous le nom de parallélogrammes to check if Chebyshev polynomials are correct.

So, if a result is already well-established, many people have seen it, checked it and built their work on it - you don't have to read the original paper, if you don't want to. If you really want to understand how some details were presented originally (for methodological or historical purposes), you can check if some colleagues in your University can read this language. If they don't, you can hire a translator, but it is not easy to find one who can also read understand math arguments.


What are the most credible rankings of US computer science departments?

Very few computer scientists (or academics in general) think highly of any ranking system. The main reason for this is that rankings are pretty arbitrary, highly biased by personal opinion, and not super informative. There's very minimal feedback pressure on rankers to get it "really right," and there's no particular reason to think that they do.

The methodologies vary widely, and small differences can result in wildly different rankings because the gradations between schools is usually not very big. In the US News and World Report Ranking, five schools all got a perfect score. Their methodology is to solicit rankings from researchers on a scale of 1-5 and then average them. So there were five schools that everyone gave top marks to. But there were also 17 schools that received higher than a 4.0 without receiving a 5.0. Due to their methodology, that means that there are at least 17 schools for which at least half of respondents said it was a 5/5. It seems unambiguous that all of those 17 schools are outstanding, because at least half of researchers gave them a 5/5. However, it likewise is very unclear what a 4.1 vs a 4.5 actually corresponds to.

This also shows how much the presentation of the results matter. The following three statements are all true of the USNWR ranking:

UIUC is ranked 4 slots behind CMU.
UIUC's ranking is five times that of CMU.
UIUC's raw score is 11% lower than that of CMU
UIUC is a top 3.3% school and CMU is a top 2.8% school.

Other sites use a weighted system that scores universities on a variety of factors and then take the weighted average. The issue with this methodology is that the results are highly variable with differing weights, and there doesn't seem to be any principled way to decide if "mean impact factor of faculty" should be weighted 0.3 or 0.1. Even choosing to measure "mean impact factor of faculty" could be disputed, and one could use median instead of mean or only look at the 5 most active professors. There are arguments for and against myriad tweaks like this, and again there seems to be no principled way to decide which is best. This wouldn't be very concerning if it mattered little, but it matters a lot. This is easily seen by looking at 5 random rankings and observing that there's a very high variance in the ranking of universities from site to site. This issue is exacerbated by the fact that universities try to game ranking systems (note there are two links there).

How your school is ranked can also vary massively with the discipline or sub-discipline.  My alma mater had a fabulous CS theory program, a less-reputed systems program, and (at the time) a non-existent AI program. Someone who says "I studied theoretical computer science at Stella's alma mater" gets a very different response than someone who says "I studied programming language theory."

Not only is your discipline going to matter a lot, who your adviser is will as well. Sometimes the word experts on fields or subfields work at universities that are, in general, not thought as high of. But if you can go study the problem you're interested in with the world expert on it, you should jump at that chance, even if it means going to some podunk school you'd have never heard of if your adviser wasn't located there. And these kinds of concerns are entirely ignored by rankings. Some rankings have breakdowns by sub-discipline, but there's no real way to get them nuanced enough to be particularly meaningful.

University rankings are also comically America-centric, and actual perception of the quality of universities widely varies by region, both within the US and across the world.

Finally, university ranking doesn't matter that much compared to other factors.


Should biomedical engineering/ biotech academics aim to start businesses?

The NIH seems to take the opposite view of you. The NIH provides funding for the training of a large number of biomedical engineers. The individual NRSA mechanism (F31 and F32) provides some of the most prestigious funding for PhD students and post docs. This funding comes with a pay back obligation such if you leave academia for industry within a few years of receiving NRSA funding, you can be required to pay back the funding. The NIH is in essence saying "do not leave academia" to the best biomedical engineers it trains. If the NIH thought more people should be starting up companies, I believe it would drastically increase the funding to the SBIR mechanism and rework the pay back mechanism to encourage individuals to leave instead of stay.


How to leave a PhD without angering my academic references?

Note that I have exhausted all the logical possibilities

It doesn't sound like you have, though. You need to explain, in very clear terms, that you are unhappy enough to leave the program and apply somewhere else.*

Don't hold back, but I would avoid using vulgar language (you know, like in your titular question), and would otherwise strive to be professional about it.

Now, most academics are sane, understanding people. If your advisor comes up with some potential solutions that, after reflecting on them, you decide are not satisfactory, then you should make your decision to leave the program and ask your advisor for a strong letter of recommendation. (I would encourage you to be patient when working through the potential solutions with your advisor, though, as there may need to be some iteration.)

The key here is to really, really, really make every attempt to find some common ground with your advisor that works for both parties before deciding to "jump ship." I don't see how a sane, understanding advisor could possibly hold against you wanting to put yourself in a better situation, so long as you make every possible attempt to make things work out where you currently are first.

* I don't mean to be rude, but from the comments below your question, you seem to have an answer for everything, so I want to minimize that type of interaction here. My impression is that you are beating around the bush with your advisor, and not really giving them the "full scoop." Just basically tell them what you have told us here, but in a professional manner.


What Affiliation to put for Amateur scientist who is an alumni out of school for 15 years?

Do I put my undergraduate university as my affiliation because I was educated there?

Absolutely not.  That could be considered fraudulent, since it would suggest you are still affiliated with this university.  You should only list an affiliation if it applies now or applied while the work was done, and in the latter case you should note if it has changed (by including a current affiliation or address).

You don't need to include any affiliation at all.  It's perfectly reasonable to publish a paper with a private address rather than a work address, in which case you can avoid this issue.  If you don't want to reveal your address, you can always get a P.O. box or the equivalent.  The main points are that people can distinguish you from others with the same name and can get in touch with you if needed.

You should not list your current employer unless they are OK with being listed.  If the research is not part of your job, your employer may not want to be seen as sponsoring your research, so you should ask if you don't know their policy on this issue.


What should I do with a paper I've translated?

If the paper you are speaking about is a published research paper, you should contact the publisher (e.g., Springer), as they do deal with copyright issues. If the paper is a technical paper, written by a set of authors about a subject, and those papers are hosted on an university website or a research-based company, then you need to contact the authors.

If the paper is not a research or technical paper, then well the question is not related to the Academia section.


COVID-19 - how do I navigate this situation with my advisor?

As someone who's been out of academia for a while, I would like to offer a different perspective. Yes, occupying your co-advisor's attention when the roof is on fire is tone-deaf. However: you have acquired skills that are obviously in high demand these days, and are thrown into a (hopefully) once-in-a lifetime situation to apply these skills. Especially since you're not on a strict deadline with your thesis, there are now more important things than finishing the thesis at the scheduled time. See this as an opportunity, not an obstacle.

Check if this is okay with your primary advisor, then send a mail to your co-advisor saying that you would be glad to put your thesis on ice and help her with her COVID work if she has anything you could be of help with. If you are a capable student, she probably will.

Then, when things have calmed down, reevaluate the situation, see what you have learned in the meantime, and continue from there.


Some weirdo is harassing me via e-mail and knows my physical address at uni; What do I do?

How about:

  I have told you not to contact me on this matter. If I receive any more threatening emails I will go to the police.

The best case scenario is they stop after receiving some form of the above.
Depending on exactly how alarming the emails are, you could also go to the police now, as well as taking it up with someone else in the University -- check your university's grievance procedure and support services. While your supervisor was unhelpful, there should always be some way to escalate or someone else to ask. You can talk to your fellow students and researchers, people you trust, to find someone who is supportive and helpful. Try to get a restraining order against this person.


No response from Professor; how should I remind him about writing a recommendation for me?

I would send an email along these lines (taken from Cindy Au on Quora):

  Dear Professor [Professor's name],

  The deadline for submitting letter of recommendation for [name of
  program/ fellowship] is quickly approaching. I would like to
  inquire if there is still any document I can supply to make your
  writing easier in addition to what we discussed during office hours 2 weeks ago.

  I understand that this is a very hectic time in the school year and
  thus can't thank you enough for your time and support.

  Respectfully yours,

  [Your name + ideally a link to some website containing your photo]


How long it takes for GRE score to be delivered to graduate school?

Per the ETS website, for the online general GRE (emphasis mine):

  About 10–15 days after your test date, your official scores will be available in your My GRE Account, and your scores will be sent to the score recipients you designate

It is up to the receiving institution to decide how they want to receive those scores: online (which doesn't add additional delivery time), or paper mail (which adds some additional shipping time).


Can my university revoke my degree after it was granted due to (corporate) data having changed?

Revoking a degree is rarely done and, then, only for the most extreme reasons such as explicit dishonesty and such. Any results in any thesis are subject to revision as new information becomes available that was not present in the past. It doesn't mean that the work was wrongly done, but only that what is known has advanced.

Since you re-did the experiment and came to the same conclusion, you may be able to publish something based on the new results and, when citing your unpublished theses, mention that the conclusions there were verified with new data.


Why are the acceptance rates for publications in subfields higher than others?

You can't judge a conference by its acceptance rate because you don't know what is in the rejection pile. For example, I know of a computer science conference that regulates its acceptance ratio by determining it in advance and then just setting the number of parallel tracks to fit.


In the GRE, why are we allowed to use calculators and not dictionaries?

The GRE is ran by ETS, so only they will be able to answer your question about why they don't allow dictionaries.

Your same logic starts to question the entire point of these tests. Using Google is trivial and is engrained in our day to day lives, so why can't we use it on the tests?


Are admissions offers sent after the April 15 deadline?

Yes, sometimes.

(I am the Graduate Coordinator of the UGA math department, i.e., the faculty member who is most directly in charge of graduate admissions here.)  April 15th is "the singularity" for sure: we make offers months before, many of which are held until the weeks, days or hours before April 15th.  As the deadline approaches, we try to check back in with people and try to hear sooner rather than later if they will decline.

While we try our best to get everything resolved by April 15th, it is likely that we will not entirely succeed.  E.g. for us this year we made an offer that was received (just) after April 15th.  Things tend to move very quickly after April 15th as well: we can really burn through a waiting list when it turns out that a lot of people on it took something by the April 15th deadline.

If you are still interested in a department and haven't been rejected yet by them, I would say that today is a great today to write back and let them know you're still interested.  At this time of year, knowing that an offer is likely to be accepted is worth something to us.

Good luck.


How long is the waiting time for having a phone/Skype interview?

When does the call close? I'd think likely 6 weeks after that - you could reach and ask how long they anticipate the committee search to take. Usually the committee is made up of multiple faculty members so I would imagine it would be post - holidays.


Having been, worked with, and supervised a number of undergraduate researchers in my time, a few thoughts:

If people have been working on a problem for years, it means there are pieces of that problem to work on. There is often a perception, I find, with new researchers, that the process of doing research is an on/off switch...that there is nothing...nothing...nothing...BAM! Breakthrough.

For most research, this isn't the case. Particularly good undergraduate projects are pieces of a larger whole, and generally are accomplishable over the course of a summer. Testing a particular hypothesis. Working on the implementation of the algorithm on a new platform/language, etc. Applying existing tools to new data or areas as a proof of concept. Testing the sensitivity of the results of a tool to some of the parameters used for it.

Undergraduate research, to be "successful", should produce a project the undergraduate can take ownership of (i.e. not just "Write the code one of my postdocs can't be bothered to) and helps move the lab's research agenda forward, but it's not necessarily supposed to produce flashy standalone results or major breakthroughs.


Quitting a PhD program and starting another one: who is the legal owner of my research?

Within limits, you most definitely can bring the old research with you and publish it. Unregulated digital data stored on a standard computer should be fine, but for example, there may be limitations on moving human subject data (even de-identified data) depending on what the IRB protocol said. If the research involved samples (e.g., chemical compounds) moving these may also be regulated.

You may or may not be able to use this previous work towards your dissertation. You will have to check with your new department.


Can industry experience make up for undergrad courses?

While not every place will respond positively, I don't see a huge problem in the US. But you will need to write your application materials so that people look at your "special case" positively and find strong evidence that you will likely succeed. You will be facing a lot of stiff competition at good places by people with a more standard and easy to judge set of qualifications, so you need to find a way to stand out.

Your current majors are useful in your proposed study, of course, even if you are missing some CS things.

So, don't stress the lack of additional courses in CS but the possession of skills related to the program that you want to join. Your academic record is what it is, though you may have time for some additional courses, but your other activities may, in the eyes of a reviewer, compensate for that and even give you an advantage. It is all, or at least a lot, about how you present yourself and your skills.

It might depend, of course, on which particular CS courses you took and on the kind of things you did in the internships. But like anyone, you have to make it easy to answer the main question: "Is it highly likely this person will succeed?". If you make it obvious that the answer is yes, then you have a shot. It will also be helpful if you have some ideas, even if only partly formed, on the kind of thing you want to study. Fairly specific. Fairly detailed.


Tables can typically be included verbatim (under fair use), just cite your source.
Turnitin is presumably just detecting verbatim inclusion. Assuming you've correctly cited your source, you can ignore.


I was graded unfairly on a group project

It is a good idea to ask. But you probably won't get a change in grade.

The "ask", however, should be about why the grade is lower than you thought it should be. Learn, if you don't already know, what the grading criteria was and how much each element contributed. The professor should be able and willing to answer these sorts of questions.

But it should also have been clear before the project started what the grading criteria should be and how important would be the evaluation of each part. It is possible that half the grade was assigned on the presentation.

Learning what happened gives you the chance to work on those things in which you were judged lower than the others. That is the real reason for asking.

If you really want the grade changed then get your teammates to advocate for it based on your contribution to the other part. But that will have to come from them, not just your claim of doing "half".


Why is it reasonable to believe that this student handed in a term paper from another class?

I might be having a completely different stance on the topic, however I feel it needs to be thought about. The primary goal of a school would be to asses whether the student in question has achieved a certain level of competences.
In order to test those competences you'd give all sorts of assignments to see whether the student has both competences AND skills required for their studies.

As @Significance and @DanRomik mentioned before, filing the other paper can be seen as self-plagiarism. However, if you consider that filing this paper is invalid you could also say that he never filed any valid paper in the first place. Meaning he crossed the deadline that was given for this paper.

School is a place to prepare a person to work at companies and more. So it would not be a bad idea to treat a student as if he were an employee. He filed his work late, couldn't meet the deadline and would obviously be penalized. Now since school is a place to learn from your mistakes you could throw him a lifeline. Rather than smashing him down, I'd accept his paper that was of extremely poor quality, but penalize the grade of this paper based on crossing the deadline.

Now, in the end he may still fail due to the poor quality + crossed deadline. But at the very least he would have learned to be more punctual about his work.

After all, being able to deliver good quality work on a timely way are some of the most important competences a student has to learn.


"no derivatives" clause for CC licensing

It is correct that it is very unlikely anyone is going to hack out chunks of a scientific paper and reuse them in another scientific paper - that would be plagarism, and very unsubtle plagarism at that. However, that's really not the main goal of allowing derivative works. (Plagarism tends to ignore copyright anyway, so worrying you've 'given permission' for it is a bit of a red herring...)

These are things that are (probably or potentially) considered derivatives in the meaning of that clause:

Edited or annotated extracts for teaching purposes
Translations of the whole or part of the paper into another language
Modifications of images and diagrams for reuse in other work (or in writing about your work)

Any of these, if done with appropriate permission and attribution, would not constitute plagarism - and all are fairly useful things to allow.

Some of these may be more useful in certain circumstances than others, of course.

There are also some complexities around databse licensing; depending on the jurisdiction, reusing material from a dataset could always be considered an adaptation. CC explicitly recommend against using ND clauses for datasets for this purpose. If your paper contains data tables, this aspect may be worth considering.


Is it good to work in a funded PhD project to complete it within time?

May I know what is the probability to complete it within that time. Moreover, what sort of guidance I should expect expect from him.

The answers will differ greatly based upon individual factors. Your primary source of information will be your advisor and your fellow PhD students and other researchers in your institute.

Some general points with respect to your questions, though:

Whether or not you can complete your PhD by the time your funding ends may or may not be relevant. Your advisor may be able and also willing to arrange for or help you get some other funding after your project has ended.
The project itself (i.e. the tasks mandated in the funding contract or similar documents) is probably feasible in time; especially as such documents are often kept a bit vague to allow for enough flexibility to finish things in time and work on your PhD.
It is difficult to say now whether your own research and your project are different, especially if they are somewhat related. They might remain separate, or either of them might become much more aligned with the other than it seems now.
The guidance to expect is very much dependent on the advisor and their resources. Maybe you will have weekly meetings, maybe you will have a hard time catching him to even read manuscripts before submission. Maybe he will advise himself, maybe he will delegate that to his postdocs or senior PhD candidates - or expect you to turn to them on your own.


What do you think about a part time PhD vs full time PhD, when the part time PhD involves working on my master's thesis research full time?

I can relate to your situation somewhat. I have been full time while studying my Masters and now my PhD, but in my case, there were no direct links (the job pays the bills).  The final academic transcript says the degree, not whether you did it part or full time.

While working full time, I finished my part time Masters (physics) in 3 years and are on track to do the same with my PhD.

It really depends on how much time you can realistically spend on your research so that it does not impact on your paid job, your lifestyle, family and friends and such.  Whether it is worthwhile really depends on you and what you are aiming for - it sounds like it may well be worthwhile for you, given your job is in the same field and that you are aspiring to have a career in Academia.

Hope this helps.


Whom to cite from an article: the reporter or the person who provided a quote to the reporter?

To add to Allure's suggestion, I think it would be most appropriate to make a slightly longer citation like

  According to (Corak, reported in Younglai 2016)

You stated that you didn't want to include both names, but I think it is more helpful to the reader that way. Additionally, the above citation tries to be not too wordy (compared to yours), as it is just a footnote inside the parentheses rather than disrupting the flow of text.

The ideal, of course, would be that you find a paper originally published by Corak or some other academic that identifies this phenomenon (the "theory/concept" you mention), but you may not have the time to do a detailed dig through the literature.


How is the Journal for an Annual Review Chosen

Short version: it's a money issue, at least in the case of Review of Particle Physics.

Disclaimer: I'm not part of the particle physics community, so I might get some details wrong in the following, but I think the broad strokes will nevertheless be correct.

First of all, I think the scale of what the Particle Data Group is doing shouldn't be underestimated. They are a group of more than 200 contributors, who publish a humongous, ever growing biennial authoritative and extremely well-regarded review article. With over 2,000 citations per year, I think it's fair of you to say that the article would boost most journals, rather than the other way around. Obviously just the data collection, editing, and fact checking requires a fair amount of funding.

Now, the crux of the matter is that they (PDG) also distribute the article in the form of a book, and a shorter (200-300 pages) booklet for free. We're not talking small numbers either - more than 30,000 copies of the booklet, and over 10,000 copies of the book (see e.g. this APS announcement).

As I understand it, there is a process where different publishers bid on the right to publish the review by offering to shoulder (at least) part of the cost of printing the books. (CERN covers at least some of the cost for the booklet.) This is the main reason why the article has moved around between different high-energy journals. Then in 2014, apparently only Chinese Physics put in a bid, and consequently went on to publish the article.


Guidelines for communication of machine learning methods in empirical research papers

Probably, precise communication guidelines will (and should) vary between different fields, depending in part on how well machine learning methods have been described, utilized and benchmarked in prior works within the field. However, in my opinion, every empirical field should already be able to take note of lessons learned within computer science, and also implement sanity checks on results based on both general and field-specific knowledge. Indeed, it's not all that different from applying statistical methods to a given study.

The main new challenge is guaranteeing reproducibility while using ML methods. See e.g. M. Hutson: Artificial intelligence faces reproducibility crisis, Science (2018). (Non-paywall link here.) The article stresses the need of providing code, test data, and details on training procedures, but does not provide very specific guidelines.

However, Joelle Pineau, professor of computer science at McGill, has been pushing for higher reproducibility standards in machine learning-related research. Although not published in the traditional sense, the Reproducibility Checklist on her website is the closest to a standard guideline I know of. For example, it was used for submissions to the 2019 NeurIPS conference. (A report on how this worked out can be found here.) It gets routinely updated, so I recommend checking the source. However, I will reproduce some of the points that are relevant for empirical science:

  For all datasets used, check if you include:

  The relevant statistics, such as number of examples.
  The details of train / validation / test splits.
  An explanation of any data that were excluded, and all pre-processing step.
  A link to a downloadable version of the dataset or simulation environment.
  For new data collected, a complete description of the data collection process, such as
  instructions to annotators and methods for quality control.

  For all reported experimental results, check if you include:

  The range of hyper-parameters considered, method to select the best hyper-parameter
  configuration, and specification of all hyper-parameters used to generate results.
  The exact number of training and evaluation runs.
  A clear definition of the specific measure or statistics used to report results
  A description of results with central tendency (e.g. mean) & variation (e.g. error bars).
  The average runtime for each result, or estimated energy cost.
  A description of the computing infrastructure used.

This was based on version 2.0 of the checklist, dated April 7, 2020. Note that experimental above does not mean experiment in the sense of empirical science, but in the sense of running a "numerical experiment" on some set of data.

Finally, note that this is a developing field. I fully expect more guidelines to be written over the next few years, as people realize the need for it. For a sign that this coming, see e.g. this 2019 DOE report, which declared scientific reproducibility in applications of scientific machine learning a priority research direction.


Verbatim copying of text that itself contains references - plagiarism?

If there's no reference to A, yes, that is plagiarism.  If Y has not read the papers by B and C, it's also reference padding.

It is possible that Y did read those papers by B and C and happened upon the same sentence structure as A, which is not plagiarism.  That's actually pretty easy when citing one paper.  "According to Smith (2001) blah, blah..." happens all the time.  With two authors and 25 words, it is much less likely that Y independently wrote the same thing.

You don't tell us the context.  I suppose it's possible there is a special case that would mitigate this, but I can't think of one.


How important are citations when applying for jobs or promotions?

In my experience, citation counts are considerably less important than recommendation letters, but they still matter, especially for tenure.  For fresh PhDs, high citation counts are definitely helpful, but they're not a hiring requirement for most fields in CS.  But for tenure, it's really hard to build a successful case without at least one high-impact (post-thesis) publication.

Smart committees know to gather citation counts, publication counts, acceptance rates, impact factors, h-indices, and other quasi-objective numerical data from reasonable sources and to compare them with peers in the applicant's field.  (For my promotion cases, for example, my citation counts were mined from Google Scholar, not ISI, and I was compared against other theoretical computer scientists, not other computational-geometers-who-play-with-surface-graphs.)  Alas, not every committee is smart.


Is there a term for the fact that research is done only with the means available?

In my university, people often call limitations as 'constraints'.

I have heard them saying:

"resource constraints" - availability of computers and machines, people

"financial constraints" - Money

"space constraints" - Physical space (room), lab etc.


Should my SOP be a narrative of all the events in my life that lead me to develop my research interest?

To answer your top-level question:
Absolutely not.
Your statement of purpose should be an account of what you want to do in graduate school, and your qualifications to undertake that research. Admissions officers do not want to read about everything you've done as a researcher since you were a child. Nor do we want a blow-by-blow account of your research career.
Instead, briefly summarize your history, and move on from there. The bulk of your essay should be what you plan to do, not what you've already done.


Should teachers announce the grade breakdown during first class?

I think it depends on the situation (assuming there is no official department or university policy on the matter).

For example, I am a young (math) teacher teaching a single course that has 25 students in it, at a college that I have never taught at before. I figured it was unlikely that I would be able to write exams that effectively separated the A's from the (A-)'s (say) based on some numerical scale that I set ahead of time. So I chose to not put a grade breakdown on the syllabus.

After each exam, I look at the performance of the students, and I give them an individual grade update containing what I call "a good estimate" of their letter grade thus far in the course. This prevents them from just remaining in the dark all term long with regards to their grade.

I have taught sections of courses at bigger schools where the grade scale is set ahead of time and is the same for all 800 or so students enrolled in the course. This makes sense, as the content of the courses is the same year after year, the exams are similar every year, and in general everything involving the course is somehow standardized.

I would say that, in general, it's fine to not announce a grade scale ahead of time if you don't have to. Just be prepared to have something to say about grades, because students will likely want to know. Sometimes I give myself some wiggle room on the syllabus by saying "your grade will not be lower than the following...", so they know that a 90 (or whatever) will guarantee them an A, but they might also earn an A with a score of less than a 90.


Can I quote something directly in a foreign language?

Reasons why you might want to include the original:

There are issues related to the precise wording and terms used in the original, which you pick up and elaborate on.
There is no reliable translation available, i.e. no published article contains the quote you would like to refer to. In this case, I would translate the quote myself and add a footnote along the lines of "original text" [source] (translated by this article's author).
Understanding the language the original is in is expected from the reader, e.g. in an article about the particular language. No need to include the translation in that case.

In any other case, I would stick to the translated version solely (and attribute it to its source as usual).


Given that the documentation is online (and apparently exclusively online), I would cite the website in question.

  Google and Open Handset Alliance n.d. Android API Guide. http://developer.android.com/guide/index.html. Accessed May 19, 2015.

See also this other question.


both sent "desk rejection" one saying "it was out of scope" and other one suggested couple other journals.

I am not going to lie - "out of scope" is a bit the academic version of "it's not you, it's me" in dating. Don't take this feedback as "your paper is ok, this is just not the right place for it". It may easily also just be an editor trying to be polite.

I don't know how common desk rejects are in the biomedical sciences, but in computer science they are rare enough that getting one from a regular journal (as opposed to, say, Nature or Science) is a pretty hefty red flag against a manuscript. Getting multiple desk rejects would mean that I would very critically reflect on the manuscript before trying anything further. Specifically, you say:

  Considering our findings were novel, our written language had no issues, and we tried to do our best with what we had in the lab, what do you think is the issue?

I would encourage you to revisit these assumptions. I don't think that results per se are usually what gets papers desk-rejected, but either a completely inappropriate write-up, submitting to journals where your paper is entirely out of scope, or obvious lack of scientific rigour as expected in the discipline.

I have found it to be a good heuristic to look at a random selection of other recent papers in the journal you want to submit to. Even if your results are novel, your method and paper structure should be similar to some of those. If you can't find any recent paper that resembles yours, it may be out of scope. For empirical work, also take a critical look at sample sizes. If all papers talk about hundreds of participants or survey responses and you have a dozen, talking about the novelty of your results won't get you far - it may still be rejected for lack of rigour. Similarly, if (almost) all other papers are empirical and yours is completely theoretical, or the other way around, look elsewhere.

I am aware that I have not directly answered your actual question:

  How to avoid desk rejection of a paper on novel findings?

The real feedback I have is - ponder the possibility that, after multiple desk rejects, your problem may not be that your findings are too novel. Get external, unbiased feedback, and find out why the paper appears so problematic to people not close to your work.


Is it a good idea to name some mathematical objects after my thesis advisor?

It sound as though your advisor was not the first to study/define/use these objects, but rather you just want to name them something, and think it might be nice to name them in honor of your advisor.  Please don't do this.  You'll only contribute to Stigler's law of eponymy, confuse people, embarrass your advisor and/or offend whoever was the first to study these objects.

Bear in mind two things: (i) Not every random object deserves a special name.  (ii) When you name objects, name them in a descriptive and evocative way, that will make using the terms intuitive and non-confusing (as a corollary, it also shouldn't conflict with other notation).  Many people don't even like the idea of name any mathematical objects after people, though it's common practice.

Now that naming them after your advisor is out of the way, you should feel free to consult your advisor on naming these things.


Git repo in shared folder or multiple cloned repos in each researcher individual folder for collaborative data analysis?

I pretty much agree that you've got two options:
Work as is, all in the same directory on the same system.
There are a lot of problems with this approach.

If multiple people are working at the same time modifying source files you'll step on each other's feet a lot. Two people can't edit the same file at the same time. You'll deal with annoying "that file is in use by another process" messages all the time.
Someone might make a change that affects the behavior of a function and it'll come as a surprise to someone else.

On the other hand, the issues you'll run into are fairly easy to recognize and plan around. If you all aren't familiar with Git, and expect to be making actual code changes fairly infrequently, the cons aren't too big of an issue.
I would avoid this at all costs. I've worked on projects before where multiple people were working on the same files in the same directory on a remote server and it's awful. Words almost cannot describe the frustration that it leads to.
Multiple versions of the repository
Set up the filesystem to look like:
user1/
--root/
----/functions
----/data
----/documentation
----/output
user2/
--root/
----/functions
----/data
----/documentation
----/output
user3/
--root/
----/functions
----/data
----/documentation
----/output
user4/
--root/
----/functions
----/data
----/documentation
----/output

Each user should have a directory that contains it's own clone of the repository. This lets you avoid stepping on each other's toes when working at the same time, and lets you emulate a "normal" git environment.
From there it's just business as normal, and as long as y'all can overcome the initial learning curve it'll work out much better than if you're all working in the same space.


How to present participation in undergraduate research experience programs on CV when applying for jobs in industry?

As a general note, do not use so many contractions and abbreviations. Writing terms out in full, at least the first time you use them, will never be wrong and may save a reader some time and effort.

You need to think of your resume in terms of what it tells the expected reader about your suitability for the job you are seeking.

Don't try to explain the subject matter of your research project "to a layperson". If the project does relate to a potential job, the hiring manager will either be a mathematician who understands the area, or will have mathematicians who understand the area on their technical staff, or at least will have arranged to consult a suitable mathematician on the hiring decision. If it does not relate, the reader of the resume probably does not care what the project was actually about.

A research project may tell a potential employer other things about you. Can you work independently on a specified problem? Can you write a coherent, readable report? Is your work good enough to lead to being accepted for a research project at a high prestige institution?


You're correct to want to mention them, CVs often probably only lack them because the writer hasn't done them or it isn't relevant to their career (perhaps they do not need to mention them any longer to prove particular skills). My CV included my programming/computing experience and was well received as the programming I had done was relevant; I was applying for computationally demanding PhD programmes.

Relevance is key so when including the projects, make sure the skills you gained from completing the open source projects are clear to the reader. Make sure it is also clear how these same skills are relevant to your application.


What are my chances of being accepted in a Ph.D. program with poor M.Sc. grades?

You need to talk with your thesis supervisor to find out whether the department's regulations are "hard" or "soft."  Many departments have clear regulations which are "soft" in the sense that they can have small exceptions made if a professor can make a case for why such an exception should be made.  This is very often the case, and if this is the case for your department and your supervisor wants you as a Ph.D. student, then you are fine.

Sometimes, however, a department will not allow such leniency for its professors.  If this is the case, and your supervisor wants you as a Ph.D. student, then they should also be able to advise you on what to do to try to get yourself into compliance with the regulations.


Resubmitted paper is rejected by editor after two months, what should I do?

The editor's comments clearly point to three things:
1. The manuscript lacks a clear statement of its aims and motivation
2. The manuscript is too long even after revision
3. There are grammatical errors in the manuscript

Regarding the second and third points, I think getting the manuscript professionally edited might be a good solution. However, regarding the first point, for a study to have reasonable impact, its aims and motivations need to be clear. You can perhaps do some rethinking around this point and take your supervisor's guidance to make these aspects clearer.

Now let's come to your questions.

Timelines and procedures are not uniform across journals, and it is not uncommon for a manuscript to be rejected without any reviewer comments after two months, particularly, since, it looks like the paper wasn't sent for review a second time. However, you can write a polite email to the editor requesting him/her to send you the reviewer comments if any.
I think the editor has made it amply clear that the paper is not suitable for publication in the journal. I personally feel it would be better to submit the paper to another journal, but if you are very keen on this journal, there is no harm in writing to the editor inquiring if he/she would be willing to take another look at it after it is professionally edited to reduce the length and fix the grammatical errors. You should also inform him/her that you will rework on the aims and motivations to make them clearer. Regarding how much of a chance you have, I am really not sure; depends on the editor.
I don't think the editor doesn't like the manuscript at all: he/she has probably seen some merit in it; else you would not have received the revise and resubmit decision the first time. However, the editor is clearly not very satisfied with the revisions. You should actually have taken care of the length and grammatical errors at the time of the revision. That would definitely have given you a better chance.

One word of advice: even if you submit to another journal, make sure you get the grammatical errors corrected before you do so.


Do I have to cite common CS algorithms?

No.

The fact that it was first published [in] 1961 isn't relevant, you needn't cite it because it is [widely] used and [well-]known by almost anyone in the CS world.

That said, although a citation isn't necessary, you can provide one at your discretion. Such a citation is probably more important for a final thesis than for an academic publication, since it may be considered important for students to demonstrate they can cite.

Beyond citing the original source, you may like to cite your favourite textbook(s) on the topic (rather than citing the entire volume, reference a particular section, e.g., \cite[Chapter 4.3]{Textbook} in LaTeX).


Would using an application fee waiver affect my admission result in a negative way?

The people in the program will evaluate and score your application.

They won't know whether the fee was waived, nor are they likely to care.

They will know if there is no GRE score. For some programs the GRE score is important, for others it is not.

You will need to ask the programs that you are considering what there policy is. GRE waivers are usually in lieu of other evidence (such as a strong work history, previous graduate degree, performance on some other graduate test (MCAT, GMAT, etc)).


Additional data for anonymous submission

There are three criteria: the solution must obscure your identity, it must not allow you to learn anything about the reviewers, and the second criterion must be common knowledge.

Any attempt to distribute files yourself through the web will fail to satisfy these conditions.  For example, if you use a website you own (under a pseudonym, say), then you can inspect the logs.  Even if you have arranged to use a service that will not provide any logs or allow you to tag pages or link to outside services, the reviewers may not notice that you have done so, and they may not even be willing to believe that you are not doing something tricky.

So this is a problem you cannot solve yourself.  You should get in touch with the program committee chair and ask whether the committee could make this data available to the reviewers.  As long as it goes through them, it doesn't matter how they provide it.


How should you refer to yourself in a paper?

This usually depends on whether or not you paper will be reviewed double-blind or not. If it's going to be double-blind, then you need to refer to yourself in the third person (i.e. by name, "Fred, et al.") rather than using a pronoun. If it's only going to be single-blind review, then I think it's a matter of style whether you use a pronoun or refer to yourself by name, though the venue you are submitting to, or your field, may have preferences. In which case, you should ask around.


Representing independent rediscoveries of a result in a survey paper

As you said, the goal of a survey paper is to make people aware of what other groups / communities are doing and bringing them together. It would be useful to present the full history of discovery and following re-discoveries, development, alternative approaches, etc.


All of the symptoms that you describe sound like symptoms of a reading or attentional issue. My wife has a doctorate in psycholinguistics and thinks that you're describing someone who should talk to their school or university psychologist or reading counsellor.  They could give you information on how to deal with the anxiety you feel when reading and help you learn strategies to enjoy reading.

Good luck!


Why are some graduate schools' students so much more productive?

The "fundamental difference" that you talk about should arise in three things:

The fact that a student made into the top 5-10 schools implies (not perfectly, of course) that the student has acquired a good amount of knowledge in the field and that he or she works very hard. This means the filtering, and thus a difference arises even before the program could start. It's not hard to assume that someone who gets into a top 10 school has worked harder in life to get there (of course, there are always exceptions). Thus, such a student is bound to be more ambitious, and would not settle for that one thesis at the end of their course.
Even if you're not that ambitious, seeing many peers around you publishing papers may encourage you or add pressure to do exactly the same. In life, we often try to rise up to the standards around us. If you're in a less reputed college with less motivated peers, you might be satisfied with good grades and a thesis. But if you're walking amongst other motivated people, you'd soon feel lesser and try to get on par.
Good schools attract good faculty. It's much easier to write a research paper and publish it with the guidance of a great professor.

We can see that the two principal differences arises without any effort on part of the college or university at all and solely because of the peer group. And that's an important factor in academia as much as it is in the real world.


Is it appropriate to include declined post doc offers on your CV?

I've seen a few cases of people in my field (linguistics) turning down competitive funding offers and listing them in CVs with "(declined)". Some of these happen to be tied to postdoctoral positions, especially ones offered by governments and/or prestigious granting agencies.

And depending on field/location, it might be possible to list job talks as 'invited talks' for particular departments.

Beyond that, I think referring to job offers you have refused is inappropriate and likely to look only like showing off.


It's hard to answer your question without knowing the country and field. I'll answer from my perspective, which probably extends to your situation, but take it with a grain of salt.

Here's a helpful resource describing in detail a typical (successful) job search timeline for computer science tenure-track faculty positions in the US: http://www.pgbovine.net/faculty-job-search-timeline.htm

Most interview invitations are sent out by the end of February. If you haven't heard by mid April (now), then unfortunately I think it's almost certain that you won't be invited.

Another source of information: Most departments list seminar speakers on their website. When their seminar starts filling up with interviewees, then you know they have been sending out invitations.

Most places never send a formal rejection or, if they do, it comes so late that the outcome was already obvious. So don't expect to hear anything.

Commiserations. The academic job search is tough! I wish you the best of luck in your other endeavours.


Is it possible to obtain an English certification online?

Yes. You are able to demonstrate your proficiency in English by obtaining one of the certifications below. Mind you, these courses do take 120 + hours and extensive command of English (grammar) to complete. Choose properly accredited ones when possible that include a practical component. Bonus: A recognized TEFL, TESL or TESOL certification can net you a job as an English teacher aboard as it is internationally recognized.

TEFL – Teaching English as a Foreign Language

TESL – Teaching English as a Second Language

TESOL – Teaching English to Speakers of another Language


Does it look bad if I email multiple professors in the same department at once?

Yes, it does look bad. When people approach me with a generic or just marginally tailored email and do not show that they have at least thought a little bit about how their research interests possibly match mine, I just throw the email away -- if they do not put in the effort then why should I?


Thesis by monograph, Must I publish my papers?

This will probably be closed because no one here can possibly know your institution's requirements. But, I'll take a stab at some general comments that apply to most institutions:

Thesis by monograph means writing a long "report" that your university approves.

Thesis by publication means stapling together a bunch of published papers.

In general, thus, if you are going for thesis by monograph, there is likely no requirement to publish. But, there are several good reasons to do so:

Papers are very important for you if you want an academic career (or any career in research)
Papers are very important for your advisor's and co-workers' academic careers. Indeed, I wouldn't be surprised if your advisor required/expected you to publish your good results
Papers are useful to the field as a whole, as papers are much more widely-read than thesis monographs

I should also clarify that publishing a paper does not mean just submitting a chapter from your manuscript to a journal. This is not the forum to describe how to publish papers; your advisor should help you with this.


Is it ethically unsound to accept a graduate admission offer then later withdraw?

It depends on what your ethical principles are. For example, if you self-define ethical behavior in terms of whether other people act that way, then it could be. "Accepting" an offer of admission means that you tell the university that you intend to enroll in the program, although if a jet plane crashes into your head and you are hospitalized for 5 years, you may be unable to make good on your word, due to unforeseen events.

In your case, it would be dishonest to accept and then decline, because the acceptance would be a lie (you don't intend to pursue the MS, you intend to pursue the MS if there isn't a better alternative, and this fact isn't unknown to you). An honest acceptance would be a conditional one, telling them that you provisionally accept subject to a change, owing to getting the second offer. That then allows the first institution to withdraw their offer, or to accept your conditions. It also allows them to extend an offer to another candidate, whom they might not be able to make an offer to (in time) if you accept under false pretenses.


No, you shouldn't change your bibtex database every time. Bibtex converts automatically from its native format "Surname, Firstname I. and Other, Author" to whatever the journal style is (for instance: F Surname, A Other), as long as you have full names in the database. Name formatting is something that people often get wrong at first when they have little experience with bibtex.

So you should aim for having full names in the database, at least for those papers that you need to cite with an unabbreviated first name. Everything would be easier if all journals used initials, but it's a tough world.

I suggest initials for theses, preprints and submissions, and only switch to full names after the article is accepted in a journal that demands them (and after being asked by a copy-editor that demands them). This is the solution that minimizes the workload on the author.


Ethics and etiquette, and permissions of posting student work to my online "teaching portfolio"

Do I need to ask the student for permission if I post their assignment without their name?

Yes, you do.

As a matter of etiquette, certainly. How do you think your students would feel if after leaving your class, they came across your website and saw that you had posted their work without asking them?

As a matter of ethics, you should not use student's work for personal gain, unless that use also serves a legitimate educational interest. I recommend that if you do this (with the students' permission), you should wait until after the course is over and the grades have been submitted, to reduce the power imbalance and so that a student will feel comfortable saying "No" to your request.

As a legal matter, possibly. At many institutions, students retain the copyright to their coursework. If the work is sufficiently creative to be copyrightable, then you are not legally allowed to post it online without the author's permission.

As a matter of policy, possibly. Your institution may have a policy forbidding this.

But even if the work is not copyrightable and your institution has no policy forbidding this, you should still ask the students for permission as a matter of common courtesy.


What format should the Methods & Materials section of a thesis be in?

Thesis writers generally have much more freedom to format them as they please. The only real requirement is that it follows any guidelines of the department and institution to which it is submitted, and receives the approval of the writers' thesis committees.

That said, I believe that these days, space should not really be a limiting consideration for a thesis writer. The methods section should be as long as needed to convey the necessary information. In addition, since this is not normally a journal publication, there is much more room to explain things in detail—which can be very useful for future members of the lab group who might follow up the same project.


What typically happens when a research field becomes "dead"?

Topology is surely not dead. Maybe geometric topology, or its specific parts that were targeted at the Poincaré conjecture?

Even then, there are several inequivalent definitions of deadness. One meaningful watershed is when advisers stop suggesting the field to their grad students because they don't believe the students can build their career on it anymore; a lot of fields are dead by these standards. Another, more restrictive, criterion is when editors can no longer find referees for papers on the field.

None of these things dooms the field to eternal dormance (in fact, many dead fields have recovered, some many times), and in fact people do sometimes work on dead fields: some because they don't care about building their career (e.g., since they already have a steady job, or since they are too idealistic to care), some because they feel like they can revitalize the subject, some because they hope to find things of use for other fields, and some simply because they don't know that it's dead.


I begin researching in three weeks and I have no idea where to begin. What should I say in my email to my advisor?

For starters, I hope you took her advice over summer. presumably this would be your first research experience, or an early one at least. With no prior practice your lack of knowledge is understandable. Presumably, also, your advisor knows of your state of experience.

Given all that, just be honest. Where should I start? What should I read? I suspect, strongly, that she is experienced in getting people started. Otherwise you wouldn't have been accepted in the first place.

But better than an email, expecting a long reply, would be a request for a meeting, asking for guidance. Don't try to overstate your abilities, and don't think that your current lack is a flaw. Everyone needs to start somewhere and it is good to have some guidance.

But since she has already given you advice (which you took, of course), you want to ask her for "next steps" (rather than where to start) and mentioning your lack of experience in this whole process. It isn't a time for embarrassment. It isn't warranted.

The situations in which this might be contraindicated is where the advisor is extremely busy - too many students, for example. But if she has a lot of students, it might be possible for you to join/start a group of her advisees and see what others know of her expectations. Some professors have weekly seminars for their students if they are working on similar things. Those other students can help you ease in to the process as well.


Can you publish studies based on confidential customer data that comes from private companies?

Publishing data based on confidential private company data
Where the company consents, it is possible to publish studies based on confidential customer data. Common requirements are

Don't identify the company in any publication and possibly be broad when discussing the context of the company (e.g., location)
Don't make the raw data available to other researchers or on online repositories
Don't present individual-level analyses or small group analyses which might allow any customers or proprietary data to be identified

When you initiate a relationship with a private company to analyse their data, it is important to discuss and agree on a number of matters:

Are you able to publish research based on analyses of their data? (note that this can be done without sharing their raw data)
If you publish, to what extent do they require their details to be concealed? (e.g., no disclosure of place, companies, etc.)
How will authorship of publications work? Does anyone at the company wish to be a co-author? If so, what level of contribution do they need to make and how will this work?
What if any rights of veto or influence do they have on what can be published? Will you have academic freedom to publish results even if they do not support the company's commercial agenda?
Are you able to share their data with other researchers or on suitable online repositories?
Will they give you money or other compensation for analyses you perform or reports you write for them? If so, what are the details?

Types of Relationships:

In general, there are different kinds of partnerships between academia and companies that relate to the analysis of data. Relationships should be formed based on a shared understanding of goals and mutual benefit.

Pure consulting: In this context, while you are in academia, you can often still provide standard consulting services. In this setting, you would charge commercial rates to the company for any insights you gain.
Pure research: Data is shared with you by the company with the explicit aim of assisting your program of research. The company may be curious about the results, but is principally motivated by a general desire to assist in your research. The company does not have any explicit expectations about customised reports and so on beyond the research program that you pursue.
Hybrid consulting/research: In this model the company is seeking to gain insights into their business. Providing customised reports to them and other services may be part of the exchange for allowing you access to the data for research purposes. Alternatively, allowing you to publish research based on the data may be one of your conditions that may offset the fee you charge the company for other services you provide.

Within all these models, there are many variations. The important point is that early on in the relationship, you ensure that both you and the company agree on what model is being adopted. These matters can also be renegotiated.


Personal quote at the beginning of a PhD thesis?

Yes, it is appropriate and harmless. At worst, it will be ignored, and at best, it will serve to remind readers of your thesis that you are human, and maybe that they are, too.

More generally, academia.se seems to have many questions that follow the template "Is it appropriate to do [insert completely innocuous but slightly nonconformist action that isn't mindlessly emulating the way everybody else in academia does something]?" The answer to such questions is generally Yes. Moreover, for what it's worth, I personally have a favorable view of people who are not afraid to do things in a slightly unconventional way, and I'm sure there are others who take the same view as me.


Two Bs in significantly harder, graduate level classes will not harm your chances of admission much if at all. Your GPA will only take a very slight dip from them (assuming your other marks are high) and, really, you did fine for your level. Remember that you are a whole package, not a just GPA. Write a good statement of purpose, work on doing well on the GREs if you are talking about the US, and do some volunteer research assistance to pad your CV. You're fine!


Adding affiliation due to a 1-month visit during a salary gap

I don't think that the effect will be different no matter what you put, but the latter (...hospitality...) version seems marginally more honest. Being a visitor at a prestigious place caries some cachet of course.

I don't think that a one month salary gap is going to be any issue, if it is even noticed. But you will mention the funding agency, of course.


Suggestions (overlapping rather than mutually exclusive; different techniques may work to different extents for different people):

• Keep really detailed to-do lists. Break tasks into small pieces ahead of time in as much detail as you can envision them. Cross things off one by one so that you don't either a) get lost between tasks, or b) run into a vague item, e.g. 'do report', and drift off to the Internet because you don't have enough to go on in order to get started. Optional: buying an oversized permanent marker so that crossing things off the list strikes you as decisive and worth celebrating.

• Build some rest-time into your schedule. If you know you'll need 30 minutes to decompress after teaching that class, put that on your schedule. Otherwise you'll be trying to force yourself to work and it will probably not go well.

• Carrot and stick. This is one of the two things that helps me out a lot. I bought a delicious cookie but it has a Post-It Note on it saying that I'm not giving it to myself until I've updated my CV, finished that abstract, and gotten caught up on responding to my undergrads' emails to me. I earn a day off every week unless I'm feeling extremely behind.

• Compile  distracting ideas into a 'later list'. This is the other. I'm not a major procrastinator, but when I'm being creative and productive, I'm often hit by unhelpful urges from elsewhere in my brain. If I pursue these instantly, then they sidetrack me and I lose a lot of time to YouTube/Wikipedia/Google Images/etc. But I don't want to forget about them, either. So I write them down on a sheet of paper, and then put it aside for later. Example might look like:

Reread hilarious email that [friend] sent me about his cat.
Search for [TV show from childhood] on YouTube.
Friends having baby. Look up that pattern for a knitted DNA model.
Check email.
Redesign personal letterhead.
Check email.
Look for [long-lost magazine issue] on eBay.
Did they ever find [missing kid from the 1990s]? Ask Google.
Browse Academia SE.
Check email.
Track down [friend]'s blog and see if his wife has given birth yet.
Get caught up on [webcomic I forgot about for a while].
Check email.
Text goofy note about silly dream to [friend].
Can't remember what the word 'palimpsest' means - look it up.
Add a bunch of books to GoodReads.
Check email.
Check email.
Okay, really, what are tangerines, botanically speaking? Ask Wikipedia.
Track down email address for [friend of friend].
Check email.
Look up video instructions on how to replace a zipper.
See if I can get [Windows 98 strategy game] to run on my laptop.
Order book by [colleague] to poke through.
Check email.
Revive dead LiveJournal account and see if anyone's still around.


Listing courses to be completed along with past courses

It is normal to list things that you are in the middle of, eg when you apply for a job you include your current job. The key point is that you must be careful to make it clear you have not completed the courses. Sometimes the form will make that essentially impossible, but requiring, say, a completion date that's in the past. In that case it's perhaps best to contact the people you are applying to and ask their advice.


How do you evaluate the potential for getting funding of post doc applicants?

Do you mean fellowships and other PhD-student only external awards, or are you OK with listing "I helped write this larger project grant that covered lots of people but I was not listed by name in the application"?

I think that in the last couple of years of a PhD, students should be helping to write the project proposals, but there are lots of reasons besides failure and lack of trying that might explain why they did not. Well-funded supervisors may, in my opinion misguidedly, shield their students from grant writing so that they can focus on the research. I think that this is a failure on the part of the supervisor to properly prepare a student for future research work, but it happens all the time. Some people don't get this training until the are a postdoc. You shouldn't hold the actions of the supervisor against the candidate.

Also, some applicants may believe that if they were "only" part of the writing team but not a co-PI or Senior Personnel (in NSF-speak) on an application, that they should not list it on their CV.

Finally, even for external grants which only cover a single student (fellowships and the like), having not applied for one doesn't mean much. There are many, many more PhD students than there are fellowship opportunities.

If you are trashing CVs for any of these reasons, you may be missing out on good postdocs.

Edited to answer the question (sort of): I don't hire a lot of postdocs, but I have directly or indirectly hired 20-30 PhD-level research staff. Some of them are expected to participate in proposal writing. We gauge their ability to write proposals by looking for it on CVs, asking them about their experience when it's not on their CVs, and talking about it during interviews. Then, we throw them in the deep end and see what happens. In my organization, we have large-scale projects that fund people's time, but if they want to work on their personal research projects, they need to write proposals. Those who do, get to work on things besides the center-wide projects. Those who don't, don't.


Publishing in low quality conference vs posting in arXiv

It probably depends on the "bad quality conference".

There are some conferences that are not the "top" conferences, have relatively high acceptance rates, and don't necessarily get the most exciting new results - but still do legitimate peer review, have respected experts in the field on their committee, and generally attract good attendees from good programs, albeit not with their very best work. These conferences are very much worth submitting work to and attending. You will get to network with people who are generally doing high quality work, get useful feedback on your own work, and hear some interesting talks.

(Many of the workshops that are co-located with the "top" conferences also fall into this category. These are especially useful, because you can also attend the main conference, and some people from the main conference will attend the workshop. They have many of the benefits of publishing in the "top" conference, but have much higher acceptance rates and are often a good venue for less mature or less exciting results.)

Then there are conferences that don't do high quality peer review, whose organizers and TPC are not particularly well known or respected, that have a very broad scope (so the attendees are barely interesting in one another's talks), and whose proceedings are riddled with plagiarism and work with serious methodological flaws. I would strongly recommend against submitting to these. You will not gain any of the benefits mentioned above. You will waste money traveling to and attending the conference. Publishing in such a conference will preclude you from ever publishing this work in a more reputable venue. It can also signal a lack of judgment with respect to where to publish - while many people will excuse this as just a lack of experience, it is still not the impression you want to leave on people reading your CV.


Getting into grad school for one field by doing research in another?

Your research in computer science is "somewhat close" to computer engineering. Plus the fact that you've demonstrated your "research" capabilities. That should help your grad school application.

The big question mark would be your abilities in engineering. The way to remove these doubts is to take, and do well in engineering courses.

Getting into a PhD program, while doable, might be a bit of a stretch. It's possible to make a "lateral" transfer into a Master's program, however. That's where you should take engineering courses to prove your abilities in this area.


How hard is it to re-enter academia as a postdoc in mathematics?

The possibility of getting a postdoc starts to drop rapidly as you become farther away from your PhD, regardless of what you are doing in the meantime. This goes double (or triple) if some of that time is spent without having publications.

What is your end goal? Certainly not to hop from postdoc to postdoc for the rest of your life. Answering this question will probably help you decide what to do. Take another postdoc if you are hoping to become a professor or academic researcher. Take a software development position if you are wanting to leave academia. Don't hold on to too much hope of being able to go back to academia in pure math after leaving for more than a year.


Is it better to request a recommendation letter in person after class or by email?

My recommendation is definitely in person "after class". There are several reasons to do so. First, it is personal and you can iron out any details there and then. Second, the person you approach will have a face to go with any future e-mail conversations. Third, it is less likely a person will dismiss you in a direct approach than in an (impersonal) e-mail approach.

There are of course ways in which you can blow your hopes with a personal approach as well. Just be brief and to the point, try to be professional about it. If the person appears not to have time, ask if you can meet during an office hour or if an E-mail would be better. After all, you have just presented yourself and is now "a face".

There is of course nothing wrong with just sending an E-mail but I know from personal experience that I sometimes get mails from students who apparently have attended my classes but made no impression so I ask myself, who the ...  is this? Not a great basis for a letter of recommendation. I personally also think that a personal approach shows more initiative and drive. All this is of course from the perspective that you actually can meet with the person without engaging in long distance travelling etc.


Use of QR codes in academic publications

I think this is a matter of convention and necessity.  As you already point out, most documents are online.  If something is online or in pdf form, having a QR code that is scanned with a phone is a waste of space, as the user can just click on the link instead.

In the case you are describing, I find it rare that any document would be only available in paper form, if it was made at any time since the invention of the QR codes existence (which it would need to be in order to have one).

The question also seems to be a rare situation.  You are saying a new document is published, but it is only available in paper, but it contains other information that needs to be seen online.  It is hard to imagine a document which is in paper, that contains some valuable data that needs to be viewed on an electronic system, in which the time saved from scanning a QR code on a phone and dealing with a phone screen outweighs the use of a tiny url or permalink typed into a computer.


Including desired rank in a cover letter for an open-rank faculty position?

I suspect this is one of these questions where there is no truly "correct answer" as you can't predict what's going on in any given search committee, but I think you're unlikely to do any damage by leaving it open.  At least my understanding of these things is that a department would rather hire you w/o tenure (note that this is not quite the same as the associate/assistant distinction) as it is less of a headache with the administration; you'll get tenure if they really want you, and don't think they'll get you otherwise.  I don't think it will matter much what you wrote in your cover letter.  Concentrate on making them want you, and then worry about what they have to do to get you.


What to do when an advisor repeatedly changes graduation requirements?

My advice would be to cultivate one or more allies in the department (perhaps other committee members who already have tenure?). These allies can both put pressure on Dr Jessica to allow the student to graduate and provide accountability to both parties. Another way to pressure the faculty member is to publicize your upcoming job loudly and often. This way the faculty member’s peers start asking her about the student’s job and the defense.

In regards to scheduling the defense specifically, the student can get other committee members to “request” that a date be set. The excuse would be: “I was talking to Dr Adam (choose someone tenured to help with this) and he mentioned that his schedule is packed and he wants me to schedule the defense right now so he knows when it is. He knows that you have final approval, but he just wants a date to hold.”

I basically used these strategies to manage my reluctant chair when I had a job arranged. They only worked because my chair cared about his reputation with his peers more than he wanted to “perfect” my dissertation.

At the same time, the student needs to realize that many faculty have been burned by students who never publish their research results once they take jobs in industry. This represents a waste of good research/resources for the faculty member trying to get tenure and for society at large. The change in demands is likely because the faculty member is just realizing this possibility exists and does not trust the student. The student should do whatever it takes to assure the faculty member that the research will get published after the student starts the position.


Why do even prominent institutions hire publishing houses (Springer / Elsevier etc.) for their journals?

It's not trivial to run a journal. You need so many things:

A journal management system
A desk editor to constantly keep in contact with the editorial board, answer author queries, etc
A content editor familiar with the subject matter to identify topics for invited reviews, perform editorial screening, etc
A typesetter who can set every manuscript, no matter what format it's written in (Word, LaTeX, etc) into the journal's style
A copyeditor and proofreader to check the paper's English
A marketing executive to promote the journal, e.g. by finding related conferences and getting insertions
An epub executive to handle the journal's website, epub files and distribution, deal with copyright infringement, and so on
A sales executive to handle subscriptions, payments, and customer service
An artist to design the journal cover, its promotional materials, and so on
Someone to liaise with printers to print hardcopies of the journal, and then get them delivered to conferences / subscribers

Note this list covers a wide range of skills. It's unlikely a single person can do all of them without extensive training. But publishers already have people who specialize in all of these. By engaging Springer / Elsevier etc to handle their journal, the Institution of Engineers saves themselves the trouble of having to learn how to publish a journal. In this, it's not that different from trusting one's university's IT technicians to keep the IT network up and running. One could learn how to maintain a network and do-it-yourself, but why not just leave it to the professionals.


I can't speak for all disciplines but in biomedical science this is generally considered an inefficient way of writing because the same sentence can be simplified to

  My reason(s) of shifting to biology from physics is(are)...

It's also considered tacky but I probably have to attribute that to overuse and misuse. I will only use hypophora if the statement is highly unusual or seemingly illogical. This is a bad use because the statement is not dramatic:

  To make tea I first need to bring the water to boiling. Why? Because...

Contrasting to:

  To make tea I first need to bring the water to boiling with a silver spoon in the kettle. Why? Because...

is probably synchronizing better with the readers' mental rhythm: "Huh? Why the heck would you put a silver spoon in it?" Then the following "Why?" would serve a better role: to resonate with the readers.

Surely enough in my own field nothing is dramatic enough for me to deploy this expression. Is "shifting from physics to biology" unusual enough to raise eyebrows? I am not sure without too much context. My gut sense is perhaps not because I'd categorize them both under the school of science and they do go together quite well. I'd think "shifting to biology after spending 10 years studying physics" or "shifting to biology from classical string performance study" may probably deserve a "Why?" Although, this is purely opinion.

The part after the "Because..." deserves attention as well. Make sure it's followed by a very compelling reason, or your "Why?" may be tainted with a taste of self-doubting or still-on-a-soul-searching instead of persuasion.

In any case, expressions like such are unlikely very harmful if used sparingly. They also serve to inject some liveliness into the statement. I'd consider using no more than once in a statement acceptable.


Research Questions / Hypotheses for an Engineering (CS) Thesis

Formal hypotheses are over-rated, but still often necessary for scientific communication, especially for a pedagogical exercise like a thesis proposal.  The key question here is this: how will you know if you have succeeded in your intended work?

If the problem hasn't been solved before, then your core hypothesis is that it can be solved effectively with your proposed approach.  From that spills out a whole bunch of secondary questions:

Is the problem well-defined enough that "solved" is meaningful? This is often especially problematic in AI (e.g., "human-like behavior in a chat-bot", "good book recommendations")
Relatedly, how can you measure whether you have actually solved the problem?
What is the difference between a trivial/toy solution and an effective solution?  Again, a big problem in AI, where it's often possible to make systems that technically solve the problem but practically do not (e.g., for real applications they require unavailable curated data, or a thousand years of training time).
What sort of "partial solution" milestones are there along the way that will help you tell whether you are on the right track?
What would an optimal solution be?  Can it even be identified?
What will you learn if your chosen approach doesn't seem to be working?  Will it be possible to definitively tell that it cannot be a solution?
How will you know when you have done enough?

If you can provide good answers to all of these questions (or even just most of them), then you will have a very solid thesis proposal, built around the hypothesis of "Approach X can solve Problem Y."


I'll give it a try...:

The association should be your current association:

First, it's where an interested reader from abroad can find you, and
secondly, your previous association even might be unhappy if you continue to publish papers with their name on it. (Just imagine some former member - not you, of course! - publishing substandard papers!)

If there are more authors from different universities, such as your former advisor, you should mention their association, too. Sometimes that will lead to a lot of fine-print in the header... but that's not a bad thing, when it comes to publishing: it signifies the work is up to standards of two or more different associations. And many people like to see some collaboration, for a change ;)

As for arranging the authors #2..N, a host of obscure and regional rules is applied :) At some institutions, the last place is considered to be the most honorable ("the chair"), sometimes authors are listed in descending order of importance of their contribution... which without fail will cause trouble when a team wants to publish something. Some resort to alphabetical order, or even comment on the rules applied in a footnote (which is a little bit absurd). So, talk it over with you co-authors :)

If someone can't make a contribution to the publication, the correct way would be not to give them as co-author, but to identifying their contribution (if it is significant - another controversial subject) in the paper. Conversely, if you want someone as co-author who isn't directly involved, like your former advisor, she or he might almost feel obliged to force some (sometimes impractical) changes, in order to justify their co-authorship. - Again, talk to them beforehand, everything is easier that way ;)


Can I include an author URL as part of the affiliation block in an IEEE Conference Paper?

Sure. The IEEE conference template even includes an example of an author who gives a web URL in the affiliation block:

  Michael Shell
  School of Electrical and Computer Engineering
  Georgia Institute of Technology
  Atlanta, Georgia 30332–0250
  Email: http://www.michaelshell.org/contact.html

The variety of examples in the template further make it clear that authors can choose whether or not to include details such as email, web URL, address, telephone number, and fax (!) number in the author affiliation block.


I must say that I would have a hard time listing the pros of the first approach (separate results and discussion sections), because I don't like it and it doesn't fit my style of writing. My advice would be: if you can, write in the style that you like best, because that's how your writing will be most natural/readable/convincing.

However, the choice is not Manichaean as you make it sound. There exist a continuum between those two, because it mainly depends on what you call “results” and “discussion”. When I write for a journal that requires a strict “results then discussion” format, what I usually do is that I put most of my text in the results part, and leave some general overall discussion for the discussion part. Typically, it would given something like:

  Results

  First result. Discuss its implications.
  Second result. How it confirms result #1. Consistent with previous observations [ref].
  Third result. Again, some discussion of it.

  Discussion

  Altogether, what is the insight given by these results. It changes our view of this phenomenon somewhat. It is in line with work by X et al., but highlights some contradictions of Y’s model.

That's a bit “cheating”, but I've never been asked to reörganize any paper written in that way.


Will it hurt you to leave a tenure track position (for another) after one year?

Before committing to leaving, it might also be beneficial to re-consider the current job situation. You mentioned the reasons for leaving are:

  more related to

    the teaching load,
    the types of classes I'd be teaching,
    the background of the students I'd be teaching,
    and the possibility of advising PhD students.

Regardless of which aspects of each of these items you consider problematic, it appears your fundamental assumption is that all these things will be different in the new job.  Until you actually do get the new job and let these four elements play out as they may, this will remain an assumption.

Even if you believe the situation will be different based on some 'inside knowledge' at the universities/departments you are applying to, these are merely perceptions and beliefs at this point. There is simply no way of knowing what the new situation will be like until after the fact.

In the world of tenure-track academe, these assumptions seem risky.

Based on what I hear from peers working in the academe, and occasional reading, your issues are not unique, but are endemic to the professional lives of junior faculty in the academe.

With this in mind, the problems you are facing may be reframed as truly excellent opportunities. As the likelihood of these issues resurfacing in your career is high, what better way to prepare for this reality than wrestle with it a bit during the first years on the job? I can hardly imagine a better means of gaining invaluable experience and proficiency in dealing with these problems!

See how you might address these issues now. Whether you succeed or not in changing some things to your liking, there will be valuable lessons learned regardless. The process of this learning might involve struggle and compromise, but the result is you will become a better-heeled junior faculty member, potentially capable of mentoring other peers on such matters or becoming (with time) a change agent after spending time in the trenches and earning credibility in these matters among your colleagues.

These are not simple or quick lessons, but they may be things are will pay of time and again over the course of your career in the long term. After all, your initial years on the job are not an end but a means toward something even more fulfilling later, correct?

As you see, I got stuck on your initial assumptions before even getting to the questions at hand. But I believe it is well worth to dwell some more on the reasons for leaving, prior to investigating the pros and cons of the actual decision to do so...

What if the same issues crop up in the new job? You will be left with a strange-looking one-year-long stint in a tenure track role, stuck forever on your CV.

The fact that neither salary nor personal conflicts with colleagues are causing any problems is also not to be taken for granted. Entering a new organization always carries risk of new "people issues" (conflicts related to personality aspects/working style/opinions/character/attitudes/integrity/whatever). I would count my blessings to be in a workplace where these are not major issues. Perhaps you don't even realize how lucky you are! For these reasons, I hope you might be willing to re-evaluate your current position prior to making the decision and evaluating it purely on the groups of career move timing.

Bottom line: Unless the issues you mentioned are absolutely killing you, and you just can't do it any more no matter what, then I guess there is little choice but leave. In which case the question you ask are a mute point. But if you can see some promise in that these experiences might pay off in the long term, then I would encourage you to stick it out a little longer.

After all, what does a year after which you leave a challenging job say about your ability to persevere, adapt, and succeed despite hurdles? Not too much. On the other hand, getting a few years under your belt in less-than-ideal conditions, and potentially being on the forefront of improving the situation for yourself and your colleagues, will say a whole lot about your professional character. That is worth the time served, in my book.

Good luck!


Including positive and negative evaluation comments during job search

If teaching is an important part of the job, especially if it is the main point, then providing all of your evaluations is probably a positive thing to do. However, you might consider not including them initially, but including a line in your materials that they are all available on request. I wouldn't do anything more than highlight a few of the ones you are proudest of in your complete listing.

Pretty much everyone gets mixed reviews. Some of the negative ones are valid, and some are not. Most of the positive one, are valid, generally speaking. I think that is well recognized.

Including a few positive one, and even one or two mixed ones in the initial materials might be fine, but probably not the whole load. "Available on request" is a good compromise, I think. You might have to explain one or two of the exceptionally bad ones in an interview, but don't be defensive about it. Some students just clash with some professors.

Actually, it occurs to me that the indifferent reviews might be more harmful than the negative ones.


How to respond to "unfair to write English" comments?

For writing proofs, full knowledge of English is not necessary. Most proofs can be written using a single tense. It is sufficient (and often advisable) to keep the structure of sentences very simple; that is very similar to how logic statements are written using math notation. Arguably, this exercise requires students to use only a small and simple subset of English level. Most students are expected to have it by the admission requirements of the course they signed on.


Can a grad student take undergrad classes?

Depends on institution policies, but usually yes.
That said, the grade you get usually won't matter, and besides you might already know some of the things in the course. You might be better off just focusing on the interesting part then, by self-educating.


Write a computer science thesis in native language or English?

As was suggested in the comments, if you want to share your thesis with researchers in other countries, it is better to write it in English than in other languages.

However, I will go further than that and say that in the 21st century, English is the lingua franca of communication in most technical fields. If you want to participate in the wider technical community in a meaningful way, developing your ability to express yourself in English, both orally and in written form, is essential. Therefore, you should avail yourself of opportunities to work in English whenever practical.

It is still important to be able to communicate in your local language, but this is becoming less of an issue as time goes on: for many people, they do scientific work in English, even if their everyday workplace conversations are in another language!


Response to a reviewer for a duplicated paragraph

Say that it was a mistake and the extra paragraph was removed in the revised version.

I can not see the need for going further in this issue. You should be pragmatic, I bet that there are several important points to address in your revision and this is not one of them.


How to handle students not returning borrowed equipment?

I add an assignment in the grading system with a single point: "returned all borrowed equipment."

I don't actually use it in the calculations, but seeing it in the gradebook (which students can access) encourages compliance.