Plagiarism of code by other PhD student Abit about my background first: I'm currently undertaking a PhD but have previously worked in healthcare for around 4-5 years. During this time I developed a suite of code to produce results from clinical sequencing data (a NGS pipeline plus filtering steps).

Recently while looking for example PhD theses to use as the basis for my own write up I came across a recent PhD thesis that contained a reference to a github account, which contained code I had written.

The code in the repo is over 97% direct copy of code that I had produced while working in my previous employment - the remaining 3% appears to be a cut and paste of lines from my original pipeline into a popular pipeline management system.

edit I should note here that this remaining 3% had previously been submitted by another ex-colleague as part of an external qualification - for which I was the internal assessor, this person claimed sole authorship at the time.

edit I should have noted that development of this code started a year before entering the employment that I mentioned, as part of a postgraduate qualification that I completed, submitted ironically - along with prototypes of the discussed code - to the same university. Just to clarify the IP issue, the university in question assigns ownership to the student in these cases.

There is no direct reference to my own Github repo which contains the original code (with GNU public license) and no acknowledgment of my authorship (I am mentioned indirectly as a maintainer of the code elsewhere in the thesis). I had no knowledge that the author of thesis was using my code as part of their thesis.

The author of the thesis was in the same department as me, however was at no point involved in the development of the code while I was present. They have since submitted and passed their PhD and are now employed as a PostDoc in the same department.

I can show continuous development of the code over a period of 4 years previously via my Github logs. The author of the thesis has only a single commit and no history in the github logs.

The person in question has essentially written a PhD chapter based on analysis of sequencing data that I did. The code is just part of the story, since the person also claimed that in addition to writing the code they used the code to produce the results in that chapter. They didn't - since I know that I ran the batches in question (this was around 2 years of work).

What steps should I take (if any)!

This is a tricky one. It probably sounds like academic plagiarism, but your licensing concerns are probably not going to resolve the problem at the core of this. There's two sides to this, the academic (plagiarism) side and the commercial (licensing) side. They're almost entirely separate, so I'm going to break them up.

Academic/Plagiarism Claim

  The code in the repo is over 97% direct copy of code that I had produced while working in my previous employment...

Without attribution, this is plagiarism, and may be grounds to have the PhD rescinded, but this would be a serious procedure as it's likely to have life-altering affects on the PhD student in question. You'd need to be 100% sure of what you're doing and the validity of your claims going into this. Even if the case was black and white (which I don't think this one necessarily is), the student's University isn't going to take rescinding a PhD lightly as it reflects badly on them.

Additionally, it sounds like there is a some attribution within the work:

  The indirect mention of my name is as a maintainer not the sole developer

...which might well be sufficient for the University to write this off as a referencing error, maybe requiring the student to make a small addendum to their thesis.

  The code is just part of the story, since the person also claimed that in addition to writing the code they used the code to produce the results in that chapter. They didn't - since I know that I ran the batches in question (this was around 2 years of work).

If you can prove it, the experiments that they claim to have run, that you performed while under the employ of their department are probably your strongest leg to stand on here. But you'd have to have good evidence, and be able to show they haven't run the experiments themselves. If yours were not published previously, and they've generated the data themselves using your code, this may well be null and void.

Commercial/Licensing Claim

The licensing perspective of this is completely separate to the plagiarism side - if the work was published as GPL, they can basically do what they like with it, without attribution, provided that any code based upon it remains GPL. This bit is important, as it's probably where you have a leg to stand on, based on this comment:

  although the person has also removed the GPL from the repo, which I thought was against the license terms

That is absolutely in breach of the terms, which is why most industrial entities won't touch GPL code with a bargepole (due to what's commonly called "license bleed").

Based on this, you might have a valid claim to get their repo pulled, but that's not going to solve your actual problem.

Again, from the comments:

  ...I feel that the supervisor (who used to be my boss)...

I understand this to mean that the PhD student in question is supervised by your old boss, which means you had a contract with their institution. Depending on the contract you had with them, they could therefore own all the rights to it regardless, making your initial GPL license in breach of your contract with them without prior stated agreement. This wouldn't affect the legitimacy of your plagiarism complaint, as that's a genuine academic concern, but might affect how the department deals with your request.


Role of math in Computer Science I've been wondering this for quite some time and decided to ask finally. What really is the role of math in computer science on higher levels like master's and PhD? Currently I am working on my BSc and hopefully get it done next summer. I have done like 5 math courses(linear algebra etc) + 5 statistics courses. I also did calculus in high school(integrals, derivatives etc) as I took the longer version of math which typically increases your chances to attend STEM programs here(EU country). Some of my professors have spoken how important they think math is in computer science, but is it really unless you go to some very specific fields like theoretic computer science? Because I haven't found it that useful outside of a few specific courses.

I am not sure whether I would like to pursue a PhD in the future but I've been leaning more towards it lately. Security research has gotten my interest and I've done some reverse engineering + vulnerability analysis and working on a small JIT assembler. Sadly not many undergrad courses teach these things so I've worked on them largely by myself. I haven't had any use for university level math on that, maybe I've just scratched the surface?

In some ways I feel bad for not taking more math courses and it's something that keeps annoying me but it's very hard to try to convince myself that some proofs about integrals are going to be useful in my future work/research. It would be nice if someone could elaborate what kind of role math plays in higher level of computer science studies. I have never honestly liked math that much but instead seen it as a something that you just need to know. What are some really useful math courses one should take?

As Galileo has said, "[The universe] is written in the language of mathematics," and it is no different for computer science.  To be a strong computer science researcher, you need to at least be fluent in the forms of mathematics that describe the work you wish to be engaged with.

Mathematics, however, is not a single thing, but a broad domain, and what you need to know will depend on what sort of research you are engaged with.  For example, if you go into computer vision, you'll probably need to know a lot of complex geometry, whereas if you go into cryptography, you'll probably need really deep understanding of number theory.  In some particular paths of work, you might in practice need very little mathematical knowledge at all.

What you absolutely must have, whether for computer science or for any other scientific pursuit, is a comfort with mathematical and scientific thinking in general, enough general mathematical fluency to acquire new expertise at need, and a solid working knowledge of statistics and data analysis to aid in interpreting experimental results.  In almost all computer science work, you will also be greatly aided by fluency in algebra, general discrete maths, Boolean logic, and asymptotic complexity theory.  Beyond that, it all depends on what you're doing.


Referee access to a not-yet-public URL cited in a paper? I am reviewing a publication, in which the authors give the URL of an online tool (data analysis and sharing) they have developed. This URL has apparently not yet been publicized, as searching for it in Google didn't bring any result. Because of that, I'm worried that the paper's authors may identify me as a referee when I go check their website (after all, the logs must be clear). That probably wouldn't be very ethical, but I have no way of being sure they won't do it.

What I am supposed to do about it? I thought of contacting the editor asking for guidance, using a private proxy[1], or logging from an internet café somewhere. Do you have any other suggestions? Or am I just worrying too much?

I don't know which anonymizing proxy service to use, and I welcome suggestions in comments, but that probably isn't particularly relevant to this site.

First, I think you are worrying too much. Second, I think it is bad form on the part of the authors. If the material on the website is critical for the paper, it needs to be provided in an archival form that the journal can keep track of. I would evaluate it based on what you have been given.


Restricting details in privacy-related research to prevent abuse I'm starting to do research in machine learning on sensitive datasets, which sometimes seems like a double-edged sword. For instance, some projects involve showing how a company/organization/government can infer sensitive information about you and abuse it. I feel that this has to be published as it may already be abused somewhere or will be soon. At the same time, if I publish too many details then some corporations etc. may find it easy to implement and start abusing.

Do some conferences/journals accept papers that have scarce details on some parts of the modeling such that it may hinder abuse? It should be noted that while the code may be sent to the reviewers for a check, the data is sometimes of a sensitive nature such that it cannot be handed over.

From a practical perspective, even if you omit the implementation and mathematical details from your paper, large companies like Google and Facebook, or state agencies have significant amounts of manpower and talent. And if they really wanted to they could probably get very close to the results that you are obtaining in a short period of time.

So it is unlikely that any obscuring on your part would halt these entities from following through with whatever agenda they have. On the contrary, omitting too many details will only make it harder for you to publish.

On a more philosophical note, any machine learning model can be used for good or for evil. Linear regression models I'm sure have helped people to win wars as well as eradicate diseases. As a result, one can easily argue that any attempt to prevent abuse is equally preventing progress in other domains.


Is it okay to ask to "waive" the stipend when offered a fellowship for PhD program? John just got accepted to a Ph.D. program in Computer Science. He also received a fellowship in the form of TA-RA-ships which comes with a stipend of $34,000/year for 4 years.

However, John is currently receiving Disability Supplemental Security Income (SSI) from the U.S government which prohibits him from having any income.

He is only interested to have his tuition covered without receiving extra money.

1) Is it okay for John to ask the university to forfeit the stipend? (or for any other reasons than the above).

2) Can John ask rather to receive the stipend, to have the amount apply to his tuition after the 4th year?

John appreciates your thoughts on this... Thanks :)

You can certainly ask for the stipend to be withdrawn. Most universities are happy to spend less money. They may not be happy if this also means that you are not doing the TA/RA work, depending on whether they have enough TAs/RAs.

You can also ask for the stipend to apply to tuition - no harm in asking. Less likely that this will be granted than just stipend withdrawal.

Volunteer work is usually accepted, so if you want to do the TA/RA work you may be able to, even without the stipend. The legal status of such work is the question, which you should ask a lawyer about.


Possibility of Changing Bad Impressions Long story short, I'm a struggling first year graduate student. I considered myself very lucky when I found out that I was accepted into one of the best programs in my field, but didn't realize at the time how steep the learning curve would be to work alongside the best. I work in a wet lab, which I joined three months ago. However, given that I had very little research experience in undergrad, I've had a rough start. I don't think I fully realized the level of critical thinking skills that would be expected of me, and still depended on other people to tell me what to do and what to work on. A lot of science conversations I've had with people in the lab have also been completely over my head. Like I should be the one developing novel knowledge, yet sometimes I can't even understand someone else when they describe something to me (not just older grad students either, a lot of the undergrads also know more than me)... As a result, people in the lab have started treating me like I'm stupid or inferior, and my PI is slowly decreasing my level of responsibility.

I've spent the past few months in complete depression and anxiety, which is making the problem even worse. I would really like to change this situation, and have been working really hard on my project, but I'm not sure whether it's already too late to change the impression of my labmates and PI. So I guess my questions are as follows:

Have you ever had/known any grad students who started slow, but have reversed bad first impressions? How much harder did they have to work to achieve the same level of respect?
What do you think of students that on average take longer to learn the same technique or concept? Should such student still stay in research given the amount of competition that now exists in academia, or is it realistically a waste of their time?
How would you recommend I go about making changes. Work harder and push out more experimental results? Dig into and understand literature broadly? How should I go about changing people's impressions of me?
For any PIs out there, what do you think of your students that are not meeting your expectations? Do you wish you never took them on as a student, or are you still rooting for them to make changes?

The truth is, even though people don't like to talk about it, that most graduate students start out like you do. As advisers we see it all the time, and the better ones among us have conversations about these sort of things with our students and/or to our research groups. Many students, and not a few of those who later make it into the professoriate, have at times struggled for weeks or months with frustration, depression, and general unhappiness with their progress in graduate school.

In other words, what you're describing is, if not a normal, a common experience in graduate school, even among some of the best students. I like to thing of graduate school as less of a way to filter out the best than a way to filter out those who can deal with frustration and yet persevere with their research.

So keep going on. If you want, seek out the postdocs and/or your adviser to talk about this. You'll find that you're by far not the only one to encounter such feelings.


How to add a citation to a sentence that has parentheses at the end? How can I add a author-date citation to a sentence that ends with parentheses? That can occur when using parenthetical remarks or when an abbreviation is introduced:

However, methane has a higher Global Warming Potential (GWP)(IPCC 2013).
Most environmental impacts were due to methane emissions (which has higher GWP factors)(IPCC 2013).

Having two parentheses next to one another sure looks awkward. Is there a "workaround" or should I work harder and restructure the sentences.
Update: I am writing my thesis and the university does not recommend any citation style.

This depends on the writing and citation style you are using. In APA you should use a semicolon to separate the citation from the acronym:

However, methane has a higher Global Warming Potential (GWP; IPCC, 2013).
Most environmental impacts were due to methane emissions (which has higher GWP factors; IPCC, 2013).

Source: http://blog.apastyle.org/apastyle/2013/05/punctuation-junction-parentheses-and-brackets.html


Postdoc salary. Fair offer? I was just offered a postdoc at 34 000 USD a year.

I am wondering whether this is an ok offer. Can someone give me feedback on this?

It sounds like it's on the low side for the sciences, but not unheard of.  For comparison, NIH NRSA postdoc stipends start at about $39k for people with no previous postdoctoral experience and go up from there.  Postdoc salaries can vary a lot by field, location, institution, etc.; if you have no other offers to compare with but want to know what's typical, I'd recommend searching online to find information that fits your background.

As Paul Garrett pointed out, you also need to consider the cost of living.  According to CNN Money's cost of living calculator, $35k in Nashville is the equivalent of nearly $70k if you were living in Brooklyn.  Of course these calculators are far from perfect, but they give you some indication of how prices and rents vary across the country.  If you are going to live on $34k, Nashville is a good place to do it, and I would expect typical salaries there to be lower than in more expensive locations.

Ultimately, unless you believe there is discrimination or bias involved, I wouldn't worry too much about abstract notions of fairness, or even comparisons with other people in different circumstances.  Instead, I would focus on three questions.  What do you need to live happily in the short term?  What are your long-term goals and prospects for achieving them?  And what other options do you have, including not just similar postdoctoral offers but also career changes?  Only you can weigh these considerations and decide whether a given offer is acceptable to you.


What is more important in choosing a research advisor? How would you weight each factor below on choosing an advisor?

1 - My interest in the advisor's research topic.

2 - How well he/she dedicates time and effort to guide me.

This is a Hobson's Choice as stated. In reality you need both.

But in reality each of these ideas is defined by a wide range. Your interest can be a little or a lot. The more interested you are the better. But if your interest is zero it is a big mistake to choose that.

The support provided by a professor can be a little or a lot. Even if it is "low" the needed support may be provided by others, say post-docs or senior lab researchers. But if the support is zero (in time/effort), again, it is a big mistake to choose this. Moreover, the kind of support provided by different advisors can vary widely. They can be the source of a problem that you solve, or they can be a collaborator.

In realistic situations you need a balance. Moreover, the balance is partly determined by yourself. How wide are your interests? How flexible are you? Are you driven to a particular sub-sub-sub-field or are you willing to explore anything "interesting"? How much guidance do you need? Are you a dedicated self studier or do you need a kick to get moving in some given direction?

Think about your own personal situation and make a choice. But zero on either of the two indices you are looking at is probably a bad choice.

However, at the undergraduate level this is a less critical choice since you have a variety of things to do beyond research. As you are just getting started in research, it might be wiser to choose someone who will give you more help rather than less despite a low interest in the specific topic. At the doctoral level, the topic becomes more important.


How can I get a paper if our library is not subscribed to the journal? I am a PhD student writing my thesis, and desperately need some specific papers which are not accessible via our library subscription. I contacted the authors to get a copy from them but some didn't reply. There were not available in free repositories and buying the articles from the publisher is too expensive for me.

Is there any possibility for getting a few papers you need?

My university has an inter library loan system where I've been able to submit requests for copies of an article. It requires entering citation information about the article and I have seen requests returned in a week or so. Sometimes the requests are digital, sometimes they are physical.


Possibility of doing Masters in astronomy with only bachelors in CS I have a bachelors degree in Computer Science & Engineering and currently employed in s/w industry in Pakistan, but have no degree in physics. For long, I've been interested in doing research in physics, especially in astronomy, astrophysics or in particle physics.

Are there good institutes or universities in Europe ( Germany,
Sweden etc) which accept students without any degree in physics to
Masters program in astronomy or astrophysics or joint with computer
science? If so, do they also offer financial assistance or some form
of scholarship to such students to meet at least one's tuition fee
expenses?
Where I can find some research article that some teachers are working on so I can contribute them? I want to help through my coding skills. How to found those teachers who are working on research based on astronomy and contact them?

I can't speak for all the institutions, but in general, you're out of luck. It's true a lot of modern astronomy is programming, but there's also a lot that isn't. You need to be familiar with things like the Fourier transform, vector calculus, and classical mechanics / general relativity.

Here's an example of the entry requirements for astronomy at Lund University in Sweden.

  Bachelor’s degree of at least 180 credits in physics or the equivalent. The degree must include at least 90 credits in physics. Proficiency in English equivalent to English 6/B from Swedish upper-secondary school.

You'll have to get the physics training if you want to pursue this, unfortunately.


What do I do with a write-up of possibly folklore knowledge? Some months ago I was trying to wrap my head around some classical constructions in homological algebra. I spent quite a lot of time with this, and decided it was worth it to write it down. I did, it's almost 20 pages, and it's been sitting there in a file since then.

It starts pedagogically enough, reproving well-known results, and then it gets into "surely folklore" territory, i.e. not hard results about well-known objects that I have never seen in print (and I did search quite a bit for them). Then it goes on to prove an auxiliary result which is taken for granted in a recent paper (this was my motivation to do all of this).

It might be hidden in Cartan-Eilenberg (a quite hard to read book nowadays, in my humble opinion), it might not. At any rate, I don't know what to do with this file. Should I forget it? Be happy that I understood all of that, and keep it for personal consultation? Post it in my website? In arXiv? Submit it somewhere? I thought I could try to remove the certainly well-known stuff at the beginning, and only keep the "folklore" stuff; then it could be a less than 10 pages note.

The question is, then, how do I deal with "possibly well-known, possibly unwritten results about some well-known construction"?

I could speculate here, but I think you need advice from an expert in that particular field. It may well be that there is journal out there that would gladly publish such a paper, but also the converse may be true. It may also be that there is some special issue coming up where such a paper would be a good fit. However, these things are only known to experts in the field and hence, your best bet would be to contact one. These could be people in your department, editors of journals on this topic, plenary speakers at conferences or authors of books in the field. Knowing this person personally prior to asking would probably be better (but not necessarily so).

If you do not know anybody to contact, you could also look for a journal that seems to fit and write an email to the editor (or a suitable associate editor) with the write-up attached and ask if this would be suited for said journal. It is not uncommon to sound things out that way. (Beware, that a positive reply does not tell much about chances of acceptance.)

If publication in a journal is not important to you or you don't want to risk another frustrating rejection, uploading the thing to the arXiv is the way to go. You get some publicity and some people will read it…


Kavli Frontiers of Science: is it a worthwhile use of one's time? I recently received an invitation to a "U.S. Kavli Frontiers of Science symposium."  I have to be honest, when I first received it, I kind of thought it was conference spam, but investigating further, I came around to thinking it seemed legit (in part because it is organized by NAS and they offered to pay expenses).

But "is a legitimate scientific activity" is a pretty low bar for deciding whether it is worth expending one's limited time to attend a conference (at some minor personal inconvenience), which at least for me is not obviously connected to my research or even necessarily my discipline.  Does anyone here have experience with it?  Are the talks interesting for outsiders to the disciplines?  Is it actually a good networking opportunity?  Is it the sort of thing I should be bragging to my dean about (I'm about to go up for tenure, so bragging rights are somewhat relevant)?  Is it just sort of a glorified TED?

Yes, it's definitely worth attending and you should mention it to your dean.  (It's only a minor honor, but a minor honor is still worth highlighting.)  I did this some years ago, and it was a great experience.  Not particularly valuable for my research, but I met some fascinating people in other fields, some of whom I had more in common with intellectually than I had expected, and I learned many interesting things.


Should I decline a request to tutor a class I will be taking? I am a first semester master's student. A professor has sent me an e-mail with an offer to tutor a bachelor class (this would be a paid job). I do not know him personally but he told me in his e-mail that I was recommended to him by a professor whose class I took this semester.

Now here is the conflict: I did my bachelor's at a different institution and in my country, it is normal for universities to require students who switched institutions to take 1-2 bachelor classes in the first semesters of their master. Among the classes I am required to take is the very same class the professor offered me to tutor. As a tutor, I would be teaching exercise classes and grading other student's solutions to the problem sets.

Can I decline this offer for the above reason or could it be seen as making excuses? I do want to pursue a career in academia so I am afraid that this could be misunderstood as me not being willing to tutor classes or do work for the deparment in general.

You need to tell the professor. I would suggest that you tell them you want to tutor the class and believe you have the skills and knowledge, but that you are being required to take the class for credit. Then ask if it might be possible for the tutoring to satisfy the requirement.


Include F1000Research publication on CV I am a biostatistics postdoctoral student. I recently participated in a coding festival and our work was published in F1000Research (https://f1000research.com/).

In your opinion, should I include this publication in my CV along with more typical peer-reviewed papers? Similarly, what are the pros and cons of adding this to my CV?

Thank you for sharing your thoughts!

Personally, I think that one should include all of one's significant scientific works in a CV.  What you do not want to do, however, is to give an impression of "CV-padding."

Accordingly, I recommend that you do what is done by many researchers (including myself) who publish not just in journals but in multiple different types of scientific venues: divide your publications list into different classes of publication, e.g., "Journal Articles", "Thesis Chapters", "Peer-Reviewed Conference Papers", "Non-Refereed Articles", whatever fits.

Thus, a work in something like F1000Research, which is citable archival publication but without traditional peer review, would be listed as a non-refereed article: noted as a possibly significant scientific work, but clearly labelled as different than your traditional peer-reviewed articles.


What does it mean to be a co-author? What does acting as a "co-author" entail, and how common is it for first year undergraduate students to be added as co-authors to a paper being prepared by a professor?

Almost any published work has one or more people listed as authors: they are those people who made a significant contribution to the creation of the work.  If there is more than one author, they are called co-authors, and one might say they co-authored the work.  Usage like "become co-authored into a paper" would be non-standard and perhaps non-grammatical; one would instead say that a person became a co-author of the paper (typically for having contributed to it in a significant way).


Editor of manuscript assigned after reviews were completed Recently, I submitted a paper to a journal. The paper was reviewed and the reviewers asked for some changes. I revised the paper and sent it again. The paper was reviewed again and after a few months the status was shown as "reviews completed". But the status was again changed to "editor assigned". Could you please explain to me what does this imply?

Each journal has its specific take, but the most likely explanation is that the peer review process took longer than usual and the same editor had expired and had to be reassigned, or that he was no longer interested in handling your manuscript and it was thus assigned to another editor.

In most busy journals several associate editors cooperate with the editor-in-chief, and it is likely that your manuscript was switched from one associate editor to another one.


I absolutely hate my PhD and I don’t understand the purpose of it I am in the fifth year of my PhD and seriously depressed. In my first year of graduate school I was not funded. In my desperation for funding I chose an opportunity that came my way even though I did not like the topic. The research I would say is pretty mundane, I was providing experimental support for an FEM group. I did t have any freedom until the end of my 4th year. Also my advisor was the co-PI and the project was not in his area of expertise and he had no clue about the work being done. Whenever I get lost and ask him for advice, he would commonly uses the phrase “Do what the industry sponsor wants, keep him happy ”. I literally felt like a contract employee and not a PhD researcher. As expected the work did not yield any papers. My lab mates working on other topics (areas of my advisors expertise) get to present at academic conferences and are writing journals. When I point out this fact I get chided for comparing myself with others and  that my work is “unique”. At one point my advisor himself said that the project was ill conceived. You can understand my frustration.

Now I am depressed, lost, and hardly do anything. I wake up, go to the lab and pass time. I absolutely hate my “thesis”, I don’t have anything meaningful or useful for my future career. I don’t even know the purpose of my thesis topic. initially I was scared to leave, now I feel it is too late to leave.

please advise me on what to do? Thanks.

Now I am depressed, lost, and hardly do anything. I wake up go to the lab and pass time. I absolutely hate my “thesis”

This is the problem; you are stuck in a vicious cycle. You need to meet with your advisor and come up with a solid plan - including a timeline - for what will happen in the next year or two.

Given that it has already been 5 years, I suspect this plan should involve you finishing your current work, writing a dissertation, and graduating. But, you and your supervisor could also choose a different direction (i.e., starting a new topic or choosing a new advisor).

  I don’t have anything meaningful or useful for my future career. I don’t even know the purpose of my thesis topic.

At this point it's probably time to decide what your career goals are and make sure your plans are aligned with reaching those goals.

This could mean spending 1/3 to 1/2 of your time learning skills that will be useful for an industry career, and spending the rest of your time preparing for graduation. Given your level of burn-out, I suspect this is the wiser course, but I'm just guessing.
Or, it could mean switching topics / advisors / institutions so that you will be competitive for academic positions in topics that interest you more.


Is it possible to defer graduate admission for one year? I got accepted into the Phd program at a Top 3 university in US.

However, as I have an external scholarship (full funding for PhD study), I have to defer my admission to work at the scholarship sponsor research institute for one year.

I wrote to the department explaining my situation, but was informed that deferral is not allowed and I have to reapply next year.
Anybody had a similar experience as me? Is there a chance to appeal for my deferral request?

As I have my own fundings, technically speaking I do not occupy a quota in current cohort.

You have no 'rights' in this matter.  You apply, they accept you or not, under their own terms.  So all you can do is ask again, maybe giving fuller details of your situation.


Quoting Keynes in a lecture I am teaching mathematical statistics and part of this is large sample theory. I would like to discuss some methods that do not focus on asymptotics and refer to J. M. Keynes quote

  In the long run, we are all dead.

I am a bit afraid some students might find this quote a bit too strong.
 Could this quote be considered a bit too strong to be presented to 3rd year undergraduate students in the UK?

Opinion, of course, but I think it is fine. It is often quoted in fact. While your students probably still think of themselves as immortal, they almost certainly aren't. No one should really take offense at basic biological certainties.

It is, in fact, a corrective on much illogical thinking, which is why it has lasted.


Do PhD advisors allow students to collaborate with faculty from other institutions? I would like to know if PhD advisors allow students to collaborate with professors from other institutions in a major way. The context for me here is that I will be joining a Top-50 institution for a PhD in Physics. Considering the job prospects in academia, I think it would be worth collaborating with the topmost people in the field directly (who generally reside at topmost universities like Stanford, MIT, Princeton, etc.) to get solid recommendations from them along with my advisor's recommendation (assuming I produce good quality research with them). I would like to know how such an arrangement can be made possible without making my advisor feel bad. Are such arrangements common?

Of course, my current institution has brilliant professors as well and I would like to do my best to produce good research with them too. This is why the consent of my advisor in whatever I do is very important to me. I just want to make things as productive as possible in my current PhD program and have the best people in the field write recommendations for me so that I could continue working in academia.

Interesting thought. I will try to offer some factors to consider related to the approach you are suggesting.

There's a risk of spreading yourself too thin. All things held constant, I would expect it to be more difficult on average to build relationships with faculty at institutions other than your PhD "home base." The time and effort spent building these relationships would thus be re-routed from what should be your main thrust, i.e. developing a reputation as an excellent student in a place that actually voted to have you and invested resources in you.
Faculty at top institutions are extremely busy and inundated with queries from all sorts of places and people who want their time and attention on collaborations of various types. Successful faculty are very strategic about where they invest their energies (especially in Physics? sorry, bad pun). This partly explains the uphill battle presumed in point #1. They usually have plenty of students and postdocs of their own who want to "collaborate." The returns from such one-off partnerships with this or that individual who met them at this or that conference are dubious, and typically high-flying faculty end up collaborating on high-visibility/payoff projects. Unless your work will fall in that category, I think productive sustained collaboration with quality attention and care invested in the relationship on both sides is highly unlikely.
The only relatively common, accepted form of collaboration with faculty from other institutions that I am aware of is IF those individuals are  members of your dissertation committee. Colleges (at least in the U.S.) often require that at least one committee member be from another department at the home institution. Along the same lines, it is typically viewed as OK if there is another, additional committee member from another institution, as long as their being on the committee is well justified, e.g. by filling a gap in expertise or being in a unique position to contribute something given their specific context/resources. In contrast, collaboration on side projects can cause some minor (which could become major if left unchecked) issues involving your Advisor wondering what the heck is taking up your time that you could be spending in his lab and writing his papers...

This being said, it is possible that in some disciplines such collaborations are more frequent and more accepted than in others, and may pay off in some ways. However, the though I would like to leave you with is to carefully reflect whether such collaboration will in fact help your career plans, over and above similar collaborations with faculty at your home institution. If you find yourself in a situation/project where the answer is a clear YES, well, you can at least give it a shot and see what happens.

However, if by looking over the fence (where the grass typically looks greener) you might end up missing some gems on your own lawn, I would say stick to the familiar environment and try to make the most of the opportunities under your nose.

Lastly, collaboration can take many forms. It may not be necessary to go it alone and try to carve out an independent project with someone from another university/lab. Being on a research team (as a Research Assistant) that has some external partnerships with teams at other institutions can be enough to develop some contacts and build some name recognition in those places. Being considered a valuable member of the research team at home, and being valued by your own Advisor can speak louder than trying to convince someone on the outside that you are wonderful and totally worth their attention. When you will be close to graduating, if your Advisor believes in your potential, s/he will go a long way to help you network with various other labs/teams that s/he has relationships with. I personally would recommend this more "organic" route.

The academe is a big boat that doesn't like to be rocked, and stability is generally considered an asset. Having a reputation for dedication to one or two large-scale, complex, team projects is probably going to help you more than having 10 separate fledgling solo projects/partnerships. (Note: If you were an undergrad with a major in Business/Entrepreneurship, this advice would be the opposite. But a PhD in Physics seems more aligned with the solid/long-term academic paradigm.) Whichever way you choose to play your cards, good luck!


What's the purpose of a PhD defense? It looks like everyone has it's own theories on what's the function of a defense. People say that it has to be a contribution to knowledge, other people say that it has to reflect 3 years of work, other say that it has to be a work of publishable quality.
Given that "contribution to knowledge" is kinda a difficult ground to judge for some humanities, how are examiners approaching a PhD defense in the humanities?

The ‘defense’ is part and parcel of the work itself. Typically you must first produce some novel work, and at the very end, you must ‘defend’ this work in an act of oral discourse. The defense is mostly a rite of passage in most disciplines. Your advisor and committee usually won’t let you get that far if the work is sub par and you’re likely to ‘fail’. Officially, you must be able to speak intelligently about the work and address criticisms on the fly, proving your scholarship and deep knowledge.


What should I do if I think a researcher in my university is intentionally employing incompetent people? In our university there are a lot of great researchers and a very competent people in general. I've discovered today that one of our researchers is intentionally employing people who are totally incompetent. I think that he's doing this to appear as a great teacher and supervisor, because, as far as I know, he was a supervisor for all of them in the past.

I personally know some of these incompetent researchers, since their first year of undergraduate studies. They were those people who find it incredibly hard to pass every course, especially maths.  I've been giving one of them remedial lessons to make him able to pass a database course. He finally made it on the 3rd attempt. His other courses weren't much better - he failed literally EVERY maths course until the last possible attempt.

Today, I discovered that he and several people similar to him are employed as researchers.  Some of them were there even before completing their B.S (which is usually not allowed even for the most talented students).

What should I do to notify others of this situation and without worsening my position in my colleagues' eyes?

The researcher is a man of a great reputation (or at least, much greater than I am as a postgraduate :-) ), so I'm afraid of being just considered malicious and jealous man. On the other hand I'm pretty angry about all this, because there are some very expensive international projects, where money for these people are completely wasted and a research progress is much slower than it has to be. Those positions could be occupied by really talented and competent people and not just by somebody, who was supervised by one specific man.

My suggestion is that you let it go for three reasons:

This is hardly the last time you'll come across this problem, inside or outside of academia.
There are factors here you might not be considering or know nothing about.  Maybe the person you're tutoring in math has excellent people skills, or is the instructor's nephew, or the Dean's. Whatever the reasons they're really not any of your business.
As you say, you will indeed end up being considered a malicious and jealous man.

If it really bothers you you should probably find somewhere else to work where this isn't a problem, but then see point #1, above.


Acknowledgment to friend in research article I have a research article that has been accepted in reputed journal and is in final stage of publication. Now I want add acknowledgment in my article, as I independently written this article so nobody has academically contributed to my research. But I strongly believe that my research could been effected very badly if my close friend had not been there for my help(not academic of-course).

Can I add his name in acknowledgment?

This sort of thing is quite normal in books. In articles, one frequently sees the author(s) thanking a colleague for fruitful discussions and such. If you really feel so strongly about your friend's impact on your work, I think it would be perfectly appropriate to include it. Just avoid specifics such as "X helped me deal with the effects of my depression and drug dependency". (In other words, use common sense.)


Motivational Letter for Work placement I'm an italian student,attendig the university, and I have to apply for a Work placement during this year, in order to complete my path and graduate. I have already found a firm in London and I would like to send as soon as possible my request. The point is that it's my first time and I have some doubts:

Should I send, with my CV, a motivational letter in order to introduce myself or this letter should be done only for jobs or accademic application like PHD and Masters?

I read this thread below very carefully, and I loved it!

A good motivation letter

Could be the first answer from @penelope a good structure also for my application?

Thank you so much!

I'd send a CV and a motivational letter - it might be a good idea to call as well if you are unsure exactly where to send it.

Penelope's answer is good, but recruiters can spot a 'template' motivation letter a mile away - I'd try and do it from the heart as much as possible.

Also, make sure you include contact details on both your CV and covering letter!


Is getting into MSc programs in Europe easier than PhD in US? PhD programs in US usually include an MSc degree and many of the admitted students don't have an MSc. In Europe however, with just a few exceptions, everywhere requires an MSc for a PhD. There are also quite a few differences in the structure of the undergrad in US and Europe.

I was wondering if it is easier for someone with a US undergrad degree to get into an MSc in Europe than PhD in US? Are the PhD admissions in US more competitive?

If I have an offer from a couple of top US schools (by "top" I don't mean Harvard and MIT, I mean around a dozen (national) ranks below that... say, top 30-40 in global rankings), should I be confident that I can get into one of the few MSc programs in Europe I've applied to? (The programs are top/best programs in Europe, but the universities are essentially on par with the US school in global rankings. Perhaps some of them have a better global reputation in the specific field.)

Note:

1 - By Europe I am referring to Western Europe, excluding UK. More specifically, Germany, Switzerland, France, Belgium, Holland, Austria.

2 - The field is Mathematics, if that makes a difference. (I think it might, given the reputation of places like Heidelberg, Bonn (Hausdorff Institute), and the universities in Paris have in Mathematics.)

Master's education in Europe is largely considered an "undergraduate" degree that follows the bachelor's degree, rather than being the prerequisite for the PhD. Thus, admission to a European master's program tends to be much less competitive than PhD admissions in the US. Now, if you're applying to a top program in Europe, it can be as difficult and competitive as in the US. But the average master's program in Europe has a lower bar to admission, so long as you've done the necessary undergraduate studies considered a prerequisite of the bachelor's degree program.

The rules about what is considered acceptable varies, but a few rules of thumb apply:

In a “consecutive” master’s, which requires a bachelor’s in the same discipline, you need to be able to catch up with coursework in less than one year (sometimes one semester, if the program is competitive).
In a non-consecutive master’s, you just need to have a suitable bachelor’s degree to enroll.


I have a degree but it isn't actually what it looks like it is. How do I list it on my CV? Due to various department sortings and organizations, I have a degree that is, functionally, a computer science degree but because it belonged to the College of Mathematics, the degree is formally "Mathematics".

Unfortunately this leads to many employers thinking that I have a mathematics background when the reality is far from this: I don't think like a mathematician or particularly enjoy its work.

Is there something I can do with my CV to reduce this bias? Is it as simple as changing "Mathematics" to "Computer science" even if it isn't the official title of the degree? Are there other options?

I would list it directly with the degree. I have a similar issue in that my degree is Geodetic Science, but my focus was in (at the time) computer-assisted mapping, now known as GIS. People try to call me a geodesist, but I'm not really. I would use something like:

M.S. Mathematics (specialty: Computer Science)

Edit: I finally remembered what the various tracks were called in our department--a concentration, not a specialty. Other synonyms include focus, even research or research topic.


ratemyprofessors' alternatives for francophone or German-speaking countries Are there some equivalent/alternatives for the sites like ratemyprofessors.com for francophones or German-speaking countries?


As an international instructor, should I openly talk about my accent? I'm an international, teaching at an American university, and I have an accent, which can be strong at times. I'm working hard at it, have always been, but still, the accent is there.

This has never been a problem in my career as a researcher because I was most of the time working with senior researchers and grad students. And even if they were native, they've never expressed any concern about my accent.

I'm sure that several times they didn't understand a specific word I was saying but they catch the meaning from the context. Sometimes, people asked me to repeat in an informal way by simply saying "what's that?" or "say it again".

Last year, when I started to teach undergrads, which are unlikely to have experienced different accents, I had some issues.
Some students asked me to repeat and I gladly did. My concern is related to those students that didn't ask, either because they are shy or because they thought that by asking I would be offended.

This next semester (yes, I'm going to teach in the summer) I'm thinking to tell my students in the very first minutes of the first class about my accent and tell them that I'm totally fine if they need me to repeat some words.

I'm not sure about it, because I've read that the first 6 minutes with a new class are the most important ones, and by showing this "weakness" they will conclude that I'm not capable, knowledge-wise, to teach them.

A mentor of mine told me I should talk openly about my accent, and add that in addition to English, I fluently speak two other languages and can understand two others. Trying then to make a balance between my "weakness" (my accent when speaking English) and my knowledge with languages.

Accents are tricky, especially in large lecture halls where students hear you over a mic, and can't see your lips. Different regions might have different opinions on what accents are difficult, depending on what other native language groups the undergrads may have been exposed to.

In my opinion, it would go a long way for your undergraduates to say something like:

  As you may have noticed, English isn't my first language. I know sometimes that makes it hard to understand certain words. Please don't hesitate to ask me to repeat something.

This might help with students who are shy or don't want to offend you by asking.

If you like, you could mention the other languages you're familiar with to encourage speakers of those languages to connect with you, or just as a fun fact (personally, I'd be curious to know). I wouldn't mention it to make yourself seem somehow better than them, as that could needlessly add feelings of resentment.


Conference Title - shall abbreviation and year be listed uniformly? I'm just had a look at my citations and they are in an aweful state. Most conference papers that I imported into my citation manager have different styles, e.g.:

IEEEE Conference on Emerging Txxx Bxxx Qxxxxxxx, 2009 (ETBQ 2009)
IEEEE Conference on Old Wxxx Yxxx Sxxxxxxx (OWYS), 2009
IEEEE Conference on Txxx Txxx Xxxxxxxx, 2009, (TTX 2009)
IEEEE Conference on Gold. 2009 (Chicago)

Am I allowed to bring all conferences into the same format?

What format would you recommend? Should I drop abbreviation, year, or place of the conference as it is repeated? I think the year might have to stay because e.g. a coference might be held in Dec. 2009 and the papers are only published in Feb. 2010, hence the 2009 date would be lost. I also like the abbreviation as it helps my to identify the coferences in one glimps.

Second question: Should I add "Proceeding of the" in front of every conference?

There is an important and unfortunate caveat for managing citations that I bring up because this refers to IEEE.  In IEEE, ACM, and many other computer science and electrical engineering venues, it is often the case that there are strict page limits and the citations are counted toward that limit.  This happens mostly with conferences, but sometimes even with journals.

Because of this, I often find it necessary to maintain both a "master" reference database and an ad hoc "abbreviated" copy of the database used for a particular paper.  In the master database, I keep the full everything in all its bibliographic detail to the best of my ability.  In the abbreviated copy, conference and journal names get shortened as necessary to purge the bibliography of widow and orphans
and extract those last few lines necessary to get the text to fit.  It's a nasty, undignified practice, and I consider it the lesser of two evils if it can preserve technical content without decreasing the ability of a reader to locate citations.

The ability to find the citation, though, is sacrosanct.  Authors, title, year (and volume and issue if available), must never be trifled with.  As such, the shortening targets that tend I use, in order, are:

"Proceedings of the..." can always go, as can the location of a conference.
"International Conference on" goes to "Int'l Conf. on" and then vanishes
Most EE/CS conference have acronyms: an exceedingly well-known conference can be entirely replaced by its acronym.

Thus, for example, "Proceedings of the 23rd International Joint Conference on Artificial Intelligence, Beijing, China" can ablate all the way down to "IJCAI", saving 1-2 lines in typical IEEE format bibliography.  It's an ugly business, and maybe I shouldn't admit to it out loud on the internet, but it's a useful practice that I still find ethical as long as the spirit of readily locatable citation is preserved.


Which undergraduate research experience will help more for graduate admissions in mathematics? I was recently offered a six-month undergraduate thesis at two places. Let us call them A and B.

I am looking to apply abroad for my Masters in pure math next year. Hence, recommendations are important to me.  I am not sure which offer will yield a more useful recommendation.

The professors who have accepted me at A and B are both the leading experts in my field of interest (Algebraic Geometry), and have won the highest honour given for Mathematics in my country. The professor at B seems vey encouraging and helpful, and has found the time to go through my math blog and offer feedback, while the professor at A has a reputation for being abstruse, and hence perhaps not ideal for a person not experienced in research. However, A is a much more reputed and well known school than B.

Should I go to A or B?

Will a recommendation from a well-known professor from a less well known school matter as much as one from a well known professor from a well known school?

Should my personal equation with the professor be the most important factor for me?

I understand your question as: Which will be more useful for graduate admissions (all other things being equal): a recommendation from a professor at a well-known university, or a recommendation from a professor at a less-known university with whom I have a more personal connection?

There is no one-size-fits-all answer here. The answer depends quite a lot on the degree of the difference (both the difference in reputation between universities, and the difference in how well each professor will end up knowing you personally).

As you have intuited, a recommendation from someone at a well-known institution is worth a lot more than a recommendation from someone at an institution that is not well known. On the other hand, a recommendation that describes your specific talents at mathematics in complimentary detail is worth a lot more than a perfunctory letter that says "Algebraically speaking did a thesis in my institution."  (Meanwhile, you know nothing at all about the letter-writing skill of either professor, which is another important variable.)

There is also the impact on your development as a researcher. You would likely benefit from working with someone who takes a close personal interest in you. You would also likely benefit from being at a well-known institution that attracts many talented students and has a very productive research atmosphere.

Your decision will ultimately be a personal one, and we can't give personal advice on Academia.SE. However, since your goal is to go to graduate school abroad, I would suggest the following:

Find out where undergraduate students who work with each professor end up.

You can ask them directly, or talk to their students. In either case, you'd like to know:

how many of their undergraduate students want to go on to graduate school in mathematics? How many of these actually do?
for the students that went to graduate school, where did they go? Are these institutions you would consider attending for graduate school?

The "road less traveled" can be great, and rewarding, and all that. But it's also more difficult. If there is a well-traveled path that leads to your desired outcome, get on that path if you can.


When is it appropriate to use a university seal as a graduate student, post-doc or research scientist? I am applying for tenure-track positions at other universities after having recently completed my PhD.  I am still technically a graduate student until my degree is conferred in a few months, and I am employed and acting as a post-doc in the meantime.

After wondering if it is acceptable to use my current school's seal on the letterhead for my research statement, statement of interest, and the like, I decided to look up general guidelines for when to use the seal, and I couldn't find much.

Another answer mentions it is unacceptable to use a school's letterhead for something totally unrelated to the university, but it does not answer the general case for when a graduate student (and above ranks) should use the seal.  In my special case, I think me going on to become a tenure-track professor in the same field is very much in the interest of my advisor and our school.

With that background in place, I think the general question is the better one to ask here: When is it appropriate to use a university seal on a letterhead?

It is my personal understanding as a professor and former chair of a program that you can use the letterhead for job searches as long as you retain a position of some kind at the university: postdoc, doctoral candidate, visiting professor, lecturer, research scientist, etc.

As an appropriate proxy, use the letterhead as long as you have a university e-mail address (that isn't an alumni one).

Once you're no longer affiliated with the university because you graduated or separated, then you should not use the letterhead.

[Note that use of letterhead for job searches is a special case. Do not use the letterhead for other personal purposes - such as writing a letter to your congressperson - if you're in a liminal position as the possible blowback can be hazardous to your career].


Is it wrong to repeat yourself in the abstract, introduction and conclusions? I find that when I writing a paper,
I use the same phrases and sometimes the same sentences
in the abstract, introduction, and conclusions.

When I compare this to non-fiction writing
(e.g. Malcolm Gladwell or Michael Pollan),
my impression is that they do not repeat themselves
in the prologue and epilogue.

However, I realize that they are writing non-fiction books/articles,
whereas we are writing scientific articles,
for a different audience and a different purpose.
My questions are:

Does using the same phrases and sentences
in the abstract, introduction and conclusions
make my paper boring to read?
Or is it easier to read and understand a paper if it repeats itself?

The three things are doing pretty different jobs, and so should be pretty different in content.

The abstract is an advert for your paper.  Someone might read a list of titles and abstracts (for example on arXiv) and decide on that basis whether it's worth their while downloading and reading the rest of the paper.  The abstract has to be attractive, but not fraudulent ('truth in advertising'!).  When you read an abstract, you're trying to find out: (i) is this paper in my area?, (ii) is it asking a question I care about? (iii) does the conclusion sound interesting?  You don't have to summarise the whole paper, but you do have to answer those questions.

The introduction gives your reader a map of the paper.  By the end of the introduction, your reader should have a pretty good idea of what they're in for, and where they're going to end up.  They should know what sections they're probably going to skip, and which ones they look forward to disagreeing with.  A paper is not a detective novel: you don't need cliffhangers or mysteries.

After that, the conclusion doesn't have a lot of work to do (at least in my experience).  It might be the last thing the reader reads of your paper (that is, unless they care enough about its contents that they'll re-read it), so this is an opportunity for you to frame their memory of it.  "We have shown that ..." is the sort of thing you'd find here.

Key points:

Remember the reader is a human being, just like you – talk to them, as you'd like to be talked to (far far too many people bizarrely forget this).
Make it easy for them to read the paper, and easy to agree with you (that's why the introduction has a map of the paper, to ease the reader's way through your golden prose).
Your reader is asking themself "why am I reading this paper?"  Make sure they have a good answer to that question by the end of the introduction. If you get a colleague to read your draft, get them to answer that question at that point.  If they don't give the answer you want them to, it's your fault; so edit.

There will probably be some overlap in text in the three parts.  That's OK, but it probably shouldn't be cut-and-paste.


Important questions to ask yourself when writing research paper I remember I read somewhere four (at least I think it was four) important questions to ask yourself when writing research paper, such as "What is the problem?", "Why is that important?", etc.

These questions were named after some guy or something whose name I don't remember. Please help me remember the name.

It's probably not exactly what you're after but it's commonly recommended to answer the three standard questions what-why-how:

What is it? What is the object of the work and what is the context? Are there any similar questions already solved or studied in the literature?  How does your goal/question differ from existing works?
Why does it matter? What are the motivations for doing this work? What problem does it solve (or contribute to solve)? what use cases does it apply to?
How? Which method can be used? Why this method in particular? What are the potential limitations of this approach?


Seriously conflicted about a graduate program option I graduated in 2013 with a degree in Botany from a state college on the west coast. Since then, I've worked for the Forest Service on a rare plants/ invasive weeds survey crew, and currently, work for the USDA as part of the Agricultural research service as a biological science technician. When I took the job, I was clear to my supervisor that I planned on attending graduate school after the two years I was committed to on the project. He was excited about this and very supportive of me. I went to work for on a number of projects involving plant physiology, plant biology, remote sensing etc. My goal with this position was
to take my academic record from my times as an undergraduate and supplement it with some applied experience, then to apply to graduate schools for the 2016/17 school year as a top tier candidate. I've worked hard to make sure my undergraduate grades, GREs, and letters of recommendation are of sufficient quality to single me out from a crowd of well qualified applicants. My thought was that this two years of experience would take me over the top, that this experience would take me from being a well qualified applicant to a top tier applicant/ the top applicant. I had been looking at applying to 3-4 top tier schools in plant genetics/ plant physiology (UC Davis, UC Berkeley, Cornell, Michigan State).

So fast forward a year and a half (this summer) and my boss approaches me with an offer. He wants to fund me to do a graduate program at the local land grant university. It would be a full assistantship and tuition waiver for the two years, which is an incredible offer. I wouldn't even have to apply to the school.

Here is my conflict: The offer is for a program I'm only tangentially interested in (weeds biology), from a department I don't really want to be involved with (crop science; but could make do), at a fairly low ranked state university.

I also feel like I've set myself up for one good shot at getting into a highly competitive program, and that taking this offer will throw that away. I won't get the chance to use the letters of recommendation, undergraduate grades, GREs, that I worked hard for, only to go to a middling school to do a degree that I'm only kind-of interested in.

At the same time, it's a convincingly good offer, one that I would be incredibly unlikely to get again.

Note also, that the offer was made at a very strategic time. The offer would be for the 2015/16 school year (I wouldn't finish my 2 years under my original contract). He made the offer in such a way that it preempts my ability to apply to other schools and cultivate a counter offer.

I'd just state that the offer, while tempting, is second selection for you, and apply to the schools that interest you anyway. Worst case, you'll be rejected elsewhere. Don't close options unless you really have to.


How to grade unequal contributions to group work as a TA bound by instructor's rules I am a TA for a freshman course in the humanities at a US university. Due to pandemic restrictions, the class is entirely online and the medium through which students learn is Canvas. Lectures are pre-recorded by the instructor and posted to the course site, as are any reading documents or assignments. Students contact me in "real time" through email, course messaging, and virtual office hours (held via Zoom).
Students complete some individual assignments and upload their work to the course site, but they have also been broken up into project groups and complete group work. It is their job to contact their group members and work together to submit assignments.
I am not sure how to grade group work when:

It is clear that only one or two students did all of the work
Each student receives the same grade as everyone else in their group (something I cannot change per my instructor's request)

I cannot force students to learn and I cannot change how learning outcomes are assessed. But how can I reward students for meeting objectives while not punishing them if students in their group do not contribute?

Restrictions:

Changing the course gradebook and ways that assignments are graded is not a viable option because the instructor has asked me not to.
The instructor is very clear that neither they nor I are to intervene in group disputes. According to the instructor, "Students need to learn to work with difficult people."
I do not see the value of group assignments in this course because (in my opinion) students aren't meeting the learning goal if they only think about certain parts of the assignment. I also think it is unhelpful and difficult to put the burden of communication on the students during a pandemic with asynchronous learning.
I do not want to encourage the "good" students to do all of the work for the group just to get a good grade because I do not think that promotes healthy behavior toward group work.
The instructor is not open to negotiating how the course is run.

Freedoms:

I am the only one grading assignments, meaning that I can come up with whatever grading scheme I want and have the entire class graded with the same metrics.
I can create content (handouts, etc.) and post to the course site as much as I please.

Note: I've looked at this question, which does not answer my question here but might help when I run a course as the instructor.

I suggest that you grade "the project" for its value and assign every student the same grade. If any student objects, refer them to the instructor. This recognizes an important fact.
You may not recognize all "contributions", but the students might value some things more than others. Not every student needs to contribute to a "team" project in the same way. The same is true for real world projects.
If you try to change things or devise some "scheme", then you will be the bad person, disrespected by everyone.
The work is the work. Grade it.

I actually think that "dividing up" the work makes it harder since the integration adds another step. I think that the so called "best" students do everyone a disservice if they do all the work. But if I give a project to a team and don't instruct them otherwise on process, then the team process is up to them. Respect that.

I gave a lot of team projects. One thing I did was have peer evaluations of the form "Who were the two most helpful members of your team and why". That would be for a team of four or so. I once had the experience that the team was unanimous in praising one person who I thought was slacking because their contributions weren't visible to me. But he actually kept the team functioning and moving forward. It may be that you wouldn't want to hire him for is technical skills, but you almost certainly would as a manager of a technical team. But that is mere supposition on my part, so don't read too much in to it.
Don't expect every student to learn exactly the same thing from a course.
I once had another student in a class who I predicted would eventually be the manager of all the "geeks" since she asked the right questions. She focused more on "why" instead of "how". There are a lot of skills.


Is it possible to get a PhD Degree in from USA or Europe after doing Masters from India I am a Chemical Engineering Masters student from India and I wish to pursue a PhD degree from some reputed US or European Universities.

I have heard from my seniors and from internet searches that generally good universities do not admit students who directly apply for a PhD after a Masters degree from India and expect them to take a Masters degree from their university before going for PhD.

It maybe that such instances would have occurred for some particular cases and cannot be generalized, but as I said that it is just what I have heard over from people and I wonder if it is true.

I have been searching all over the internet regarding this but quite a few websites exist where this question has been answered convincingly. So I thought to post it here in stack exchange so that I can get some better answers. Any help would be appreciated.

You can certainly pursue a Ph.D. in the U.S. after getting a Masters degree in India.  You can even go straight in from a Bachelor's degree.  I know a number of people who have done it in other fields---I expect chemical engineering should be the same, I just don't know as many chemical engineers.

Note, however, that the first stage of many American Ph.D. programs is either explicitly or implicitly a Masters, and you probably will not be allowed to skip that stage of the program, though you might be able to pass out of some early requirements, depending on particulars of your background and the requirements of the university.


What are the perks of being a tenured professor at U.S. universities, besides having academic freedom? For instance, one of my professors went to Princeton (for his undergrad math degree) for free, because his parents are tenured faculty at Princeton.  Is such a benefit available to tenured faculty at most U.S. universities?  This is assuming that a tenured professor's children are qualified to be admitted to the school.

Besides having academic freedom, what are some other, lesser-known, considerable perks of being in academia as a tenured professor as opposed to being tenure track?

(Main motivation for the question is to follow up on a previous question in which the OP asked about the stresses of academic life, specifically, in mathematics research.)

Universities offer all sort of "benefits" to its employees. Some of these "benefits" do  not have a monetary value (e.g., flexible work schedule). The benefits available to faculty are often different from the cleaning staff. Further there are differences in benefits between tenured/tenure track and adjunct faculty. I can only think of three benefits, that have a monetary value, for which there are differences between tenure track and tenured faculty

Sabbatical: Some universities do not permit pretenure sabbaticals. It is often hard to differentiate if sabbatical eligibility is tied to tenure or time in service. Brown University provides different sabbatical benefits pre and post tenure.

Housing Assistance: Some universities provide housing assistance (discounted homes, mortgage assistance, loans, etc). Portions of the housing assistance program at Columbia requires tenure.

Parking: Some universities provide parking passes. Carroll College provides reserved spaces for tenured faculty while other faculty and staff simply get a parking pass.

In terms of perks that do not have a monetary value, this varies widely by department. Tenured faculty often get to be chair of the department (which may or may not be a perk). Departments may also give tenured faculty priority in terms of teaching schedule, departmental and university service requirements, office space, and lab space. The sabbatical system, internal funding, and administrative support may be skewed in their favor also.


What should I do if I submitted an article to a predatory journal? Call it stupidity or bad luck but I am guilty of submitting my research article to a journal which is listed in Beall's List of Predatory Publishers.

It is my first article and I don't have much experience publishing articles. I was searching for a top impact factor journal and found this one on Google and in excitement sent my article (word and pdf files) in this journal a few days ago, only to discover later that this might be a bogus journal.

Now I am worried about that what will happen to my article. What if they plagiarize my paper, or send it to another journal not giving me credit?

My question is that what should I do now? Should I send my article to a reputable journal now? What should be the process? What if it is flagged for fraud by that journal? What are my options?

Any help would be appreciated.

If the paper has not yet been accepted for publication, you are free to withdraw the paper from consideration. Depending on the policies of the journal to which you submit the article, you may need to disclose the prior submission, and explain why you withdrew the publication from consideration.

Unfortunately, there's little you can do to stop the publishers of the first journal from doing something unsavory with your article. You will need to exercise vigilance in monitoring the work in this area to ensure that the paper isn't mishandled or worse. Be sure to maintain records of all of the correspondence you have had with the journal—and make sure of all it is documentable—phone calls won't suffice here.

However, if all the journal has is a PDF of your original article, it makes it a lot harder to do anything with it: it is tedious work to convert it into the template that most publishers use without significant effort. Thus, without the original graphics and text files, it will be difficult for them to "transmit" the paper elsewhere.


What are secondary "visiting" positions? Note that I'm not talking about "visiting professor" or "visiting lecturer" positions in the US, which seem to be full-time non-tenure-track positions offered at some US universities.
What I mean is that I sometimes see people list "visiting researcher", "visiting scholar", or "visiting professor" as their second affiliation, and seemingly they are not actually being paid by the second institution (their full-time position is at their primary place of employment) but they simply maintain a second affiliation through this visiting position. Often I see people having visiting affiliations at universities in other countries, or professors keeping a visiting position at their previous place of employment after they moved to another place.
What are these visiting positions? How does one get it, and what is the point?

A typical reason for these positions is that a person needs a formal affiliation with the "visited" university for some formal reason. This is particularly common for visiting positions at past institutions. These can be there to faciliate continued supervision of PhD students at the old instituation, or to keep existing grants. Grants can be a reason beyond this - eg by having a visiting position at some university, it may become possible to get travel there (or even to other places) paid for by a grant situated at that university.
In the short-term visiting positions can actually be just what they are called. The person may in fact visit the instituation for a while, sometimes with funding from the host institation (which would be acknowledged via such an affiliation). It can also be something mundane as needing some formal association with the host university to get a keycard or library access.
I assume that almost always the person receiving a visiting position will have a pre-existing strong relationship with either the institution or an academic at that place. There will be some formalities depending on the institution, but that is something people figure and sort out once the need arises.


Is it ok to call the professor in this situation? I had a telephone conversation with a proposed Ph.D. supervisor last Monday and he agreed that he will double-check my research proposal before I submit it. Then I emailed him the proposal. However, I haven't heard from him for a week, so I sent a reminder email to him this Monday. And yet still no feedback from him so far. I know that professors are busy and slow responders, but Christmas is coming and I do not want to miss the deadline. I wonder whether it is ok for me to call him at the same time as last time if I do not get his response before next Monday? Or are there any other solutions in this situation?

First, ask yourself whether you are sending the right email.

One of my professor mentors had a very useful heuristic for ensuring effective communication with busy people.  For any busy person, email typically gets triaged into three bins:

Email that can be safely ignored.
Email that can be responded to with trivial effort, thereby clearing it from their "todo list."
Email that requires non-trivial effort to respond, and must be put off for later... and later may be a long time, because now it's competing with their other "large" duties.

If you want a response from a busy person, write a short email that includes precisely one question, and make sure that question is easy to respond to.  For example, in your case, if you send email saying:

  Here is my research proposal, as discussed.  Can you please send me feedback?

then that might get no response until the professor has the feedback ready, and preparing your feedback may get pushed off and pushed off again.  The professor might also misremember the deadline and have a lesser sense of urgency.
If instead you write:

  Here is my research proposal, as discussed.  Please recall that I must submit before the deadline of XXX, and I would like time to revise if necessary.  When can I expect your feedback?

In this you've posed an easy question, which should get a response, and also gotten them to commit to a specific date.  If you don't get a response in a day or two from an "easy" email like this, then you need to wonder whether this person is actually somebody you want to work with.

What, however, if you send the right email, get them to commit to a date, and then they fail to either respond or tell you they need more time?  At that point, I would recommend against either emailing or calling on the phone.  Instead, go find the professor in person.  I have found that with busy people who fail on their commitments, that finding them in person is the best way to get yourself back in their queue.  Again, however, you should ask yourself whether you really want your whole Ph.D. to be this way, because it is likely to be a pattern...


Color space for papers: CMYK or RGB? This is a bit technical question, but might be frequent enough in this community.

My PI and I disagree on which color space to use for figures and manuscripts.

I like CMYK, because I care about how it prints out. Even for online-only publications, a lot of people still print them out to read them. (I also care about black & white printing and color blind friendly colors, but that's another story). My main tool for editing figures is Adobe Illustrator with CMYK default (of course I can change it).

My PI likes vibrant red and blue colors which are in RGB space and not in CMYK. I agree that it has better visibility on screen or presentations. It would also be more flexible for switching for different requirements since RGB space is in general larger.

What is the best practice for preparing manuscripts with color figures (and possibly color text)? Do you make the figures in RGB which has a larger color space, and only adjust to CMYK when sending the accepted version to the publisher? Or let the publisher figure it out? (What about self-archived preprint versions?)

(I don't want to worry about color space consistencies and do more research!)

You follow the publisher's instructions.

If your target journal asks for CMYK, you give them that.

If they ask for RGB, you give them that.

If they (are one of the few IME that) express no preference, then have a think about whether the charts will be viewed more on screen (use RGB) or printed on 4-colour printers (use CMYK).


Had the idea vs. did the work: Who should be the lead author? Dr. A came to Dr. B asking for research ideas. Dr. B gave him a thesis, explained its value, why it's plausible, and how to test it.  Dr. A liked this, got Student C to do the work, and managed the work.

Now, it's time to publish their results.  How should they determine the lead authorship?

The lead author should be the person who carries out the bulk of the research work—including the planning, execution, and writing.

If the student C is the one responsible for carrying out the experiments and writing the paper, then C should be considered the primary agent of the paper.

Who should be the "final" author is a different matter. I would suspect that this really should be professor B, who had the original idea. The role of doctor A is only as research manager, so his role is nominally weaker than that of either B or C in this process. So, ultimately, barring other negotiations and arrangements to the contrary, it should be:

  Student C, Doctor A, Professor B.

If there is some other distribution of roles beyond what is laid out above, it would need to be negotiated between everybody involved.

Note: In fields where lexicographic order is not used, the final author position also carries weight. It usually is the head of the research group or team that originated the project.


Is it appropriate for peer-reviewer to look for possible plagiarism? I'm in the second year of a post-doc, and currently participating in my first experience as a peer-reviewer (my lab PI recommended me to the editor because he's too busy to do it right now). I noticed a section of the Methods that seems to be completely out of place. It describes statistical analysis of data that were neither generated nor reported in the manuscript, and is generally a source of confusion for me as a reviewer. So I did what I would have done grading papers in grad school, and pasted that section into a free online plagiarism detector. It came back with a 100% match for the full paragraph from an article published earlier this year. My suspicion is that this wasn't any sort of intentional plagiarism or research misconduct, but rather a case of someone using another text as a guide for how to structure that section of the text and simply forgetting to make the necessary changes, or possibly even submitting the wrong version.
I should mention, for context, that it's not uncommon to follow the methods of another paper exactly in experimental biology, but that's clearly not what happened in this case. My primary concern is that I can't properly review the reported results and conclusions without information that should be provided in this section of manuscript, which I've already discussed in my review comments. I'm just wondering if I would also be expected to point out the possibility of unintentional plagiarism, or if that's considered outside the scope of my responsibilities as a peer reviewer.

I would immediately communicate your findings to the editor and do no further reviewing until you hear back from them.
In the best case, like you say, they forgot to edit it, and can resubmit. Communicating to the editor will let them stop the other reviewers so they don't waste their time either.
In the worst case, it's poorly executed plagiarism and you would have to contact the editor anyway.
To answer the title question, of course there's no issue looking for plagiarism, and you seem familiar enough with the field to understand the implications of your results.


What is the best way to merge subfigures and convert to a required format for submission to a journal? I'm currently preparing a paper for publication and so trying to construct the figures. I'm finding it more difficult than making figures for a report mainly because journals expect one figure file for each figure, regardless of whether it contains subfigures or not. This leads to some problems/hurdles:

I can't use LaTeX's \subfig package, so I have to manually place an (a), (b) and (c) on the figure and keep track of the caption if the ordering of these changes.
Journals' rules about figure submission vary quite a lot, some can take pdfs, some want vector graphics, others raster.
I have to somehow merge the output from various programs into a single file; for example diagrams made with Tikz make up the same figure as a graph plotted with python's matplotlib.
With having to merge subfigures in such a way, my workflow becomes quite convoluted if I have to modify one of the subfigures, and then regenerate the single figure file.

I don't know how well this will apply to you because I don't use tikz much. But if you can save them as say a pdf, this might work for you.

I use illustrator (but inkscape is similar and free), and I link in the files so that if there is an update to any component it will update. And I merge them all together.

Then I can just save it as a pdf or svg (or whatever format the journal wants). I found this a little cumbersome to start off with, but now that I'm used to it, I have a hard time reverting.


For applying to math postdocs on mathjobs, does "N Reference Letters" include one for teaching? I'm a graduate student in the US, currently applying for postdoc positions on the mathjobs website. The format of the job postings is basically a description of the position, followed by

  Application Materials Required
  Submit the following items online at this website to complete your application:

  Curriculum Vitae
  Research Statement
  ...
  N Reference Letters (to be submitted by the reference writers at this site)

  And anything else requested in the position description.

(where N is usually 3 or 4).

Sometimes, the position description says explicitly

  N letters of recommendation, one of which should address the candidate’s teaching qualifications.

My question

If the position description does not have an explicit statement asking for a teaching recommendation letter, is it supposed to be one of the N letters I submit to them anyway? Or, should I submit N letters all having to do with my research? Is there any harm in submitting N + 1 letters in order to include my teaching recommendation letter?

In my experience serving on large numbers of pure mathematics search committees at a couple of different research universities, people who read the files are often only dimly aware of what the ad requests.  The vast majority of files will contain 4 research letters and 1 teaching letter.  Even if they only ask for 3 research letters, it is a poor idea to not include a 4th if you have one since most people will have 4.

Some people go overboard and submit a ton of research letters (I've seen 8-9 in a single file).  This can also cause problems: 1. usually when someone has that many letters they are not uniformly strong/informed, and 2. it looks weird, sort of like a violation of implicit social norms.  Probably you won't cause yourself problems if you go as high as 5, but don't exceed that.


Sharing content from thesis online, before submitting thesis I wrote some piece of code early on in my PhD. It is not genuine research as such but just implementation of already published paper (no public domain code for that paper exist). Because I spent considerable amount of time on it, my guide wants to include it in my thesis as an appendix.

I want to put it on github as well for which my guide has given his blessings! However I am confused about its documentation. I wrote complete introduction and implementation of the problem and code etc which will go in the appendix. Now i want to put that documentation on github as well. But I havent submitted my thesis yet.

Our departmental policy is that thesis go for plagiarism check before submission. I am afraid during that check my own github repo will show up matching word to word. Is this acceptable? Or shall I wait till I submit?

TLDR: Can portions of thesis be put up online before submission? will it count as plagiarism during plagiarism check?

Ethically, I think you would also be fine. Theses in many fields include content from published papers; GitHub doesn't even count as 'published'.

Practically, it depends on how much blind faith your department places in the plagiarism checker.  Plagiarism detectors should only be used as a first-pass, and humans should evaluate the detected potential plagiarism. If the authorship of your GitHub documentation is clearly labeled, then they will hopefully see that it is your work.

Navigating the details of this in a department-specific setting is what your adviser is there to help you do.  If they've given their blessing, and they are aware of the policy, and they are a good adviser, then I would also expect them to be willing to go to bat for you if it does come up in thesis review.


Handling PhD funding offers that come before hearing back from all schools I applied to So I applied to several PhD programs at different schools of probably different levels of selectivity and prestige. From a few of these schools I have been admitted and in contact with certain professors there who are suggesting that I will receive full funding to go there. In one case, this funding will be in the form of a fellowship from the school. The only hang up is that they would like me to make a decision on these offers quickly. In one case, I think they want to figure out if I would accept the fellowship if offered to me so they can extend it to someone else if I wouldn’t accept.

The problem is, the two schools I am most interested in have not yet admitted me and no professors from those schools have reached out to me. I would like to know what the result of my application to these schools will be before deciding. Should I just tell the other schools to wait? I worry that I may not receive a fellowship offer from one of these schools for delaying my decision too long (and would maybe be funded through some other means). Another option I see would be to reach out to the universities that have not admitted me yet and try to initiate conversations about working in professors groups and gauge how they perceive the strength of my application.

To summarize my question:
What is the best course of action when a grad school (or specific professor you want to work with there) pressures you to make a decision on their offer before all other schools you applied to admitted or rejected you?

I am located in the US, sorry forgot to mention it

This answer applies if your schools of choice are in the United States:

Most major universities in the US are signatories to the "April 15th resolution," which gives students until April 15th to accept offers of admission/financial aid. A full list is here: http://cgsnet.org/ckfinder/userfiles/files/CGSResolution_RevisedOct2017.pdf

  Students are under no obligation to respond to offers of financial support prior to April 15; earlier deadlines for acceptance of
  such offers violate the intent of this Resolution

If the schools you are applying to are in the US and signatories to this resolution, they are not allowed to offer and then withdraw admission/financial aid prior to April 15th. Before that deadline, you can politely inform them that you are waiting for all your offers before making a decision. They might want to pressure you to commit earlier, but you are not compelled to do so.

You are correct, though, in assuming that they would like to offer the fellowship to someone else, if possible. Therefore, the polite thing to do is to inform any school that is no longer in contention as soon as possible, that is, as soon as you have another offer you plan to accept, and no sooner.

You could reach out to the schools you are waiting to hear from, but I wouldn't pester them, it is still fairly early in the acceptance calendar (again, from a US perspective) and admissions committees are still meeting to make decisions.


Are PhD Students and PhD Researchers the same thing? Similarly to how a Postdoc researcher is a researcher, I think that a PhD student should be considered a researcher. Especially when:

A salary is obtained for the research that is done as part of the PhD studies. Per definition, I would say that students pay, they are not paid.
A research master has been studied before and there are no lessons, classes, exams, etc. So in fact the person is not a student, but "at least" an "apprentice".

I know that naming things in one way or another may not make a big difference for those in academia that read the CV, but it may evoke different ideas for those out of academia that read it.

AFAIK, they are absolutely equivalent, even if one is more used than the other (mistakenly, IMHO). Nevertheless, I would like to get confirmation, if possible from an authoritative source (like a dictionary for titles), and at the same time I think that the question may be useful for many people.

I don't see the point in your distinctions in either bullet. Some students get a salary, some do not. Neither of these is determinative of whether a student is a researcher. Not every PhD student did a Master's degree before the began their PhD studies. I certainly did not.

Why do you care if PhD students (who I agree do "research") are "researchers" or not? Of course they are researchers because I think that anyone who does research is a researcher (paid, student, or otherwise). Are you looking to validate your ego, to overcome an officious rule that says that only "researchers" may do some thing or other, or are you looking for something else? Except in a few places, titles matter little. If titles matter where you are, then find the law or bureaucratic codes that define "researcher" and follow them. If you don't like the answer you find, you can either live with that, find a workaround, or fight (presumably through a legislative body if that place has one) for change. You haven't given us enough detail about why you care for us to helpfully answer your question.