text:
Is the Nature publishing group's "Scientific Reports" journal well regarded?
The Journal "Scientific Reports", published by the Nature publishing group, is gaining popularity with time (impact factor now around 5.2). It highlights its editorial policy as one that is focused on scientific rigour and validity, rather than perceived impact.
My question is:

How well regarded is "Scientific Reports" in the academic community compared to other more-traditional ones, especially in the physical sciences and engineering?
Also, does the fact that it imposes article processing charges and publishes only open-access articles reduce from its perceived rank as a journal?
Is its high impact factor a result of these factors, or is it actually due to high quality articles published in it?
Many researchers know that some well-regarded specialist journals might have relatively low impact factor, but their reputation is still top-ranked. Say, for example, that I have a paper in physics or engineering, and I could either publish it in a specialised Physical Review or IEEE journal versus Scientific Reports, which one would be more well-regarded (assuming the first two have less impact factor than Scientific Reports)?

Personally, I have not been impressed by the papers I have read from Scientific Reports.  Physical Review publishes good quality stuff, but can be challenging to deal with sometimes.

I don't think IF matters too much, people will search, find the article and look at the journal later. Especially if it's not among the highest ranked journals in the field. Also, over time the impact factor will drop (take a look at PLOS ONE: https://en.wikipedia.org/wiki/PLOS_ONE#Community_recognition_and_citation_information)

Is the Nature publishing group's “Scientific Reports” journal well regarded by whom?  There isn't a singular, monolithic academic community.

Indeed @JeffE brings up a good point. Some disciplines, like mathematics, seem to care a lot less about these metrics, especially for non-mathematical journals. However, a lot of biological disciplines seem to really care about IF, and discussions of IF of publications comes up when people are talking about new potential hires. Ask your colleagues/adviser for their opinion since it's the local opinion that matters.

Please see this link to understand the whole matter.

I just came across a paper published in Scientific Reports that is incomprehensible to me, even though I am familiar with many of the scientific ideas to which it refers. This gave me the impression that the paper is of low quality, or at least poorly written.

My take: any journal that considers rigour and validity only, and not perceived impact, will be less well regarded than an equivalent journal that has a good reputation for rigour and validity and also considers impact.
On the plus side:

Page charges are normal for open access, and open access is a positive, so I don't think there's a problem there.
As a Nature journal, Scientific Reports inherits a little of the "glow" of Nature, which will lift its reputation relative to other journals that don't consider impact (e.g. Helyion and PLoS).
Nature journals employ full-time professional editors, which means that people submitting to Scientific Reports can also expect fast, professional review and editing. This help's the journal's reputation, too.

An impact factor of 5 is very high in many fields, but nothing to crow about in other fields. So I would expect this journal to attract higher quality papers from those fields in which 5 is considered a high impact factor, and lower quality articles from fields that typically have high impact factors.

Based on my experience, this journal is very good for publishing interdisciplinary research works and the papers in this journal are highly noticed by researchers. Also, the Nature publisher is a very important factor that you should consider in your's decision.
About IEEE, it depends on which target journal you think about it? IEEE have several journals e.g. in computer science, you opt to choose among IEEE TKDE, IEEE cybernetics, IEEE man, systems, IEEE PAMI, and etc.
I could say that the Nature SCi REP is better than IEEE TKDE but not better than IEEE PAMI.
About Physical Review, the same argument like IEEE! For example, the physical review letters is better than Nature SCI REP.
In order to recognize the validity and impact of a journal, several metrics should be regarded along the impact factor, including the H index, Eigenfactor Score, and Article Influence Score.

IEEE TKDE is a top tier journal in the field of data mining. You can never compare a mega journal to a good journal in specialized field, let alone top tier journal like TKDE.


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Just starting in grad school, I haven't heard from my advisor in three weeks …
I just started grad school this year. I met with my advisor over three weeks ago, on the first week of school. We talked about the school, she told me a bit about the department and showed me around the office. She also talked to me a bit about putting together an advisory committee, but that's it. It lasted an hour, but we didn't really talk about my research project. She told me to get settled into grad school over the next couple weeks. She did recommend I watch some videos to help me get more familiar on the nature of the project, which I did.
I'm worried I haven't heard from her in so long. She's someone who likes to set up weekly meetings for her students, too. And now I'm worried to email her because she may have been expecting an email like two weeks ago. What do I do? Should I email her? What should I say? I was thinking of mentioning to her that I watched the videos she recommended. I think I'm already making a bad impression in grad school.

"I think I'm already making a bad impression in grad school". FYI, just have a look at Impostor syndrome and try to change the way you think.

How does your graduate school work? Do you have other obligations beside your research project, such as coursework?

For clarity, is this in the US, or somewhere else?

Just send her email.  Better yet, just go to her office and talk to her face to face.

Depending on course workload and the turnover in graduate students the first weeks of the academic year can be a busy time for advisors. For new grad students, it is a time to get your feet under you, learn about your project, and get a good start on any coursework. Three weeks in is a good time to set up how you are going to operate normally.

" And now I'm worried to email her because she may have been expecting an email like two weeks ago". This about how this will feel in 3 more weeks of waiting anxiously.

@Wrzlprmft yes I have coursework for the first 2 semesters (the program is 6 semesters)

I had to constantly bother my advisor for help or else I would have been ignored for 4 years until he showed up and asked "where's your dissertation"

Let me add to something that's already been mentioned here but can't be overemphasized: "And now I'm worried to email her because she may have been expecting an email like two weeks ago. What do I do?" Email her! This is true for any kind of human communication: sometimes for whatever reason we take more than we should to reply and the later we reply the worse it is, so just get through with it ASAP. There's no other way.

It is very important to have frequent communication with your advisor, even if you think you have nothing new to say. And it is NEVER too late to email her. Just tell her the truth, just like you described above. Advisors want students who are honest and can make adjustments as needed. I am well aware of how awkward it can feel to meet with your advisor when you haven't accomplished everything you think you should have or when you think you're running behind schedule, but that's what weekly meetings with advisors are especially good for - evaluating what the next steps should be and how to change things around to get things done.

What do I do? Should I email her?

Absolutely. If you don't contact your advisor now, the 2 week delay will quickly grow into a 3 week delay, then a month of no communication. Then your advisor may decide to reach out to the department to check up on you. Contacting your advisor ASAP is the only reasonable action in your situation.
If you are very nervious about writing an email, here are a few things that may help (as someone who used to suffer from severe social anxiety I was in your shoes a few times, too).

Put aside all your other assignments and entertainment until you finish and send the email.
Don't try to guess what your advisor thinks of you or how she will respond, just find your strength in realization that what you're doing now is the right and responsible thing.
Show that you are willing to learn from this communication mishap and make sure it does not repeat again.
If you are still too anxious, try mindful breathing, it may help to focus and reduce the anxiety.

She told you to get settled into grad school; presumably, you've done that, at least to a reasonable extent. She told you to watch certain videos, and you did that. And presumably your schedule of classes and other recurring obligations is reasonably fixed by now. So write an email telling her that and asking to set up a regular meeting time.

Every advisor is a bit different. Some may want you to take the initiative. Of course, she is also busy. If she has regular office hours you can go visit again. It is especially valuable if you want some specific guidance on your project or have some initial ideas that you want feedback on.
You can also ask, directly, how often you should meet and how to arrange it. If the meetings she has are group meetings, you probably want to be included in that also. Ask. Face time is best.

In addition to what everyone else has said, another reason it's very important to contact your advisor, is that you are responsible for your education and for the pace at which you learn and proceed. This was one of the hardest aspects for me to get used to when pursuing my graduate degree. I kept waiting for my advisor to make corrections, give regular feedback, and guide both my project and my education while at school. I learned quickly, and repeatedly, that this expectation was both unreal and my invention.
If you need something, you have to ask for it, clearly, and sometimes repeatedly. Your education is not your advisor's responsibility. It is yours and will succeed, or not, by your actions more than any other factor.

You were instructed to do a thing. You have done that thing. Now you go forth and inform your supervisor that you have done that thing and ask what you should do next. Simply initiate that communication.
You're not at high school any more: you're an adult and are expected to be proactive with social interactions. Sometimes that means starting a conversation, rather than waiting for the other person to go out of their way to do it for you!
tl;dr you're overthinking it just reach out

From Buffy's answer: "Every advisor is a bit different. Some may want you to take the initiative..."
Now for the bit from personal experience: you want to make sure that you set up a relationship with your supervisor that works well for you. If you don't get in touch often early on, your supervisor might assume that you just like to work more independently and leave you to it, figuring that you'll report back when you need help/have published a paper etc. It is difficult to change that dynamic later on. It's definitely worth setting up regular meetings from the start.

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I begin researching in three weeks and I have no idea where to begin. What should I say in my email to my advisor?
I have been accepted to a funded master’s program under an advisor. I already came up with a research proposal months ago with the advisor’s help as I needed one in order to apply. The last time I spoke to my advisor was about two months ago when we discussed courses to sign up for and anything that I should review over the summer. I have since signed up for the courses.
However, I have no idea where to begin with the research and how any of that works. I am thinking of emailing my advisor on Monday to ask her where to begin because I am so lost at the moment. So, in my email, what should I say to my advisor to help clarify my confusion about where to begin with the research?

You are not the first, you are not the last. It is Ok not knowing what and how to do stuff three hours after your start. You should, however, know in 6 months.

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.

Oh yes, I absolutely took her advice which was just to review a couple of undergrad courses. I'm still working on it, but about 75% of the way done. I do have some experience from undergrad, but I was under extensive supervision and just did what my supervisors told me to do. So I don't have any independent experience. Thank you for  your reply, I'm already slightly calmer. I guess I will ask her if we will be meeting up in early September and just ask her where to begin with the research. Thanks!

Don't push too hard on an early meeting date - just ask to meet. The first week or so of the academic year can be crazy busy. You can concentrate on getting a good start on your courses, and learning your way around.

You've done just what you should have done. You could probably just show up at school and find out then what to do next. If you want a little reassurance, send your advisor a short email telling her that you've followed her advice and reviewed the material she suggested. You can then ask if there's anything else you should do in the next three weeks before the semester starts. No need to say or even suggest that you've no idea what comes next.

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Post-doctorate or equivalent "entry level" job
I'm a PhD student in pure math hopefully defending my thesis in 9 months. This is exactly the period in which one has to look for post-doctoral positions or for an entry level job. I have recently become intersected in machine learning and learned some basics of it myself. I have some raw project on Github and an idea for another one in my head. The university even gave me to TA a machine learning class for Bsc so I guess I know a thing or two. I'm now in a crossroad  -- I wish to take a job which includes some "research aspects" but related to ML as I think it's quite cool and helpful "to the world".
The last few years have been very difficult for me due to challenging relations with various people in my group and my advisor calling me an imposter several times ("Are you idiot? Do you live in a fake reality like the last POTUS?!"). That made me take a decision not to look for a tenure track position in academy and to look for a place in which my skills are more appreciated and in which I can work out research problems in larger collaborations.
I wonder whether I should take nevertheless post-doctoral position in machine-learning, to strengthen my background and knowledge or apply directly to an entry-level job outside academy. I will have 3 papers by the end of my phd but none of which are related to applied math (albeit 2 of which are related to pure probability). I also have an offer from the guy I'm tutoring to work under him next year but I feel like doing post-doc in another campus of the same university is not precisely "a decent leverage" for future positions/jobs.
What would you do in my place? More importantly, can one with similar experience (moving from pure to ML for instance) can elaborate on his/her path including the difficulties?

Is it just that your advisor has extremely poor people skills? Otherwise known as a jackass?

@Buffy, he's very social with other people but with me somehow he is a bit tough. I had with him a talk on my future last year and he said something like "Indeed  I'm a hard person but that's because your education was poor albeit I'm partially accountable for not asking you to retake your Msc from scratch. As a matter of fact you have no future in our group so either go to industry or take another direction in your research. That's why we changed our initial problem to one more achievable to you". Speaking of which, his last student dropped as the problem was too hard, so I don't know.

There's no shortage of individuals with some sort of background in machine learning, and as you no doubt know it's also a field exploding rapidly in its core ideas, algorithms, and software implementations. In an industrial setting an entry level position tends to implement senior researchers' ideas and do lots and lots of training of models. To move beyond that you will understand the organization's goals, identify appropriate projects and sell them to leadership, then execute with the help of new entry level staff. I'm sorry for you if your advisor is half as crass as he sounds in your post.

@Aruralreader I agree there is no shortage but on the other hand, the domain advances so fast because many people bring their own eyes and perspectives for large collaborations freely, unlike in pure math. Also, I know that my home country is quite strong in ML but they don't have "that" strong academical community like here so I can bring my own unique perspective after all. Words cannot explain how much I learned from my advisor, regardless of his horrendous attitude.


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What happens to the application materials sent/submitted with graduate school applications in US after admissions decisions are made?
After the admission decisions are announced, accepted students made their decision, and the list of next year's graduate class is determined, what do graduate schools and respective departments in US universities typically do with the application materials (electronic or paper), including recommendation letters, transcripts and score reports, that they received from each individual applicant, in particular, rejected applications?
Do they keep them, in their entirety, for future reference or statistics? For how long, typically? Or, do they keep a summary of each application and the reasons for rejection and discard the rest?

My department keeps them for one year, and then deletes/shreds them.

At our school, we never keep written reasons for acceptance or rejection. These are made in a final faculty meeting with voice votes of yays and nays for each candidate that made it to the semi-finalist list.  Only the finalist list is recorded.
As to materials, they were shredded sometime after admissions season is over. It's a moot point now that everything is electronic.

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Citing a work authored by “A. Smith with B. Jones”
I have a book, for simplicity’s sake let’s say it’s written by “A. Smith with B. Jones”. Note the with, not and. This how the authorship is credited both on the cover and inside the book.
This is because one of the writers did by far the majority of the work. So, how should I cite it? I am considering the following options:

In-text citation:

(Smith & Jones, p. 11)
(Smith with Jones, p. 11)

Reference:

Smith, A. & B. Jones 2020. A book's title. Chicago: University of Chicago Press.
Smith A. with B. Jones 2020. A book's title. Chicago: University of Chicago Press.

Take the 'with' as the authors seem to have made nonstandard choices for reasons which are probably important for them.

Cite it according to the LOC listing.  You're not responsible for any nonsense put on top of that.

@ScottSeidman: I have no idea what LOC is referring to in your comment. Also please do not post answers as comments.

Same for @user111388 …

Library of Congress

@Wrzlprmft. https://meta.stackexchange.com/a/4271/274872

The main point of citation style is to allow the reader to identify and find the work in question, not to please the authors, correctly represent their contributions in detail, or reproduce how the authors were listed on the publication in absolute detail.
In fact, hardly any publication has equal contributions.
Probably the only reason we do not see other conjunctions very often is that most citations are to papers where the journals control the style and nip any trend towards this in the bud.
On the other hand, the odd with may be confuse the reader. Consider:

Smith with Jones (2020) established …

As a reader, my first assumption would be that you made a mistake and I consider the following “corrections” equally likely:

Smith & Jones (2020) established …
  Smith (unknown year) with Jones (2020) established …

Hence: Ignore this peculiarity for citing. It does not hinder the reader to identify or find the paper. It is only confusing and unnecessarily complicates things.
Some illustrative examples leading the alternative ad absurdum:

In a paper with alphabetical author ordering, you do not try to figure out who contributed most and name them when citing. Not only would this often be unfeasible if not impossible to find out, it would also strongly harm the identifiability and searchability of your reference. Aaronson’s contribution to “Aaronson et al.” may be minor; they were just the first in the alphabet.
If a paper has co-first-authorship (“these authors contributed equally”) and further authors, you still cite it by only naming the original first author. Taylor may be a co-first author with Williams on “Taylor et al.”.
You can imagine arbitrary complex authorship phrases. Would you honour the following?

A. Smith together with B. Jones and some contributions of C. Taylor as well as a chapter by D. Williams

Depending on the journal’s style, a paper by the same group of authors may list them as:

A. Smith, B. Jones, C. Taylor, and D. Williams
  A. SMITH¹, B. JONES¹², C. TAYLOR³⁴, D. WILLIAMS¹⁵⁶
  A. Sᴍɪᴛʜ*, B. Jᴏɴᴇs†, C. Tᴀʏʟᴏʀ§, & D. Wɪʟʟɪᴀᴍs♠ [sorry for Unicode abuse]

This should not affect your citation the slightest.

The only exception I can think of is if you are Jones and this is your CV, which should humbly reflect that your contribution was only minor.

Cite it as they have authored it. Preserve the “with”. (That’s rough in LaTeX, I know!)

Welcome to Academia.SE. As discussed here, we generally require more reasoning than a simple "yes" or "no" (or in this case, "A" or "B"). Would you consider expanding your post to explain your reasoning?


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Is it acceptable to ask for a first review midway through the review process?
I have written a paper on COVID-19 with data that goes up to the 31st of July. I would say that the interest in this paper will reduce significantly as time goes on. I submitted the paper to a fast-track process of a relatively high-profile journal on August 5. This is the second time I have submitted to the fast-track process of that journal. Last time, both reviewers were assigned in a single day, and the first round of reviewing was complete in two weeks.
This time things were much slower. Reviewer 1 took over a week to assign. According to status updates, Reviewer 1's review is in as of August 20. A second reviewer still has not been found. I asked the journal whether there was any way I could assist, and they asked if I had reviewer suggestions. I thought a bit and provided a suggestion. That was before the weekend and I have not heard back.
Here’s my conundrum: If Reviewer 1 has recommended rejection, then the paper will not be accepted, so I think waiting any longer is a waste of time. I would like to see Reviewer 1’s review and feedback, implement it, and submit to a different journal ASAP, preferably still in August (so the data is less than one month old). I feel this is an unusual thing to ask: “Based on Reviewer 1's report, is the paper likely to be rejected? If so I'll just withdraw, make the changes, and submit to a different journal now.” If we wait till a second reviewer is found, that review takes time, and then the paper is rejected based on Reviewer 1's report, then I will be quite frustrated. I will have waited for little purpose and the paper will now be out of date and less likely to be accepted by another journal.
There's always a certain amount of chance with submissions. Do the reviewers like your paper – that's often quite subjective. If they don't, I'll roll the dice again, and would like to ASAP.

I'm interpreting your question as whether it's acceptable to ask for a decision based on the single reviewer report received so far. You could certainly ask but the editor's reaction is probably unpredictable. Some will be OK sharing the report (this gets more likely if the report isn't controversial), others will not be hurried.
The problem with sharing the report is that the decision might not agree with the report. There are all sorts of reasons why the first report might be rejected, e.g. (and this is an intentionally egregious example) if the reviewer says "this should cite A, B, C, D, E papers, aside from that it's acceptable". In that case the report effectively says nothing except ask for some citations. The second reviewer report will likely be the decisive report, and showing the authors the first report is rather pointless (other than to show how bad our journal's reviewers can be, i.e. not desirable).
Even if the first report is an honest and relatively positive report, the decision still might be reject, if the second report is sufficiently poor. In this case I would be more inclined to share the first report with the author before the decision, but I would stress that there is no decision yet.
It sounds like you're considering the case where the first review is damning enough to cause outright rejection. If that's what happened, the journal doesn't need to invite a second reviewer, they can already reject your paper. If they haven't already rejected your paper, then unless the editors are too busy to look at your submission, your paper still has a chance.
tl; dr: "Based on Reviewer 1's report, is the paper likely to be rejected?" is not an answerable question, unless Reviewer 1's report is well and truly damning, in which case they would already be able to make a decision. You could still ask for the review, but not every editor will show you the review.

You should not request special treatment because your paper is about a major current event.  Journals will have many papers about the event, and they already know those papers are urgent.


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Is the prestige of a university correlated with how rigorous its undergraduate courses are?
How much harder is it to get an undergraduate degree (say, in computer science) at a highly competitive university compared to a less rigorous institution?

It depends on the state university, but generally yes. The students at a place like Stanford or MIT are simply more able than those elsewhere, and this is reflected in the difficulty of the coursework.

Given that "state university" also covers, say, Berkeley and Ann Arbor, I'd consider removing the reference (not only as you might step on some toes), replacing it with something like "...compared to a less highly ranked/less competitive university."

There are a lot of different ways to compare the difficulty of programs.  One is the minimal standards: if you're willing to seek out the easiest possible courses (and take hard courses only if they are absolutely required), how hard is it to graduate?  Another is the typical difficulty, which can differ substantially from the theoretical minimum.  And then you could ask how many students challenge themselves with particularly demanding courses.

I'm not exactly an impartial observer, but my impression is that Stanford's CS program is actually easier than Illinois' CS program.  Admission, on the other hand, is a different story.

The word "correlated" sounds exactly right to me: there must be some positive correlation between the ranking of a program and its rigor/difficulty.  To say more than that you'd have to give much more precise definitions of all the terms involved: they are all a bit fuzzy.  For one thing: the least you can do to get a degree at a university can be very different from, say, the average amount of training/learning/work that students do, which in turn can be very different from what the best students / students who plan to go on to graduate study do.

There are several enormous presumptions in the question, and I disagree with most of them. E.g., "getting into" a university is not the same as "completing the program", which, if done minimal-istically, is invariably stupid in all cases, and this is not the same as "what is possible?" at a given place, or "what are the limits of the human resources at the place?" or ... So: wrong, irrelevant, misguided question, unfortunately. But de-fragging a bad question is good?

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How much duplication is permissible in letters of recommendation?
Anybody has idea, how much copying is allowed in a recommendation letter and whether they really run a copying test on the letters of recommendation?

I would expect that if the top 10% of the professor's students applied to grad school then he would say "this student is in the top 10% of my students" in all of them...

I am not even sure a letter of recommendation can be plagiarized, merely copied.

I edited the title from enthusiastic student's version. S/he used the phrase "copyright" which isn't applicable. No one is disputing the copyright status of letters so it's a moot point. The question is whether letter writers should write letter de novo, whether they should recycle text, or whether they should 'borrow' text (from the student or from posted letters of recommendation).

Copying WHAT and FROM WHERE? Nobody expects you to retype the name of the applicant and the exact formulation of his theorems (or whatever) or, God forbid, try to be "inventive" about the way you present them. The letter of recommendation consists of two parts: the publicly available information about the candidate (where the closer you are to how it is presented in CV, publication list, etc., the better) and your own opinion about it (where any construct starting with "copying" will be an oxymoron by definition).

As to "running a copying test on letters of recommendation", all I can say is that the set of people who lost all touch with common sense and reality after reading our written "academic honesty policies" in our class syllabi is certainly non-empty... In short, "No". In long: "What a novel and fascinating idea!"

While our university occasionally submits statements of purpose, research statements, and writing samples through plagiarism detectors (and gives the admissions committee the results), I have never seen this done to letters of recommendation.
There are just very limited ways of saying nice things about students. I use the same variation of an opening for all my letters, with only minor changes in intensity (I am very/slightly/marginally pleased to write this letter of recommendation) and close with the same sentence on all of them.
I wouldn't worry.

Addendum given the changes to the the original question: I don't know if people have seen the output of plagiarism detectors but they don't provide  a simple YES/NO answer. Instead, they provide a statistical quantification of how much unquoted text might be drawn from other sources (e.g., 3-5% of the text appears duplicative). Each report is several pages long with parts of the student text highlighted and possible prior sources highlighted.
The reports are quite "noisy" with many false positives -- notably in one case that I remember, highlighting text in the bibliography because the citations matched citations in other bibliographies. [facepalm]
Running LORs through plagiarism detectors would serve no useful evaluative purpose in terms of how the admissions committee views the candidate.

Oh man, I would be absolutely crushed if someone gave me a letter that began with, "I am marginally pleased to write this letter..."

That's why you always ask your professors if they will write you a strong letter of recommendation.

@Asad:  That is why I decline, politely, I hope, to write letters for students when I cannot write "recommend" or "strongly recommend."  I say, "You should ask professors in whose classes you did better than you did in mine."

There isn't much creativity involved in most recommendation letters. And frankly, that doesn't matter. The important thing to a school or employer is that the individual who signed the letter believes it accurately describes you.
Yes, it would be nice if every letter was rewritten completely de novo. It isn't very surprising when it doesn't happen that way.
Don't worry about it. The worst that will happen is that they'll contact the recommender, he'll say you're a good candidate, and that'll be the end of it.

-1: It's important to me that recommendation letters are written by the ones who sign them.  (This is my opinion as someone who has had a lot of involvement with graduate admissions over the years, at UGA.  If you are involved in graduate admissions elsewhere and make a practice of not caring about this, I would be very interested to know.)  On the other hand, I don't agree with "[I]t would be nice if every letter was rewritten completely de novo".  This is really not required.  But taking too much of someone else's writing and claiming it as your own is never okay in an academic environment.

@petelclark: this isn't  an academic document; it's a near-form-letter endorsement, modified for the particular case. It may be the same letter, essentially,that he uses for all similar references.  I honestly see no harm here other than the risk that the admissions comittee may get bored if they see: the same text too many ti mes. Gods know that the students are always looking for boilerplate they can model their applications on; why isn't this equally legit?

Form letter endorsements for PhD programs make for poor recommendation letters, of the sort that significantly hurt the student's chances.  And yes, this is a kind of academic document.  May I ask again what admissions experience you have?

And in any case, that's something you should debate w/ the recommender,rather than faulting the applicant on,  if you care at all about fairness.

"[I]f you care at all about fairness." Of course I care about fairness.  What is it that you are suggesting?

Also, if you read my answer, you'll notice that I said that using boiler-plate language as part of a recommendation letter is okay.  However, in order to be a good letter thee needs to be something there beyond the boiler-plate.  If the distinctive part is stolen from someone else without attribution, that is problematic.  And again, what I'm disagreeing with is "The important thing to a school or employer is that the individual who signed the letter believes it accurately describes you." I am (a representative of) the school, so I am pointing out that it doesn't work that way.

Remember, the whole letter wasn't borrowed, just a portion thereof. We haven't seen the letter, we don't know, we don't even know whether it would in fact be recognized as reused language rather than just somewhat hackneyed.... We agree that we disagree. And, again, would you blame the kid for the fact that the letter wasn't 100% original? If so that isn't fair to him; if not your objections are entirely (pardon the pun) academic. A difference which makes no difference is no difference.

I'm not sure what you're asking that my answer doesn't already address.  I already said that in this case the OP very probably has nothing to worry about.  However, your answer makes a broader assertion about what schools find important.  I am telling you, as a graduate admissions representative, that this is not the case.  When you say you disagree, what do you mean?  That in your experience PhD admissions are handled differently?  If people followed your advice and, for instance, wrote their own letters, it would almost certainly hurt their applications.  That is a real risk.

You misread me badly. I never suggested people write  letters recommending themselves. I'm leaving it there.

You wrote: "The important thing to a school or employer is that the individual who signed the letter believes it accurately describes you."  The use of the word "signed" implies that it is not important to those who process admissions who wrote the letter so long as the signer believes it is an accurate description of the candidate.  Since I and the vast majority of other faculty doing graduate admissions I know vehemently disagree with that, I am commenting.  If that is not your intended meaning, perhaps you should edit your answer.  I ask  once again: how do you know what we find important?

We agree that we disagree.  Stet.

Let us continue this discussion in chat. Or not. (I was hoping the move-to-chat would actually move some of this chain to chat and clean up; apparently not. Oh well.)

I find it fascinating that the admissions process would actually care if the letter was actually written by the endorser, rather than the fact that it was signed by the endorser.  I guess its time to write a pseudo-random recommendation generator macro, and quite frankly @PeteL.Clark, writing your own letter is apparently the only way to get a fair review from someone like you.

@Jim B: I have explained elsewhere on this site why a student writing their own recommendation letter for a PhD program would be a very poor decision.  I take issues of fairness very seriously, and the position that I am taking here is identical to that of the vast majority of my colleagues at American universities.  What is your experience with PhD admissions that leads you to give such divergent advice?

I do not believe anything unfair has been suggested here except an arguably unreasonable  demand for complete originality in recommendation letters ... which is an issue to take up with recommenders, not  one the student should be judged upon. I agree that an exceptionally specific recc will stand out and carry additional weight, of course; that's entirely appropriate. But if the recc  simply says excellent candidate for program X, and comes from someone with authority in that area, how much do you reallly want to downgrade the application... unless it's english dept, maybe.

@keshlam: I don't see that anyone here has suggested (let alone demanded) "complete originality in recommendation letters".  If you have followup questions about the nature and meaning of academic recommendation letters, feel free to ask.  Most of the people who write these letters understand the culture and requirements of the form.  Those who don't write letters that are less effective than they could be or than they are intended to be.  I hope you now see why it is not helpful to make assumptions about what a good letter is without having familiarity with the graduate admissions process.

Assuming that you are in fact interested in the truth, I'll start you out with this: an overly short or completely generic letter is often intended as -- and even more often read as -- code for a lack of enthusiasm about the student.  What (based on past direct experience on this site) many outsiders don't seem to realize is that faculty have a direct stake in placing their students in the best possible programs: doing so is part of our job.  So even really famous, busy people write enough to give their students their best chance....if they think the students deserve to be there.

Anybody has any idea, how much plagiarism is allowed in a recommendation letter and whether they really run a plagiarism test on the letters of recommendation?

I have read literally thousands of academic recommendation letters, and I have never run one through plagiarism detection software.  I don't understand why you did that after the letter was submitted: what were you hoping to gain?
You also sound slightly naive about how "plagiarism detection software" works.  Such software does not directly detect plagiarism; it only makes a more or less compelling case for it according to the degree of similarity.  The letter is a highly structured, ritualized writing style.  Having 10% of a letter be the same as some other letter is not itself problematic, and it certainly need not imply "10% plagiarized".
A recommendation letter is not an academic paper, and most people who write many (graduate school) recommendation letters keep a basic template and fill in information accordingly.  Therefore a lot of recommendation letters are going to be a lot more than 10% alike without there being anything problematic.  This is another reason why putting a graduate recommendation letter through a plagiarism detector is not a very plausible thing to do.
In summary: I think it is overwhelmingly unlikely that anyone except you will know what percentage of this letter the plagiarism software reported as copied.  I doubt you'll have a problem.
On the other hand, I am not quite willing to say that including an entire paragraph in a letter that one found on the internet is a good practice.  It depends a lot on what the paragraph is.  If the language in that paragraph is boiler-plate or standard, then I certainly don't care.  (In particular, I hope you would have told us if the copied paragraph was the very last one, e.g. something like "In summary, Ms. X is a very strong candidate and deserves the highest consideration.  Please do not hesitate to contact me if you require further information.") However, if the paragraph contains distinctive, poetic or especially clever language and your writer lifted it from the internet because he liked someone else's clever language better than his own: well, it has nothing to do with you, but I don't think is a good practice, and it doesn't fill me with confidence about his writing skills or professional ethics.

Almost every prof I know uses a template for recommendation letters, and adds a paragraph or two specific to the student.  I'm not surprised a about the reuse of a paragraph and similar wording.
Remember, the purpose of a letter of recommendation is to make the case that you are a good student, and will be a dedicated, ethical researcher, not to introduce new research or new ideas.  A letter of recommendation would likely not pass several requirements of publish, professional research as it does not present a novel idea, nor does it have external references.
A recommendation letter is a vote of confidence in the individual.  Its difficult to see how similar content between letters would hurt either the recommend-er or the recommend-ee, so long as the recommendation accurately reflects the opinion of the recommend-er.

One person who could be harmed by a plagiarized recommendation letter is the person whose distinctive language and/or ideas the plagiarist stole.

@PeteL.Clark is right - and the reputation of the plagiarist could also be severely harmed, I would think.

Come to think of it, it could also do harm to the person being recommended, depending on the amount of content that's copied.

While all the comments would be true about plagiarism, most recommendation letters (in my experience) don't meet other requirements of professional writing as they do not usually have any novel idea or new research presented.  Its the opinion of a current researcher usually without references, which would be unpublishable anyway.

The concept of plagiarism doesn't just apply to academic papers.  The practice of copying others' distinctive language or ideas without attribution is viewed as unethical by (e.g.) academics in whatever context.  As I (and others) have said, whether the duplicated paragraph is problematic depends on what it is.  We have already said that this hunting expedition is poorly motivated, and the paragraph would have to be something truly artful and distinctive for it to be even worth shaking a finger at.  But, for instance, lifting a whole paragraph from someone else's short story would be bad.

Consider this example.  You and a few friends are planning a trip, and one of your friends suggest inviting someone you don't know.  You want to make sure this person you don't know will not detract from the trip, so you politely ask about this new person.  The person who suggested it vouches for his "coolness", then a few other friends add in they've meet him, and say he's cool.  In this example, everyone who knows him will probably say "he seems cool," followed by a brief explanation.

This seems like a strange question to me, because if I were a new-ish prof asked to write a letter of recommendation, the very first thing I would do would be to type "letter of recommendation template" into Google (12.9 million hits), and use the first one that seemed to fit.  Since I think I am not much lazier than the average new prof (and in STEM, have the advantage of being a native English speaker), I'd expect the majority of letters to be created the same way.

I am surprised that nobody has mentioned the possibility that the supposed "plagiarist" recommender used his/her own text, which was also coincidentally found online.
While a cut-and-pasted paragraph of 50 words strongly suggests copying of some kind, it is not necessarily the case that the 50 words were plagiarism (i.e. usage of another person's text without attribution).
It could very likely be the case that the recommender posted up one of his/her old recommendation letters online, and it got picked up as a template text by the anti-plagiarism software, which then detected the similarity. I would not at all find it surprising that my recommender(s) were reusing parts of their old recommendation letters, as they clearly have much better things to do with their time than write a completely new recommendation letter for each application.
In fact, it could even be the case that your recommender did not even post his/her letter online. Assuming your recommender has also forwarded their recommendation letter to his/her past students, it is not a stretch to consider that the student could have posted that letter online.
With the limited information, I find it rather uncalled for to immediately jump to the conclusion that your recommender has committed plagiarism.

Well, the title isn't quite asking the same question as the question body.
The direct answer to "Is there any copyright on letters of recommendation?" is that it depends on the country you're in (because copyright law differs from one country to another), but if you're in the UK or the USA then copyright automatically attaches to the creation of an original written work such as a letter. No need to register the copyright or declare it. Letters of recommendation are not exempt by virtue of their subject matter.

copyright in the United States automatically attaches upon the creation of an original work of authorship

WP: Copyright law of the United States
So the general answer is: Yes, letters (whatever the topic) do fall under copyright law.

"how much copying is allowed in a recommendation letter"?

Copying from oneself is fine (so long as one still owns the copyright in the work being copied). Copying from someone else is not, unless they've given you permission to do so.


text:
Applying for tenured positions while on sabbatical
I plan to apply for a tenured position at school B.
I am currently on sabbatical at my school, school A, for the fall semester of 2015.  According to the rules of school A, I have to stay with school A for the whole year of 2016 (I heard that this is the case for most universities: you have to stay for at least six months or one year after you receive a sabbatical).
Therefore, if I get an offer from school B, the earliest time I could start working would be the spring of 2017.  School B is hiring for the tenured position starting in September of 2016. And I am afraid that school B will not have openings in future after this hiring.
So my question is: Should I apply to the position at school B and telling them: "I can only start working with you starting the spring of 2017"? Also, if I say this, will it affect my chance of getting the job? Or, would it be the case that I will not be considered and I should simply apply for academic jobs that advertise a start date of September of 2017?

Welcome to Academia SE. Unfortunately, my problem is not completely clear to me: You are on a sabbatical from school A right now and want to apply to a tenure position at school B? Also, if that was correct: Can you really not just stop working at school A during a sabbatical?

I am sorry if my question was not clear. I have modified it and hopefully it is more comprehensible.

@Wrzlprmft For my sabbatical, and I guess this is standard, I signed an agreement to the effect that I would return the salary for my sabbatical year if I did not return to teach the following year.  Though if I had died, I don't think they would try to get it back from me, but who knows.

Your sabbatical time may be able to be "bought out."
If you leave your job after your sabbatical, the school may just want reimbursement for your salary. It is possible that the new school will be willing to pay that in order to hire you.
One case of this happening, I believe, was when Matt Welsh left Harvard after getting tenure (although he left for a company).

I weakened your statements slightly, since I suspect some schools might disagree.

In the light my limited experience, if I was in your position, I would apply normally to school B and, if I get the position, ask them to defer my integration until the spring of 2017. If they accept (which they apparently tend to do), all is good. If they don't, then you cannot accept the position, but there was no clean way for you to get it anyway. This strategy does not affect your chances of getting the job in theory, since you already have the position when you ask for deferral. Of course, if the selection committee is aware of your situation, they might ask for your intentions during the selection process and your (honest) answer could impact the outcome. However, it would only be a sooner way to know whether the defferal is possible for them or not.

Thank you very much for the answer. As far as I know, most of the schools will ask in the application form: "If appointed, when could you start work?" So I have to reveal my plan of deferral when I apply.

@Paul, You might explain your situation in the answer to that question. For instance, "I currently have a contractual commitment through Spring 2017 but may be able to 'buy-out' the remainder of my commitment, and would work hard to negotiate an earlier release."

Personally, I would apply, but making the situation perfectly clear from the go. It might hurt your application, but it is better than to be interpreted as malicious by your potential future colleagues... Not the best way to start anything...

I would apply and not even mention this until it became a problem.  You may not be interviewed, and you may not be offered the job even if you are interviewed.  Cross that bridge when you come to it. I also doubt that the school would litigate against you, so, while it might create some bad feelings if you left, you'd be tenured at a place you were happier with, and that's what matters.


text:
How can I improve my chances of receiving PhD funding (UK, Anthropology)?
I have been accepted to UCL and Oxford for a PhD in anthropology, however I have not been offered funding for either position. I am considering reapplying next year and I would like to know how I can improve my chances of securing funding. I already have experience as a research assistant for my MSc supervisor, and she has acknowledged me in a recent paper. I have also presented at a conference, though I have not published the paper. Would publications improve my chances, even if not in top tier journals? What other things could I do to make my application stand out to funding committees?
I should add that this is my second attempt - I was in the same situation last year when I applied only to Oxford for a PhD, gaining acceptance without funding. I received my MSc from Oxford, with an overall grade of 67 and a distinction in my thesis.

Who are you asking for the funds? Research councils? The universities? Have you recieved any feedback on your applications so far?

Have you considered going overseas? Especially in the funding-scarce social sciences, the more positions and scholarships you apply for the better. There are a number of countries in western continental Europe that must, by law, employ their PhDs and pay a salary. You might find greener pastures elsewhere.

Funding is extremely scarce, especially in Britain. Since you have been accepted, I would write to the person who you suspect would be your adviser if you matriculated and ask them for advice. The program clearly has an interest in bringing you in. They may be able to find fellowships or paying jobs within the university that can help you financially.

Each of Oxford and UCL has an ESRC-funded social-science Centre for Doctoral Training (CDT), which would be a suitable funding route for a new anthropology PhD student.
As a backup plan, consider an inter-disciplinary PhD: apply your anthropology to a subject that is well-funded.
Both Oxford and UCL have inter-disciplinary PhD students. You'd typically have one supervisor from anthropology, and one from your applied subject.
Hopefully there's a subject that really interests you, for which either Oxford or UCL have a CDT; in that case, they'll have funding for PhD students. But be sure to pick a subject you can be really passionate about: remember, this is going to swallow a big chunk of your life and your energy, and you're going to have to be motivated to work 12+ hours a day for weeks or months at a time on it. So don't pick something that just vaguely interests you, or you'll risk never completing.
(disclosure: I supervise inter-disciplinary students in one of the CDTs linked to above)


text:
Typographical emphasis on text is ambiguous
I am writing a paper and part of my thesis, and I need some advice to improve the readability of my manuscript(s).
Working in computer science and machine learning, there is a lot of technical stuff going on: I have to write definitions and set the terminology of my work. So, for instance, I have to explain the reader that a training set is a set of example on which my system learns to model some phenomenon.
Now, please, focus on the previous paragraph. As you can see, I used the italics to stress the new piece of terminology, namely the expression “training set”, and to emphasize some other words, namely the word “learn”.
So, having the same style for these two things, with a different semantics, sounds a little confusing to me (and to my supervisors). And there is a lot of this stuff in my paper/thesis.
How can I improve readability in this respect?
--
EDIT. The focus of my question is not if the word "learn" should be emphasized with respect to what it means or not. It is just an example. Idem for the "training set" with respect to the expected background knowledge of the reader. In abstract terms, my question can be generalized to: how to emphasize both the terminology that I am introducing and words that need proper emphasis? A more fitting example could be the following:
We call training set the set of examples on which a Neural Network learns to model some phenomenon. (omissis) At each timestep, our network has to decide if the symbol will be chosen from the first or the second list. In both cases, it has to decide also which symbol will be chosen.

I'm in a different area but I've seen only new terms emphasized when they are defined. Emphasizing words like "learn" just for the sake of it doesn't seem natural in academic texts; have you seen that elsewhere?

Just as a head's up, SE.TechnicalCommunication looks like it may be entering private beta soon, if you're interested in stuff like this.

Can you please [edit] your question to specify why you emphasise learn in said sentence? You said that it’s for a different reason but you do not specify which.

@Nat Looks like a bad idea to me, conflating two very different targets (documentation and scientific papers). I wish I could downvote Area51 proposals, but apparently the SE folks are just interested in finding out how many more users it can attract, not in whether it is a good idea. :(

“[It] sounds a little confusing to me (and to my supervisors).” — Weird. Why is that? It’s pretty much the norm, and not generally seen as confusing.

Is boldface out of the question? Or underline? Or small caps?

Also, what about colors? Here are two lines of LaTeX preamble that are making circles in the combinatorics community:
(line 1:) \definecolor{darkred}{rgb}{0.7,0,0} % darkred color
(line 2:) \newcommand{\defn}[1]{{\color{darkred}\emph{#1}}} % emphasis of a definition
Then, everything inside \defn{...} will be italicized and dark red at the same time, which neatly tells it apart from mere emphasis.

@darijgrinberg ... until somebody prints the paper.

Are you already using quotation marks for some other dedicated purpose?

Perhaps you don't need to italicise the word learn: you could just say "a training set is used to train the system to model the particular phenomenon".
This means that the italics are reserved for the words or phrases that you are setting the precise meaning of.

Agreed. Develop a style for definitions, where it is immediately clear that you are now defining a new term (e.g. by a big Definition 2.5 above) and decide on a style for the new term to be defined; e.g. bold, italic, etc. Then stick with that and do not use it elsewhere. If you want italic for other emphasis, then better take bold for new terms. If bold is also preoccupied, you need to put some more thought.

Thanks for your reply. The "learn" think is just a excuse to explain. A more realistic scenario could be the following:
We call training set the set of examples on which a Neural Network learns to model some phenomenon. (omissis) At each timestep, our network has to decide if the symbol will be chosen from the first or the second list. In both cases, it has to decide also which symbol will be chosen.
I will edit the original question.

For what it's worth, "our network has to decide if the symbol will be chosen from the first or the second list" is ambiguous to me. This could mean (1) or (2), where: (1) the network has to make a choice of whether the symbol will be chosen from one of these two lists [this further bifurcates according as to whether "exactly one" or "at least one" is meant] or the symbol is chosen from one or more other lists; (2) the network has to make a choice of exactly one list from among the first list and the second list.

First of all, your university or target journal may have a style guide which specifies how they want such things to be typeset.  So check whether they do, and if so, follow it.
My personal preference is to use boldface for terms which are being defined, and italics for general emphasis.  This is because it is pretty common for a reader to need to refer back to a definition, and it is helpful if they can glance at a page and immediately spot the term they are looking for.  Boldface is eye-catching and can be immediately picked out from a page or block of text, so it's good for that.
When you just want to emphasize a word, you want it to be noticed by someone who is already reading that sentence, but it isn't so important that they be able to glance at the page and jump immediately to that word.  In your example, somebody might be skimming the page looking for where you have defined training set, but nobody is going to be skimming for the word "learn" which just happens to be important in that sentence.  So italics is fine in that case.
As illustration, you might look at the following two paragraphs.  In which one is it easier to spot the specific word?

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur in luctus dolor. Pellentesque orci ante, pulvinar ac leo ut, venenatis commodo tortor. Proin faucibus tincidunt nisl, quis semper tellus ullamcorper ac. Mauris quis tellus eleifend, condimentum diam id, posuere eros. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Donec bibendum auctor tristique. Donec justo odio, commodo id elit vitae, efficitur dictum massa. Phasellus placerat convallis ipsum et fermentum. Pellentesque urna mi, malesuada sagittis vehicula sit amet, auctor sed leo.
Phasellus ante quam, convallis eget vestibulum id, rutrum sit amet libero. Duis ultricies ornare semper. Nunc cursus aliquam ultricies. Morbi tellus neque, euismod sit amet tincidunt eu, volutpat interdum massa. Nunc eu elementum massa, sit amet vestibulum metus. Quisque hendrerit nunc feugiat ligula elementum, in mollis felis aliquam. Praesent hendrerit dolor id nulla lobortis fringilla. Aenean non dictum risus, id molestie lectus. Donec id ullamcorper nunc. Proin eu risus vitae leo hendrerit luctus. In scelerisque, purus scelerisque convallis imperdiet, leo nibh tempor ante, at ultrices ligula diam a dui. Ut eu risus id justo vulputate sagittis eget et tellus

This is exactly the approach I've come to prefer, but there are certainly publishers who will change all your boldface to italics.

Boldface does work well for terms being defined but I've never seen a pure mathematics or theoretical computer science journal use anything other than italics. And I think the intended purpose of the typesetting is to make it clear exactly what term is being defined. If I write "A proper colouring is..." then it's not clear whether I'm defining "colouring" and contrasting it with something that I feel to be improper or defining "proper colouring". But "A proper colouring is..." is unambiguous. You'd find the definition by scanning for Definition 7.

@DavidRicherby: I'm in pure math, and I've been able to use boldface for definitions in a number of my published papers.  Example (needs subscription).  The problem with Definition 7 is when you see "proper coloring" elsewhere in the paper, you don't know which definition number to look for.  Also, I often find it nicer to define a number of terms in a prose paragraph instead of giving each one a numbered definition.

Typographical emphasis is typically used for the following semantically different aspects:

introducing a new term
titles of works
referring to a word/term as such
species names
stress
highlighting an in-paragraph heading
person names
phrases from another language in English
…

As you typically only have limited number of types of typographical emphasis available (boldface, italics, small caps, …), you inevitably have to overload at least one of them in any larger work, usually italics.
However, in most works and cases, it is easy to deduce from context which of the above cases applies.
While this may not appeal to the structure-loving scientist in you, this kind of overloading is a common feature of human communication – and compensated by redundancy.
Consider for example the different meanings of the word that in the English language.
That being said, if you really think your texts benefits from a clear distinction, you have to get creative in terms of emphasis.
For example, some philosophical works use a zoo of quotation marks to distinguish different types of referring to a term.
However, going by your topic, you almost certainly shouldn’t do something like this as it would only make your work more difficult to read.

Thanks for the suggestion. I would like to "keep it simple" too.

I think small caps for introducing technical terms is somewhat common

@sgf I think so too, and like it, but if you have a lot of acronyms/initialisms they'll be in caps or small caps which makes it less clear.

I agree with @Solarmike's answer, but on a more general point of view, if this is a concern for you then it may be the case that you over-use italic for emphasis. For instance, I realized in the past that I tended to over-use quotation marks and parentheses: since then I try to avoid them whenever I can, and I think my prose has improved. When you re-read your text, try to go over each instance and see if you can remove it.

You're italicising training set and learn (sticking to your original example) for the same reaon -- to draw attention to them.  So using the same emphasis for both is fine.  If you have a long section on terminology, perhaps much of your introduction chapter is devoted to this, you can try paragraph headings:

Training set
We call training set the set of examples on which a Neural Network learns to model some phenomenon. (omissis) At each timestep, our network has to decide if the symbol will be chosen from the first or the second list. In both cases, it has to decide also which symbol will be chosen.
The choice of training set is of particular importance because...
Test data
The test data set is another dataset.  Can you tell I'm making this up as I go along?

But I suggest doing something slightly different: instead of putting the term you're introducing as a paragraph heading, draw attention to it in a margin note.  This acts almost as as index to the terminology section.  Here's an example from Ohanian -- physics (an undergrad textbook I keep on the shelf):

This is all in addition to any glossary, as this terminology section will contain much longer descriptions and will be sorted in a logical rather than alphabetical order

It's a nice suggestion in a book, but I suspect margin notes will not be allowed by most journals / proceedings, especially if they are going to be physically printed (printed journals don't like to waste paper and so aren't likely to have wide enough margins to contain a margin note).  And for a thesis, it's pretty common for a university to have strict formatting guidelines, including a requirement that margins be of a particular width and empty (so that text is not cut off when converting to microfilm or other formats).

"to draw attention to them": No. He emphasizes "training set" because this is the notion being defined. It is common to italicize words that are being defined, and this is semantically different from merely stressing the word.

@NateEldredge I was concentrating on the thesis aspect.  Here in the UK guidelines don't tend to be all that strict so the option would be there

@darijgrinberg if it was structured like a dictionary, I would agree with you, but in this case it's just emphasis; the reason for the emphasis is the novelty of the term

Here is an example of confusion: "While a presheaf cannot generally be expected to [...], a sheaf will always have this property.". Is this a definition of a sheaf, or just a property that holds for all sheaves but perhaps for some presheaves as well? The only way to tell is by checking whether sheaves have already been defined before.

I’m with Solar Mike that learns doesn’t need to be italicized. Still, the cleanest solution seems to me to be adding a glossary section somewhere. You should certainly have the space in a thesis. If you can’t do it in a paper, you could still have a paragraph in the introduction along the lines of

In this paper, we use training set to refer to ___ ...

and from that point on, never italicize training set. Finally, you could try using quotation mark to define the terms instead of italics.

Improve readability by not over-using italics for emphasis.
Text gets difficult and very annoying to read if the author keeps emphasizing words that they feel to be important. Especially if their emphasis doesn't quite agree with where you'd put it (you'd probably find it more natural if I'd emphasized "very", rather than "annoying", for example).
If you look at well-written, well-edited text, you'll see that typesetting is almost never used for emphasis. Technical and formal writing isn't intended to mimic the spoken word and it's better to use sentence structure or vocabulary to give the emphasis you need.  For instance, you could describe something as "crucial" instead of "important" or "very important".
In the example you give in the question, you don't need any emphasis: "learns" is a verb and we naturally see verbs as important parts of sentences.  If you feel more emphasis is needed, then contrast the learning of the training set with the use of other data: "The training set is a set of examples from which the system learns to classify data, as distinct from the whatever-you-call-it data that it will be deployed to classify." (I've kept "training set" italicized, since it's standard in computer science to italicize terms at the point where they're defined.)

Other options are bolding, different font, quote marks, a colon, or, if you really want to set it apart, a separate line.

Expect your reader to have some knowledge. Somebody who reads a new paper about a machine learning topic hopefully knows what a training set is.
Reduce the points that are basic knowledge for the target audience and your problem should solve itself.


text:
Decline for and reapply next year?
I applied to a professional program that I had been striving for in my undergrad, at a top school, but I've since felt overwhelmed with how to pay for it and incurring so much debt. I think I should wait a year so get into a better place financially. I've become so anxious, thinking I've ruined my opportunity with this school if I don't go.
I am considering withdrawing my application, but I'm very worried about how it might hurt me in the future when I reapply. Or I may wait but need to decline if I am accepted, and reapply the following year. I feel like both will hurt my chances in the future. How will admissions consider me the second time?

How is this different from your previous question?

You might ask to have your application (or acceptance if they've already decided to accept you) "deferred" for a year.  It's not at all uncommon for something to come up (illness, family issues) that prevents a student from starting a program that they've been admitted to.  The thing that would be most damaging would be to get admitted and then wait until the last moment to withdraw- let them know as soon as possible.

I would wait until you know the outcome first. It is possible (and not that usual from what I hear) to defer an offer of admission, which means you may be able to take up an offered position in the following academic year.
Since you do not know that you have been admitted yet, I would wait until you get a response. If you are rejected, there is no harm in re-applying next year. If you are offered a place, a request for deferral will not be looked upon badly.


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Does rigor/thoroughness of undergraduate program matter (for graduate/PhD applications)?
I am an undergraduate at a large public research university in the US, finishing my second year. I have done some theorycrafting around my graduation course requirements, and I have realized that it is possible, with some work (and generous CLEP testing), to graduate with a double major, Math BS + Physics BA, by next May. I would be meeting the bare-minimum requirements for both majors (in particular, for math, I will have only taken the 4-semester calculus series, lin. algebra, and the 2-semester abstract algebra series; plus some extraneous ones e.g. game theory).
If I were to stay the extra year, I would comfortably qualify for a double Math BS + Physics BS, and I would have 3-4 more math classes under my belt (perhaps the 2-semester topology series, graph theory, advanced abstract algebra, real analysis, etc). (edit: this option, Physics BS rather than BA, stresses a more thorough physics courseload; 15 hours of upper level physics classes are required for BS over BA)
edit after several answers: Another 4-year option is to get Physics BA + Math BS, leaving my course load open to taking 3-4 math classes per semester. This, hypothetically, could put my post-lin-algebra courses at 2 sem. abstract algebra, 2 sem. topology, 2 sem. intro analysis, graduate level courses of the above, intro complex analysis, intro graph theory, etc
My intent, if I were to graduate next year, is probably to take a year off from academics, and then apply for graduate/PhD programs in math.
Will it be an issue in being considered for these programs, that I have only taken a meager selection of the course offerings in my undergraduate studies? And might it be offset by the fact that I graduated in three years with a double major?

The only person who will be impressed by your finishing in three years is you.  School is not a race.

I'm confused. You want to get your undergrad finished as quickly as possible, spending half of even that short time doing something other than maths. You then want to take a year out, again not doing maths. One minute, you're saying that you want to spend four years of doing as little maths as you can get away with; the next minute, you're talking about a PhD in the subject. That seems inconsistent.

If a you did not need a full load of mathematics for getting a PhD in mathematics, it would not be worth the paper it's printed on. (For reference: in Germany, you typically study 5 years (or more) before starting your PhD. On one subject. To be fair, our (classic) PhDs don't include taking courses.)

@DavidRicherby - My aim is not to do "as little maths as [I] can get away with"; if it were up to me, I would be taking an all-math courseload for the remainder of my undergrad career, it's the only subject I enjoy. What I do want, is to do as little undergrad as I can get away with. Unfortunately the need to meet general-education and graduation requirements means that cutting down on UG time would mean sacrificing math classes to do it, which according to the answers here is gravely detrimental to my value as an applicant to post-undergrad programs.

I have to ask: if math is "the only subject you enjoy" (which I hope is an exaggeration; there are lots of other interesting things in the world), then why are you so set on getting that physics major at all? As far as grad school and a career in math, it may hurt more than helping. Of course, if there are a couple specific courses that really interest you, you could certainly take them.

It also might be worth exploring why you are so anxious to get out of college...

@NateEldredge The physics major's already complete, save one class. Might as well finish it. I came in as a physics declared major, not math.

@NateEldredge this city's very cold in the winter, it would be great to go to school somewhere where I'm not forced to stay indoors and sad for 1/2 of the schoolyear :( I don't have an aversion from classes or anything, I just would enjoy a change of scenery, why not sooner rather than later? (question answered)

Honestly, with your correct set of courses it’d surprise me if anyone would consider your application. You absolutely need real analysis of some kind. Complex analysis is pretty essential too. If your linear algebra course wasn’t sophisticated and from a book like lay, it doesn’t count. Taking topology would be helpful as well as loads of math grad schools assume you know it or have absorbed it through osmosis, unless it’s algebraic topology, and I can’t see you doing that unless you take the advanced algebra class. I do not mean to be pessimistic, but my suggestion is take course that year.

Your question makes me a little sad.  You are obviously a bright and ambitious student, and you have spent almost two years at a US public research university.  You are trying to "theorycraft" your future career, which is good.  But somehow no one has managed to communicate to you the basic goals of an undergraduate math major and the requirements for graduate study: how did that happen?
To once again answer the title question (the other two answers are completely on point): "Does rigor/thoroughness of undergraduate program matter (for graduate/Phd applications)?"  The answer is yes, of course.  Not only does it matter, but together with indications of your success in these courses -- course grades together with recommendation letters from your instructors -- it is what matters the most.  Your question first proposed graduating early with a double major in physics and math, with coursework that to any math PhD admissions committee member looks extremely minimal.  This is a terrible plan for getting into a PhD program in mathematics (not just a top one, but any one that I know).
Let me be clear: I am not scolding you.  I am lamenting the total lack of advice you have somehow been subjected to.  You are not the first bright, ambitious undergraduate who has asked a question on this site which evinces the misconception that the best students get through undergraduate degrees in as few years as possible.  This is quite the opposite of the truth: does anyone know where these misconceptions are coming from?!?
Here is my opinion (as someone who served on the graduate committee of a top 50 PhD program in mathematics for four years): unless you want to work cross-disciplinarily in math and physics, the second undergraduate major in physics is not directly helping you get into a PhD program in mathematics.  On the other hand, it seems to be stopping you from taking the deeper and more advanced course offerings that are essential for you to even get consideration at a good (or even decent) PhD program in mathematics.  If your postgraduate plans include a career in which knowing a little bit about several different things will be beneficial -- and I can imagine that many careers in business and industry are like this -- then a double major could be desirable.  However, for a future PhD student, all else being equal a double major is time taken away from the one thing you're supposed to be devoting much more time and energy to learning.
In your case, you absolutely need the fourth year of your undergraduate program in order to be considered for a top program.  Unless you absolutely load yourself up with challenging and graduate-level math courses in that last year (which may not be the best idea for other reasons, e.g. it works against the level of your success in these courses), I would in fact be thinking about what to do after you graduate in four years in order to make your grad school application more competitive.  You say that you want to take a year off before going back to grad school.  If you still want to do that after a four year degree, then thinking about how to get some additional mathematical training in during that year off might be a good idea.

Unfortunately, I've already completed all the course requirements (except one) for a physics BA, so at this point I might as well complete the degree instead of leaving 20+ credit hours wasted. The physics double major is not really an "option", it's a decision already made. I came in as a physics major, not math.

The people who have (mis)represented math undergraduate study and beyond, that would be my generic arts&sciences adviser, and my adviser in the physics department (physics having been my major for 3 of my 4 semesters). The physics adviser's attitude toward math was one of my first indications that I might not want to continue physics; one quote I specifically remember from my advising sessions, "A physicist isn't concerned about why there aren't solutions to fifth degree polynomial equations." What? Why not?

Update from more than a year later. I ended up doing as your answer suggests, I decided I won't be finishing the physics major, in order to focus on more math advancement. Just like graduating in three years, if I'm never going to use physics again, the only person impressed by a physics degree would be myself. In the meantime I've gotten published in a journal. Now just to take the GRE + math subject test, perform well in my classes these next semesters (possibly 2 graduate-level courses in fall, algebraic topology and a seminar), and see how I fare in PhD program selection.

I think those misconceptions come from popular mythology around mathematics. A lot of people assume that to be a mathematician, you must be an incredible child prodigy like Tao. Of course June Huh was no such thing, and won the fields medal. Math has a mystique in the popular imagination that is unhealthy and gets a lot of people to set ludicrous expectations of themself in many cases. In undergrad, someone told me they wouldn’t go to grad school because they didn’t think they could prove the ABC conjecture… profs need to be show they’re human too and point out their embarrassing blunders.

This would be a great question to discuss with your advisor, or another faculty member at your school whose opinion you respect.
My opinion, for what it's worth, is that the "bare-minimum" 3-year program you describe would be woefully inadequate to prepare you for graduate study in mathematics, and I think most admissions committees would agree.  The fact that you did it in 3 years with a double major won't mitigate that.  A year of analysis is pretty essential, some topology would be very helpful, and taking a significant number of upper-division math electives will be a great way to build what people call "mathematical maturity".
Your 4-year program sounds better, but honestly still a little on the light side.  Keep in mind that many applicants to top grad programs will have taken practically every undergraduate course their department offers, and maybe a couple of graduate courses besides, in addition to often having undergraduate research experience.  You also want to make sure you get to know (and impress) your mathematics professors well enough that they can write you strong letters
of recommendation, and taking more math courses is the biggest part of that.
The physics degree on your diploma will be nice, especially if you are looking to do a PhD in mathematical physics, but it may not go a long way to making up for weakness on the math side.

Another course of action for the 4-year is to just stay Physics BA instead of BS (this cuts off 5+ strenuous classes and labs) and focus more on fleshing out the math BS. This may be the best choice for me.

While Nate's answer mostly covers it, let me be a little more concrete: I just went into the files for graduate admissions at my own institution (the University of Virginia), and looked at the double majors we had admitted or wait listed.  I can't give details obviously, but I can say they are all way ahead (curricularly) of where you propose being at the end of your 3 year degree, and probably of the 4 year degree you suggest (6 classes beyond linear algebra is actually not very many).  I don't think there's any way that the 3 year degree you suggest could get you admitted into a top 50ish school (in USNW or NRC rankings) without some sort of exceptional factor, and if you have 6 post-linear-algebra classes, your background will still be a big disadvantage, unless you are looking specifically at applied math programs where your physics background will actually be taken into account.
To answer your general question: yes, rigor/thoroughness of undergraduate program makes an enormous difference.  Graduate programs are under pressure from university administrations to graduate students in a timely manner, and generally don't want to have students with weak backgrounds who will hang around in the program for a long time (or flunk out).   Most schools have a set of exams you need to pass before moving on to your thesis, and (just as an example), at UVA, you must pass a topology or analysis exam within 2.5 years of starting the program.  Thus, admitting someone with no topology or analysis background would just be setting them up to fail those exams.
While obviously, there's some sort of nebulous notion of talent that schools put a higher premium on (so you also want strong grades, and strong recommendations), background is relatively easy to measure, and is a very important factor in admissions decisions.

Thanks for your answer. I've edited my question to note another option which allows me to focus on, as you put it, "post-linear-algebra courses".

Seconding the other good answers, I would reiterate that, unless you are doing massive amounts of documentable self-study (which is entirely possible modulo the documentability), the senior-level undergrad or beginning grad-level courses you take substantially affect the appearance of your grad school application in at least two ways. First, your documented exposure to something approaching real mathematics. Second, the letters of recommendation from the faculty who taught those courses, testifying to your (presumably...) excellence in beginning-serious mathematics. Letters of recommendation are a very serious component of grad school applications, and if people can only refer to things scarcely beyond linear algebra, it won't help you.
Indeed, as @Pete L. Clark observed, you are being dis-served by lack of advising about the goals of your undergrad program, and about preparation for grad school. I realize that there are many ways for young people to disconnect from useful-but-official information, and many ways for institutions to fail to communicate effectively, but, either way, you're missing a bunch of critical info, which a site such as this can only nudge you toward.
One more time: the "minimalist" version of a math undergrad degree will doom your grad school applications. Finishing in three years versus four doesn't matter at all.


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Is it ethically questionable for me (an undergraduate) to hire "research assistants"?
I am an undergraduate student being paid a (relatively speaking) hefty monthly research stipend. I need only some of this money to pay off my university fees and living costs, since I have wonderfully generous parents.
The research projects I work on officially revolve around applied problems in math biology. Lately, I have been interested in Baez's work on "network  theory", but  because of full course load, along with the research project I am responsible for, I don't have the time to explore these ideas as I'd like to.
I have some ideas for pure math projects that involve extending Baez's nascent network theory ideas to problems in biology. I also have some ideas for tools that could be made in order to help a researcher formally analyze interaction systems.
These ideas are completely tangential to my own work (for the moment), although if I were able to set up the groundwork for them to the point where I am able to see that they do have potential, I'd love to bring it up with my professor.
One idea I have had recently is that I could hire my own "research assistants" out of my stipend (I am allowed to spend it as I like, right)? I could provide them with my motivations, and give them "guidance" (I don't know how capable I would be of this) through ongoing communication. This way, I would be able to explore my ideas, even if I don't personally have the energy and time to see them through right now. The alternative of course, is that I buckle up and find time from somewhere (e.g. by not writing this post) to work on the ideas, or put them away for a later date when I do have time.
So, is hiring my own research assistants at this time ethically questionable?

You may not realize this, but supervising and training research assistants from scratch often requires more time and effort than actually doing the research yourself.

@ff524 Yeah, the fact that I was entertaining that idea is probably born out of a good deal of inexperience :/

Why don't you just make a friend in the math department and discuss your fun ideas over some lunch and see if that inspires some collaborative work.

Why pay them? Maybe you can make a connection with a professor or student from your university or another that would be interested in this tangential (for you) project. Spark their interest! If it interests you so much that you'd pay someone to do it, there is someone who will be interested enough to do it by themselves free-of-charge.

Be very careful. Someone might come along who'd love to be your research assistant. You explain your ideas to them, give them money, and have them go off and do the research - and then publish it as their own work, since that's what it is. You apparently have no degree and no academic standing. You might fund the work - but you're not doing the actual work. If this is really an idea worth pursuing I'd say you'd be a class A fool to hand it over to someone else. YMMV...

I am wondering: If you're not sure enough of the validity of your ideas to discuss them to your professor, how can you be certain that it will be a good project for your research assistant? Making them work on a ill-grounded project could be a disservice to them.

Unless by generous you mean filthy rich, why aren't you using the stipend to fully cover your costs, which is presumably what it's intended for?

Here's another practical reason for avoiding this: depending on your legislation, hiring someone may come at substantial additional cost and/or burocratic work. Possibly even if you don't hire, but make a contract with a freelancer.

No, there are no ethical concerns, as long as whoever you hire is given the appropriate credit for the work she/he did.
There are economic reasons why this situation is unlikely to be fruitful, but that is another question.

I would add, "and you are honest with them upfront about your lack of experience in supervising research and the high probability that you will not be an effective supervisor at first."

@ff524 agreed, though the person hired is not necessarily looking for supervision, but might simply be interested in the pay.

If you are doing this for course credit or if this is part of your undergraduate thesis, you should ask your academic advisor or director of undergraduate studies. The assumption is that all work that you hand is is your own.
Many students have writing or math tutors to help them with basics or fix errors, but the underlying principle is that you did the work.
The question is what your 'staff' will be doing for you. If it is similar to what a writing tutor or math tutor is doing (checking  for errors, helping you with argumentation, etc.) then it is likely kosher. However, if it is tending towards what a paper-writing service is doing (you provide the topic and money, they provide the paper) then it is likely illegal and will get you in trouble.
Again, if what you are doing is kosher then you should have no concerns in being open about this with your faculty advisers. It behooves you to clarify this now as you don't want to be accused of plagiarism or fraud (presenting work that is not your own as your own) later on.
If this is for a project that has nothing to do with school, then: 1) you're posting in the wrong stackexchange; 2) you have nothing to worry about as long as you don't try to present it as connected to your school work.

The question explains that the OP is looking to hire sometime to do research in an area separate from his/her current official responsibilities (i.e. to do some independent research)

Independent research at a university follows the same expectations as coursework. If a student does an independent project with me, I expect them to not have disallowed outside assistance.  If the project is truly independent from academics (i.e., they are not submitting it to their university in any shape or form), then this isn't a question for a.se but for math.se or some other area.

Independent research as in "unaffiliated with his job/coursework," not the research he's doing for the professor or for any other academic obligation.

If he's never going to submit it to the university for credit, then he can do whatever the heck he wants. If he does submit it for credit, then he should be absolutely clear as to what help and support he received (and/or paid for).

Ps If he's using university funds (as intimated)  that were given to him for his research,  he needs to be extra careful.  In this case,  only his advisor would be able to say the correct answer.

He's using his own salary/stipend. I don't know of any university that restricts what students do with their money after they cash the paycheck.

@ff524: It boils down to whether that "research stipend" has been granted for conducting a particular type of research or a particular research project, or as a blanket financial support for whichever expenses the OP might have during the time while they are working on a particular type of research or research project.

When we give students a research stipend, we usually ask for a report on what they've done after they've finished. If he writes in his report, "I worked on Baez's theory of math biology and produced X results" when in fact it was his research staff that did the work, he is being misleading at best.

He himself is doing the research that the stipend is for and that the professor expects him to do. He wants to pay someone to do other, unrelated, research. All of these details I have brought up are clearly stated in the question; this answer seems to overlook most of them.

My point is that if what he is doing is unrelated to his academics, then he is posting in the wrong se. If it is entirely unrelated to his schoolwork and status as a student, he should be posting to math.se as a math problem.

Research doesn't have to be in the context of schoolwork and student/faculty status to be on-topic here; the [tag:independent-researcher] tag attests to that.

This is a very good moral question. It addresses the authority of an undergraduate researcher with respect to other students.
In my experience, as an undergraduate researcher, I found that there were times that I would have appreciated outside help that I would pay out of pocket for. Something along the lines of a consultant with regards to certain technical aspects.
I like Bob Jarvis' comment that you put your own idea at risk and someone run with it. Also take into account that instead of focusing purely on the task, you have to manage someone which is a heftier plate to be responsible for —and it already seems you have a sizeable amount.
Perhaps, as a compromise, if your advisor can promote you to a role that would take into account another researcher, e.g. senior undergraduate researcher, then probably this would work well.
To reiterate: paying someone out of pocket leaves many questions to interpretation, as far as roles and responsibilities go.

authors: Bob Jarvis - Слава Україні


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Can I get a letter of recommendation from a professor who didn't teach me BUT I did research with?
I am an undergraduate student wanting to transfer to another institution for undergraduate studies. I am a research assistant for a professor at an institution that I do not attend.
Would the university which I which to transfer to, accept the recommendation letter from this professor? Again, I have not taken any courses with this professor, nor go to the institution where he teaches.
Related (except for Graduate Admissions): Copied Letter of Recommendation?

This (somebody you did research with) is by far the best kind of recommendation.

Great to hear! But would a university accept it considering that the professor hasn't taught me in class and is at a different university than me?

@AA The fact that the professor did not teach you and is in a different university from you should not be a problem.

@AA They would prefer to have letters from people you've researched with, and as a last resort people who have taught you. You've got the priorities backwards.

The point of a letter of recommendation is for the receiving party to obtain third-party verification that you are, indeed, awesome. Generally speaking, people like to receive letters from individuals who know you well professionally. In most cases, teachers cannot write good letters, as they only know you as a face in the class, and never really got to know your work ethic, personality, and capabilities. A research advisor would be able to comment on all those things, and would be able to write a much stronger letter.

It shouldn't hurt, but I think it's only equal in this case.  If he were applying to a research program, than a research advisor recommendation would clearly be much stronger, regardless of institutional affiliation.  But he isn't applying for research...

In general. the criterion for a letter of recommendation is not "someone whose course you've taken.__ In general, the letter of recommendation is supposed to be written by someone who knows you well, and can testify to your strengths and weaknesses.
Unless there's a specific demand for a letter from someone who has taught you, you should not worry about the fact that your research advisor hasn't taught you. In principle, because a research advisor has worked more closely with you than a typical instructor would, your should expect to get a more useful letter from the research advisor, as OBu indicates.

The general answer is: "It depends on their rules regarding the admission process".
If they accept (or require) letters of recommendation, and they don't explicitely relate it to teaching relationships, they will take such recommendation letters into acount (and I personally would rate them even higher than a standard "this guy has great grades"-letter).

Thanks for the Response OBu. Universities require 'College Instructor recommendation' letters from potential transfers. I take that as "a recommendation from a college instructor"; which I would technically be providing. I guess my best bet is to ask the universities directly.