Time management and organization for PhD Student in first year? After failing the first year of the PhD program at a top university, I know that my poor performance resulted from dealing with a tremendously debilitating psychological condition, but it all was exacerbated by a serious lack of time management skills and poor organization. This academic year, I constantly underestimated the time it would takes me to complete every assignment. Consequently, I found myself asking for extensions and even then, I was incapable of making the extension. I can't use the excuse that I simply am unfamiliar with the subject matter, as I have earned a master degree in this field with honors from another prestigious university and worked for several years prior to starting the program. I also can't blame my failure on procrastination, as I  generally start weekly assignments  3-5 days prior to the deadline, and  work on term projects for at least a month prior to their deadline.  To say the least, my professors are irritated with me. Their frustration in part comes from their knowledge of my abilities. Every single one has set me aside and provided candid feedback and in their words...once I manage to complete an assignment and submit it on time, "the content and quality is pretty good". Now that my health has improved, their feedback confirms my self-assessment and I am 1,000% certain that my failure to thrive is due to serious time management and organization shortcomings.

For those of you out there that have encountered a similar situation and been able to overcome it, what did you do? What strategies did you use for completing assignments on time (specifically writing assignments or a critical and technical nature)? Can you recommend any resources that have helped you tackle these problems?

In my time as a PhD student over the past few years,  I have really benefited from the simple old-fashioned technique of just making lists on a small notepad.  Whether in lab or at home,  if I feel disorganized or anxious, I just write down the things I know I need to do. As well, I can check the list of things I have already written down earlier in the day. Putting things on paper by hand is really a simple and effective way to get things "out" so to speak. Has worked great for me in my first 3 years of my PhD.  If I am on the go and can't write something down Siri (on my IPhone) is awesome for reminders. Don't stress too much either. Work hard, stay organized, but make sure you still have time for sleep, hobbies, friends, and family. Otherwise you will drive yourself crazy. I ensure this for myself by not working on Saturday's or Sunday's. Believe me, in the long-term, a rested and clear-minded scientist working Monday-Friday will outcompete a mentally exhausted scientist working 7 days a week. I learned these things while an undergraduate student from one of my favorite professors. Not only was he an awesome teacher, scientist, and Department Chair, he was a Army Colonel working in military intelligence several weeks out out the year. I figured this guy must know a thing or two about life. I put it into practice and come to find, he was right!

Best of luck to you!


Comparison of methods in a paper with a table In my current paper I describe two methods for solving a problem in different ways. Both have advantages and disadvantages.
At the end of the paper I would like to compare the two methodologies with a table. So far it looks something like this:

 -------------------------------------------------
|           |     Method 1     |     Method 2    |
--------------------------------------------------
|Critera 1: |    very good     |       good      |
|Critera 2: | satisfactorily   |     very good   |
|Critera 3: |    very good     |       good      |
--------------------------------------------------

How would you manage that? Is such a table scientifically accepted?

Assuming that your paper describes the two methods in details (including the reasons why criterion X with method Y is assigned level Z in the table), I'd say yes, it makes perfect sense to provide this kind of table as a synthesis at the end of the paper. I would suggest adding cross-references in each cell, so that the reader can go see the details in the appropriate section for each case, e.g. "good (see §3.1)".


How to learn about a department's culture? I recently interviewed for a teaching position, but I have concerns about the department's culture. First, I learned that the department adopted a different hiring process for me. They made me jump through some hoops, but then they fell off the face of the earth. I haven't heard anything for 20 days!  Second, I learned that the department is in desperate need of new lecturers since the newly-hired experienced faculty member (established scholar!)  who had moved across the continent to work in this department left. I want to contact the-above mentioned scholar and ask him why he left, but I don't know if that's professional. What do you suggest?

I don't see a problem with contacting him, though his reasons for leaving may not be relevant to your situation. There seem to be a lot of red flags here, but it is possible that they are false alarms.

I would send him a note saying that you are under consideration for a position at the given department and asking if he has any advice he is willing to share with you. Give a sentence about your own experience or situation (recent graduate, associate professor, or whatever). Any response will probably be useful to you in figuring out your dilemma.

However, 20 days doesn't seem terribly long and might indicate some turmoil that is being resolved. Don't jump to conclusions, but stay aware.

If you have any good feelings about any of the people you interviewed with, you might send a similar note to them. "Any advice...?"


How to summarize the contributions of co-authors where they advised at all stages of the study, but technically only stepped in at the writing stage My conundrum is this. All my coauthors have provided advice from conception to completion, on the study itself, data analysis, write-up but haven't actually done anything at those stages other than provide me with advice. They have however, contributed critically to some parts of the writing. I have to complete a statement of authorship and am not sure how to accurately describe this. If I said:
"All authors contributed to conception of the study, data collection, and analysis."
This would be over-selling co-author contribution.
BUT, if I say:
"ABC conceived the study, collected the data, and conducted the analysis, all authors critically contributed to writing of the manuscript."
I am worried this undersells the input from others.
Is it better to over-sell, in this scenario?

All my coauthors have provided advice from conception to completion, on the study itself, data analysis, write-up...If I said: "All authors contributed to conception of the study, data collection, and analysis." This would be over-selling co-author contribution.

I disagree. That's exactly what your co-authors did. Execution and writing needn't be the responsibility of all authors, especially when one author is a PhD student.
One way to better appreciate the efforts of others is to ask whether work could have been completed without their input. When the answer is yes, you could consider whether their efforts are worthy of acknowledgement rather than co-authorship. When the answer is no, it is surely clear they played an integral role and merit co-authorship.
Returning to the OP's example, you could ask: Could the study have been conceived without all authors? If so, then perhaps attribute conception to only those that were needed. Ask the same for data collection and analysis. You can then write a more accurate contribution statement. Personally, I'd be generous. Err on the side of inclusion.


ieee membership discount on overlength manuscripts Does IEEE journals of signal processing society (like IEEE Transactions on Information Forensics and Security) consider a discount on overlength page charges for IEEE members?
If so, what is the rate of the discount? Should the corresponding author be an IEEE member or is it possible to receive discount by membership of co-authors?
I have heard that if the charges paid by the institution, it would be reduced from 220$ to 110$ per page. Does the membership discount considered for the overlength paid by institution?(I mean a membership discount on 110$, not 220$).
As far as I know, institutions can pay by the grant of the authors who are professors not students, is it possible to reduce the fee to 110$ by ieee rule explained above (if any!) rule by institutional paying (possibly by the grant of professors), then receive a membership discount from ieee by the student as a member?(I am not asking about institutional rules, I am asking that if there is a kind of double discount in ieee rules)
If more than one author be an ieee member, is it possible to receive the added rate of discount?

I believe there is confusion about what the charges mean. Generally, IEEE has two types of page charges:

Voluntary Page Charges
Overlength Page Charges

In 2020, for IEEE Transactions on Information Forensics and Security, the voluntary page charge rate is $110, while the overlength page charge is $220 — which correspond to the numbers in your question.
However, the meaning of these charges is very different.
Voluntary charges – are actually voluntary. They are not obligatory, usually paid by the institution, and help IEEE to offset some of the expenses incurred in publication.
Overlength charges – are different. They have to be paid for all submissions exceeding X number of pages (X=6 and X=10 for short and regular papers in IEEE Transactions on Information Forensics and Security, respectively). This small note from 2004 might explain things a bit more elaborate; I simply was not able to find the relevant page on the IEEE site directly.
I have never heard of a discount on overlength charges. Often, these charges are paid by the advisor from a grant. I once paid the charges myself as a student when I was in transition between affiliations.
With all that information, it is highly unlikely that you can get the charge lower than $220 pay page over the limit. However, in some circumstances (the reasons have to be very serious), I believe IEEE can waive the charge altogether.

Disclaimer: I serve as a Vice-Chair of Membership and Benefits Committee for IEEE Antennas and Propagation Society; however, this answer is not within my direct area of expertise — thus, posted solely as my opinion as an individual familiar with IEEE practices.


How to deal with advisors who seem to not like me? I'm an undergraduate researcher that's been doing research with another undergrad over a summer. Our project was supervised by a grad student. For some reason, sometime throughout the summer, that grad student began making derisive comments and began to devalue my work.

After I'm away, since I've barely interacted with the PI, that grad student will tell the PI about my work when the PI has to write my letter of recommendation. I figured that since I have done valuable work, it would be a good idea to tell the PI myself about the specifics of the work I've done before I go, so that he's aware. So I asked the PI if he would mind meeting at some point before I leave, and he agreed, but seemed annoyed at the request, citing that he was just going to hear what the grad student had to say.

Have I just ended up in a bad group? Is there any way to approach this situation so that the PI is aware of my work and gives me an appropriate letter? I'm afraid the grad student will say something ridiculous like that the other undergraduate did most of the work.

In my experience (which, beware, is in pure mathematics) a faculty member has very little incentive to describe undergraduate research done under their supervision in negative terms: it is hard for the reader of such a letter not to view the student's failure as their failure.  Also in my experience (which, beware...) it is quite common for an undergraduate working over a short period (like the summer) not to end up contributing anything much to the larger research project, so that even this outcome need not be described in negative terms: after all, the student still got the experience.  I am aware that in the laboratory sciences a student is working on a piece of "the real project" much more so than for student research in pure mathematics, but still....would an experienced PI really give a critical piece of their project to an all but unknown person?  Again, if they do so and it works out badly, it seems to reflect badly on them.

All this is to say that I find it unlikely that you will get a negative recommendation.  What you risk getting is a recommendation that is not positive enough to help you with your graduate school applications.  If that happens, and if as you say you did good work over the summer (both your grad student supervisor and your PI are much more experienced in this regard than you, so without further information we have to at least contemplate the possibility that their judgment, rather than yours, is correct), then yes -- you probably did end up in a bad group.

What can you do?  Well, you booked an appointment with your PI, and I think that's wise.  During that appointment your goals are (i) to the extent that seems reasonable and reasonably polite, make your case that you did good work over the summer and (ii) suss out your PI's opinion of the work to see what kind of letter you will get.  Here I will observe that if you are overly aggressive or defensive on point (i), that might hurt you on point (ii): the PI may not want to give their honest opinion if they have already had to argue with you too much.  If it turns out that the PI has a not very positive opinion of your work, then indeed you may not want to get a letter from them.  That's a bit of a shame, but the lack of it should not really hurt your application, and an equivalent way of saying that the PI's opinion of your work is unreasonably low is that all your other academic work will be evaluated much more positively by others...so go with these other, better recommendations.

Anyway, all this is just one summer: if you stick around, there will be others...Good luck.


Capitalisation of "Section" and "Chapter" in a Ph.D. Thesis I am submitting a Ph.D. thesis fairly soon and my supervisor has flagged my use of capitalisation in "Section" and "Chapter" as possibly incorrect. I have googled about a bit and I see mixed opinions.

So my question is, when writing a computer science Ph.D. thesis, what is the correct way to capitalise "Section", "Chapter", "Appendix", "Figure", "Table", ... ?

For example, what is the correct capitalisation for the following:

"In Chapter 3, it was shown that..."
"In the previous Section, a method was presented to..."
"The graph in Figure 3 shows..."

"In Chapter 3, it was shown that..."

This seems correct. "Chapter 3" is the name of the third chapter. Names are capitalised.

  "In the previous Section, a method was presented to..."

This seems wrong. "Section" is not referring to the previous section by name, therefore no capital.

  "The graph in Figure 3 shows..."

Correct. Same as the first example.

So the rule (I use) is, if it is a proper name, then use a capital. This means, if it is of the form "Section $n$", where $n$ is a number, then it needs a capital.


Is it ok to put old papers on the arXiv? In my field (I am a condensed-matter theoretical physicist) it is such a normal thing to put papers on the arXiv, that people sometimes look at other people's arXiv list of papers instead of their publication record to get to know what they do, etc.

It just so happens that a few years ago I did a PhD with a supervisor that does not like the arXiv that much (he apparently had some conflict with some authors of a paper that was very similar to one of his papers, but one was already published while the other was just an arXiv preprint -or something like that). As a result, from my list of less than 20 publications, there are four of them from my PhD that are missing on the arXiv.

I was thinking of submitting the latest versions I have of them as arXiv preprints now, four years after their publication. For this I already have the agreement of all co-authors (including my supervisor), and all the journals involved seem to allow to put preprints of the material they publish. Do you see any problem with this? I fear that some people might take it as a way to advertise as new something that was already published a long time ago (though I would of course give the full reference to the published version). There may be other issues I am not aware of. The reason why I would like to do this is that I am applying for fellowships, positions, etc. and I am afraid some of my (best) publications may go unnoticed if somebody looks me up on the arXiv.

Thank you,
Stephen

Yes, this is in general OK. The main limitations on posting old papers to the arXiv are (1) copyright considerations (i.e. you must either hold the copyright, or have permission from the copyright holder to post the e-print) and (2) the approval of your co-authors, or at least the corresponding author, which can put you in a hazy gray area if you can no longer find them or they explicitly deny it. You seem to be OK on both counts.

The criteria for publishability on the arXiv are lower than a journal, and there is no previous-publication requirement or disbarment. From the arXiv primer,

  Material submitted to arXiv is expected to be of interest, relevance, and value to those disciplines. [...] Submissions are reviewed by expert moderators to verify that they are topical and refereeable scientific contributions that follow accepted standards of scholarly communication (as exemplified by conventional journal articles).

There is no requirement that work be unpublished; indeed, post-publication posting is an integral part of the self-archiving, green open access model in the post-print variety, often with a specific embargo dictated by the publisher.

That said, each community uses the arXiv in subtly different ways, and someone who repeatedly posts old papers may get called out on it (either positively or negatively!), so if you're nervous, find someone in your field who is very active on the arXiv and ask, or simply look for precedent - it's a bit tedious but not terribly hard. For example, arXiv:1601.06054, first published in June 2014, is currently on the cond-mat front page.

One thing you should do is make sure that your metadata is pristine and complete, and to get it right the first time. This includes the DOI and journal reference - you're not there to hide anything, you're there to make your research more accessible and discoverable, and the way you do that is by having good metadata. A comment saying that this is a late posting of an old paper would not go amiss - it will defuse the people who see the posting and think it's new and would otherwise be disappointed or annoyed.

And, of course, if you're looking to make your research discoverable online, think carefully through your online presence - arXiv, Google Scholar, ResearchGate, Academia.edu, Dissemin, Mendeley, or whatever services you choose to use - and make sure that they're all what you want them to be.


How to cite software used to produce data/images? I have made a building model in an energy simulation software tool. I have taken a screenshot from this model and I want to publish it in my thesis. I'm not sure if citing the software is necessary or not. The software is not merely used as a drawing tool, but also as the calculator of the energy requirements of the building. I would like to ask for an example of how such images need to be cited. Thanks in advance.

Some software may have citation requests in their web-pages. The following are a few examples

Matplotlib: Hunter, John D. "Matplotlib: A 2D graphics environment." Computing In Science & Engineering 9.3 (2007): 90-95.
MATLAB: MATLAB <version> and <toolbox>, The MathWorks, Inc., Natick, Massachusetts, United States (<year>).
Origin: Origin (OriginLab, Northampton, MA)

Otherwise, you may adopt the following format:

  Software [version], Company, Year, Link, Last visited: Date.

Also bear it mind that you may not need to cite the software used for image production unless the software itself produces some data used for scientific inference in your work (as mentioned by @DSVA's comments).


How to balance reading the literature and just solving the problem your self? I work for a company that has several projects involving computer vision. The literature rarely has papers on the exact problems we are solving. Furthermore, the state of the art in much of computer vision is often not reproducible or not ready for actual applications. Furthermore, the rate at which new papers come out in the areas we are interested in would make it very time consuming to digest most, let alone all of them.

On the other hand, we often get stuck and would like to get answers or at least inspiration from existing work.

Our goal in the end is to get to solutions as fast as possible. Does anyone have any guidance on how to balance time spent reading vs doing?

There is a wonderful quotation by Frank Westheimer that accurately summarizes the relationship between work and reading:

  A couple of months in the laboratory can frequently save a couple of hours in the library.

If you don't know what's in the literature, you can easily spend days, weeks, or even months reinventing the wheel. It's tempting to get your hands dirty, but it can be a very expensive proposition if you later find that somebody else has already done the same thing.


which one have more importance to US PhD program ?TOEFL and GRE or publication records I have got my BS and master both with honor with good GPAs. But Now I want to know which of these have more importance to US PhD program in Computer engineering.
TOEFL and GRE  or publication records. What I am looking for is some case like this:

T : 107   G : x   p : 0
T : 98    G : x   p : 1

which case has more chance ?

Neither.

PhD admissions committees at strong departments are looking for clear evidence of potential for high-quality independent research.

Test scores only matter if they're low.  In particular, if your math score is low, there will be serious doubts about your math ability, and if your verbal/TOEFL score is low, there will be serious questions about your communication skills.  In some departments (like mine in CS), admission to the PhD requires a TOEFL Speak score above a certain minimum (in my case: 22), because all PhD students are expected to be TAs at least once while they're in the program, and the state of Illinois requires a minimum Speak score (in my case: 24) on TAs who are not native English speakers.

Publication records only matter if the papers are either good or horrible.  It's utterly impossible to tell from the number of publications whether the applicant has significant promise for future independent research.  High-quality papers, written in flawless English, published in well-known venues that are easily accessible online from the US, are definitely helpful.  Poorly written incremental results in the Inaccessible Khazakhstani Journal of Computer Stuff is at best meaningless and at worst actively damaging.


Citing private individuals without their authorization? I am writing about an innovation camp, which private individuals took part to. During this camp, they developed systems. I have analyzed these systems in my study, and thus want to credit their author in my publication.

Can I write following sentence in my paper?

  In this paper, we studied projects Fourtytwo conducted by John Doe and Erika Mustermann, and HolyGrail by Ann Onym and M. Icks.

My question focus on citing the name of John Doe, Erika Mustermann, etc. - that are private individuals - without their authorization.

I will to use the name given in the end-of-the-camp PDF report that is freely available on the web - what speaks in favour of yes. However, they are not public personalities (as politicians, etc.) nor explicitely revealed their names (as paper authors) - what leads me to this question.

Because these private individuals do not sound like they are publishing their work (in which course your questions about citation would make more sense), and you mentioned interviews with these individuals in a comment, your situation sounds more like it falls under the category of Human subject research which has all sorts of rules and regulations. Assuming you are at some sort of university, your institution probably has a Institutional Review Board that governs this type of research and includes guidelines for obtaining informed consent, etc.

In short, you cannot do research on human subjects without their consent, and this consent typically needs to be granted before the study begins. Human subjects research includes interviews, etc, you don't need to be doing medical experiments to be doing human subjects research.

If you are truly using only the publicly available resource I would still recommend trying to get permission to use the resource (and if you are reproducing any portion of the resource, permission may be mandatory), but at most all you can do is cite that resource and attribute it to the organization that has made it public, you can't attach your personal knowledge of the individuals involved.


How should I stay in professional contact with former supervisors and/or colleagues? I want to ask if anyone still keeps in touch with former supervisors and/or colleagues from previous universities and how to do it in a professional way.

I want to keep in touch with them for not only future reference letters but also potential research collaboration.

The easiest way is to keep working on projects with them. If that ship has sailed, then the next best way is to be friends with them on social media, which is to say, be friends with them in real life. Barring that, you have to work to communicate with them on a regular basis about topics relevant to your shared interests: go to conferences and strike up conversations with them, share interesting papers with them via email (i.e., "Did you see this new paper from prof X? What'd you think?"), propose joint projects and write joint grant proposals, etc. It's not hard, but it does take active work.

People definitely do this, and I think it's one of the best ways for a new post-PhD researcher to get experience writing grants and proposing projects if they haven't gotten that experience already. That being said, it's also hard. You're supposed to be striking out on your own and establishing new frontiers. Your old colleagues are either doing the same thing or using the slot you left to pay new students/postdocs to continue the work you left behind. It can be challenging for everyone to strike the right balance.


How to delay a potential advisor without burning bridge? I am talking with a professor ("Smith") in my department about doing research under his advisement.  He seems like a friendly, helpful person, and I think he has tenure.  So maybe the pressure would be lower than for an academic struggling to make tenure.  He has met with me multiple times already, way before the fall semester has even started.  Also, as far as I know, he is also one of only two faculty in the specific sub-specialty I'm interested in, NLP (Natural Language Processing).

The only issue is I jumped the gun.  I have not talked extensively to the other NLP professor ("Jones"), and briefly glancing over their papers, I think I may prefer doing research under Jones.  But I have already chatted with some of Professor Smith's Ph.D students, and again, they all seem like nice people.  It feels like every time I meet a new person and take up someone's time, I'm just going to look like more of a flake if I "ghost" them, even if I do it politely.

I have TA funding for the upcoming semester, and it's my 1st semester.  Obviously there are reasons to try to convert that into an Research Assistantship early instead, but I am worried that Smith wants more of my time than I am willing to give; I have a research passion in NLP I'm also trying to work on, one that doesn't require getting paid immediately.

So the tl;dr is:

I want to be free right now
I don't want to limit my options with Smith down the road (he may be one of the people I need to convince to get my Ph.D in the end, or he may even end up being my advisor instead of Jones)
I feel guilty about the whole situation, because it was my fault they think I want to get started right away.

I feel I should have already nipped this in the bud, but I don't know how to without burning the bridge.  I have a few ideas, but I've definitely regretted past decisions where I've just gone with my gut without discussing with others.

There shouldn't be any guilt involved since you don't seem to have made any commitment. I think there are some important points to be made in a note totem.

Thank you for your interest and support
I'm feeling a bit overwhelmed right now and need a bit of time to explore my options and further directions.
I'll be more than happy to meet with you when the term starts for additional advice.

If he has already said that he wants you to be his student then it is a bit tricky, of course.

I'm delighted that you would consider me as your student, but ... (point 2 above)

If he has not been explicit about taking you on, then don't be presumptuous, of course.

I'm currently trying to decide on an advisor, but (point 2, again)

Then, find out some more about this professor and the other. If they are, in fact, not tenured but about to be evaluated then you need to know that. It can get in the way. Look at a few papers by each potential advisor. Talk to a few other grad students if possible. The department might be able to put you in touch with a few.
Let the wording be your own, but you haven't walked through the door and you aren't closing the door.
If you want to prime the pump a bit, ask for recommendations for a paper or two that you might explore now to help you make a decision.


What kind of citing permission do I need for a research project (not a master thesis) report that I am writing? In my master program, there is a so called Research Project worth 20 credits.
This is done before the Master Thesis.

Not all the publisher website provide "reuse for technical report" option for using their pictures and tables when we want to ask for the permission.

IEEE have "reuse for report" but I found it that I need to pay for reusing the picture.

Should I just use "reuse for thesis/dissertation" option?
Or is there any more correct or better option for this usage?

I think you are mixing two issues up with each other: Copyright and Referencing/Citing sources. The first one is a primarily legal topic whereas the other one comes from scientific integrity and proper work.

Copyright prevents you from directly using material without permission. For example, I cannot simply take an arbitrary figure from another paper or the Internet and publish it in my own paper. Therefore I need to get permission to reuse such a figure in a publication. But mostly not for personal use and stuff which will not get published or spread around.

Referencing and Citing is required in science. This means that you have to give the source of any ideas, equations, figures, ...  which you have not developed and created on your own. Even if you were allowed to reuse material from another paper, you still have to cite it correctly.

For your research project, you should talk to your supervisor. Since it does not get published I assume this is far less critical from a copyright point of view. For example, if I collect information for an internal summary on a topic, e.g., by summarizing the work of other researchers, I do not obtain a permission for these figures since this is way over the top and takes away to much time and resources. Copyright is most important if you want to publish your work. I do not think that your research project requires this, but talk to your supervisor.

Nevertheless, you WILL have to cite all your sources correctly independently from how you decide to handle the copyright.


I have egregiously sloppy (possibly falsified) data that I need to correct. How should I go about this? Several years ago, I did a summer project as an undergrad with a PI not at my undergrad institution (I'm in grad school now). Now, the project is finished and he wants to publish it with data that I've gathered.
The problem is, after checking my data, that the spreadsheets that I used to calculate the data are very inaccurate, to say the least. I can't remember exactly what I did, but there do seem to be some egregious inaccuracies (as in, values from the wrong dataset) in my spreadsheet compared to the raw data from the instrument either that I was colossally bad at copying data over correctly (all of the data in my spreadsheet do appear in the raw data someplace, but not necessarily in the right location, the right dataset, etc.), or worse, I'm terrified that I may have done it deliberately at the time. (How would someone be able to tell?) I did analysis with the faulty data back then and produced graphs.
Obviously, I will have to supply the correct data analysis before it gets published. But is it ok to explain it as "I majorly screwed up the analysis and made a lot of data entry errors, here's the corrected version"? I'm hoping that my PI will just use my corrected data and analysis and just focus on that instead trying to pore over my wrong spreadsheets to individually compare all the changes, many of which are embarrassing at best and look suspicious at worst. I am not under any suspicion of wrongdoing thus far.
I redid my data analysis with correct data entry and the results look messier on most of the things I messed up, though they do not affect the underlying trends. Not sure what this means - how likely is it for honest error to have the effect of making data look cleaner than it actually is? Also, my god, I was awful - mishmashing data from one trial with another, copying data from the wrong wavelengths and/or from the wrong trial, wrong normalization numbers, etc. etc. etc.
If you were a professor and you were approached by a student who says that made egregious errors on past data analysis and the corrected data looks not nearly as good, what would you think? Would you think they were honestly trying to fix a mistake, or trying to save face and cover for past misconduct?

I infer from the question that you still have the raw data. In that case, I think you need to re-do all the steps in which errors could be introduced (such as data entry, spread-sheet calculations, analysis of trends). Then see what effect the corrections have on the conclusions of your paper, and rewrite as necessary. I realize that this sounds like a lot of work, essentially repeating most of what you had done earlier, but since you apparently did it wrong the first time, you now need to do it right.
Meanwhile, you should tell the PI about the problem and your plans for correcting it. If I correctly understand the situation, the raw data are the only reliable information currently available. You should make sure he knows that, so that he (and others working with him) won't build further research on a foundation of wrong results.


Lecturer yelled at me after class and refused to answer my question During one of my lectures today, I had a question with something he did and raised my hand to ask the question. The lecturer didn’t see me, so my classmate asked me what my question was so I whispered to her what the confusion was.

My lecturer doesn’t like this, and asked me not to do this and to raise my hand if I have a question instead of making noise and being disrupting. I raised my hand but he told me to ask it after class.

When I did so, he told me to stop and informed me that he considered my behavior very rude and would not answer my question. I tried to tell him that I’m sorry and this was how I typically would react when I’m confused with something during lectures and my other professors didn’t mind, but I was very shocked and I’m not sure how well what I was saying came across and the lecturer got more angry, saying “You think this isn’t rude behavior?” And I apologized. Lecturer said he expected me to just apologize and leave and that I should do that, so I did.

I was shaken, and very upset. I didn’t intend to be rude. I’ll admit he had to ask me not to speak with other classmates in the past, sometimes due to me just whispering to a classmate about something unrelated, but often when I have a genuine question with what is going on. So I think he believes I’ve continually been acting rude and he has been trying to politely ask me to stop and it’s getting to be too much. I do admit that I shouldn’t be whispering to my friend if it’s not lecture-related and not at all if my lecturer wishes, but I also struggle understanding the material since it’s really hard to get a question answered.

Previously, he had been mad at me once when I was confused with a result derived in the lecture and said something along the lines of “I didn’t get it what you got but I’ll take it as true.” which offended him, perhaps believing I’m doubting them or something. I feel like that’s insecure, if I’m honest.

I had no idea that whispering at a low volume to a classmate who was trying to answer my question was considered rude, (also considering I’ve never been told this before by any lecturer in the past and I’m in my final year of university) especially when it is very hard to ask my lecturer a question because he doesn’t often look at the students when giving the lecture and only asks if there are any questions once or twice a lecture.

My friend suggested I make a complaint or talk to someone about it, but I’m genuinely scared my lecturer is going to kick me off the module or something, especially if I make him more angry with me. Is he allowed to do this, and if so, would he be justified in doing this? Would I have a strong appeal if so?

I’m not sure how rude I’ve been, is the main thing. How should I act moving forward? The idea of being kicked off the module for this is very scary to me. I’m still quite hurt and shaken at the time of writing this.

I don't suppose you'll like this answer much, but yes, if you have done this repeatedly and been called on it before and have continued to do it, then (a) you are being rude and (b) she can probably remove you without any consequence to herself. She may, actually, be angry with you beyond reason, but you seem to me to be poking the tiger, which is a bit dangerous.

I'd suggest that you need to behave differently. I hope you will like this part of the answer a bit more. I'm not so happy that the professor isn't more receptive to questions (once or twice a lecture). I can find better ways to teach, but you probably can't change that.

One simple thing you can do, other than keeping quiet in lecture is to sit where your raised hand will be obvious when she does ask for questions.

But, on a deeper level, I'd suggest that you adopt a note taking style that is effective and that, in particular, captures questions you have in the lecture to be able to get answers later, either from the professor or from other students. One simple way to do that is to carry a few note cards with you at all times, but especially during lecture. Write down any question you have on a fresh card. This permits you to annotate the question and write an answer. It also provides a means of later study. You can carry those annotated cards around and review them whenever you have a moment, say waiting in line to buy coffee.

But, in order to "smooth the waters" with this prof it may be enough to just assure that you behave according to her standards, even if they aren't entirely rational. If you offer an apology, don't end it with "but...". However, I think a cooling-off period would probably serve you well.


Citing an instrument manual I am analysing data from a commercial instrument. I need to set a threshold that has to do with the precision of the instrument, so I looked up the value from the manufacturer's online specifications. How do I cite it?

The university does not have any official policy, and other papers in the field either don't mention it explicitly, or give the value without citation, but I believe this is actually a quite relevant number, and thus should be specified and quoted.

Basically, you can cite this user's manual just as you would any book-like publication. The only difference is that you don't cite the name of an author:

  User's Manual for Foo Instrument, Model Bar. Random City: XYZ Corporation (Year).

or whatever is the appropriate reference style for your work.


On the definition of research I'm writing a proposal to acquire funding for a competition to be hosted at my university.  The competitors are restricted to graduate students who are engaged in research under the auspicies of a faculty advisor from my university.  In the process of making my proposal more clear and precise, I find myself struggling with the problem of defining what exactly is (and more importantly, what isn't) research.

At first, I equated research with publishable in a peer reviewed journal, but I soon realized that the terms publishable and peer reviewed would have to be defined... And even if I do that, then I would have to define the words that I used to define those words, et cetera ad nauseam.

I want to approach it the same way I would approach mathematical set theory:  it's either research or it's not, and there should be no room for ambiguity.  But I suspect that any attempt to define research this way will certainly either circumscribe or inscribe the set of all things we call research.

I don't think this is necessarily the best way to approach defining what is research, especially for my purposes.  Is there another way I can approach clarifying what constitutes research as opposed to other publishable works in the context of academia?

For purposes like this, I would define research as loosely, broadly, and generically as possible. If your definition is too strict, then you exclude valid efforts, and you will likely be bound by the language in your proposal.

For example, if you define research to be "scientific investigation," then you exclude the humanities. If you define research as "investigative work leading to a peer-reviewed publication or conference presentation," then you may inadvertently exclude unpublishable and unpublished results.

If the requirements of the agency do not specify the need for a definition of research, then do not supply one. If you are writing to an agency that regularly supports research proposals, then there is no need to define research - they know what it is. If you are writing to an atypical funding source, like a business, local government, or charity, then they would probably rather you be inclusive (and thus generic) unless you have specific instructions otherwise. Leave the job of deciding whether an entry is qualified research to the judges of the composition.

If you feel that you absolutely need a definition, then "investigative work" is probably generic enough. Your institution's Office of the Provost may also have an "official" definition of research for your institution.


What do you need to know about potential supervisor's publications when attending an interview for a PhD? I have been advised that it is a good idea to read papers written by a potential supervisor before having an interview with them for a PhD position.

I can make sense of the summaries and introductions, but that is all.

Do supervisors ask applicants about whether they have read their papers?
Do I attempt to summarise vaguely what the paper is about?
What sort of questions may be asked about papers?
Can you just say something along the lines of  ' I find it very interesting that you did a recent article in ????' for flattery?

I would, in fact, ask the opposite question: Why would you want to work with someone if you are not interested in their work? Of course, I wouldn't hold an oral exam or something with a prospective PhD student, but I would hope to be able to have a substantive discussion about my field with the student.

Thus: I wouldn't ask "Have you read my work?" because to me, it would be obvious that the student has read some of my work. Out of interest, not because I asked for it.

BTW: I wouldn't recomment you to say something along the lines of 'I find it very interesting that you did a recent article in...'. Say something substantive, challenge me, tell me why you are not convinced by that article, ask me about it -- yes! But don't try to flatter me in a blunt manner.

Good luck with your applications!


Is it ever harmful to submit extra recommendation letters from somebody outside of my department? I'm a senior applying for admissions to Ph.D. programs in mathematics. The departments I'm applying to all ask for three recommendations and encourage (but don't usually require) them to be from math professors.

I have three math professors whom I plan to ask for letters, and I believe all of them will be strong, but perhaps not superlative.  In addition, I know a professor who is primarily from the philosophy department (whose interests are related to math) who I believe would write a stronger letter than the other three. (He supervised an unusual independent study course for me and it was fairly successful).

The subjects I studied with him were entirely mathematical (logic), but his own work is more distinctly on the philosophy side (philosophy of science/math and related topics, not mathematical logic) .

Could asking this professor to write a fourth letter harm my application in any way? I think the letter itself would represent me in a good light and highlight an unusual aspect of my resume, but I don't want it to replace a letter from a mathematician for fear of admissions committees looking negatively at a letter from someone in the wrong department.

EDIT In response to the comment: I've worked closely will all three math professors. I've done long-term research projects with two of them (my university requires a junior and senior thesis; they were my advisors), and a year-long independent study with the third. I believe they were all reasonably happy with my performance, but I'm not sure I was able to blow them away. The independent study project I did with the professor from the philosophy department was more unusual, took more initiative on my part, and I believe I made a stronger positive impression.

I read about 200 graduate applications a year. In my department we take a fairly dim view of people who do not conform to the specified application process. For one, it displays a wilful ignorance of the departments' requests, which are typically not arbitrary. Secondly, it can be construed as arrogant—as if you think you somehow deserve or require something that everyone else does not get. Lastly, each letter of reference takes about two or three minutes to read. If every candidate was permitted to flout the rules then our admissions panel members would each have to spend an extra ten hours reading redundant recommendation letters.

Others may take a more relaxed view of course, but I would urge you to submit exactly the material requested by the departments to which you are applying. That includes complying with the requested length of any research proposal, etc.

As far as letters are concerned, select whichever three you believe will make the strongest case for admission to your target programmes. It may well be that the optimal strategy is to send two mathematics letters along with the philosophy one. After all, getting a PhD is about more than subject knowledge: it requires originality/creativity, self-discipline and motivation, ability to work with the literature, etc. All of these are strengths that the philosophy professor could possibly comment on. A good strategy might be to ask a neutral party—such as the head of admissions in your current department—for advice as norms vary from discipline to discipline.


Importance of paper download statistics In an editorial on the topic of Sci-Hub, Marcia McNutt (Editor-in-Chief of Science Journals) lists a few reasons why Sci-Hub may be bad for scientists. One of the drawbacks she lists is (emphasis mine):

  Authors do not benefit from download statistics, for example, which are increasingly being used to assess the impact of their work.

This surprised me, as I have never come across any mention of download statistics being used to measure the impact of papers / scientists. Are download statistics really being used in any meaningful way when assessing the impact of scientists?

I'm also asking because sites like ArXiv does not provide download statistics, and neither do other secondary publication servers (university paper repositories, private homepages, ...), which would hurt the impact rating the same way.

The argument is a ludicrous one, defending a parasitic system that should have been buried a long time ago, and written by an individual with a blatant conflict of interest.

In theory there exist some attempts to measure scientific impact from download data. Example.

In practice, nobody cares, partly due to the fact that there are many ways to get an article without incrementing the counter. (and also because we already have enough stupid metrics).


Do I need footnotes in a Foreword if I cite something? Dear Colleagues and Stack Exchange Readers,

Hello. I am writing a Foreword for a colleague's scholarly monograph. I would like to quote from one of my own books, as well as from the recent memoir of a public statesman, and from a high-level meeting.

Forewords must be short, generally between 750 to 1,250 words. I want mine to be about 900 words.

I have not seen any footnotes in other published Forewords. What do you think? Do I need to put in formal footnotes for this memoir and for my own book and the meeting, or is it appropriate to just put the title of the memoir or book in italics within the body of the Foreword, with the year of publication in parentheses after the title?

I would like to cite a brief phrase from the minutes of a high-level White House meeting. These records were published. Do I put in a full footnote with the source, or some kind of truncated, inline reference?

If you can share your thoughts on this, I would greatly appreciate it. Thank you very much for your help.

First, to make it clear, if you use something you need to cite it. I'm sure you agree with that. The question is about how to do the citation.

For a book, I assume that there is an editor involved who will make decisions about such things as layout etc. If the book is being self-published by your colleague, then they might take on that task. But it is almost certainly someone besides yourself responsible for such things.

Thus, I would submit your Foreword with complete citations. Whether inline or in footnotes is immaterial. But they need to be complete (not just referencing a book in general). The editor can then take what you give them and format appropriately. If you make them complete then the editor will have everything they need to do the job correctly.

For what it's worth, I have seen footnotes in Forewords, but in a book length monograph, your length restriction seems rather short.


How to find ranking of textbooks by popularity used in a course? Is there a way that I can find the ranking of textbooks by popularity used in a specific course, say Linear Algebra. Here the ranking based on either

the number of students using the book (as the main textbook)

or

the number of institutions using the book (as the main textbook)

or both will be a useful resource in choosing a textbook of the course.

This question is interesting, unfortunately the question is also too broad.  (Course of an specific school or just the subject? By country or which country? At university, MBA or Doctorate level?, etc). But the way to find a possible ranking would be to see best selling books per topic. For example:

Cambridge:https://www.cambridge.org/ar/academic/collections/classical-studies-btu
Amazon's'Best Sellers in Academic & Commercial Writing Reference':
https://www.amazon.com/Best-Sellers-Books-Academic-Commercial-Writing-Reference/zgbs/books/12017
ALIBRI: https://www.alibris.com/search/books/subject/Academic

There you can add filters per subject, which do can do also with many other bookselling sites. This however will give you best sellers per subject/topic in wide.

But you could also search for the program's syllabus and the books are listed there. If it's for your current school and the school sells books, just go ask for their most sold books for your research.

However consider that:

A textbook used is not necessarily the one suggested to be bought.
Rather than textbooks, students can use online materials instead.
In some countries, teachers force students to buy certain books
and certain editions (which they receive some revenue from).
Popular for teachers is not necessarily popular for students.
Piracy always adds a level of error int he estimations.


How is a Coursera exam typically conducted? Many Coursera online courses have an exam component.  This raises the question:
How is a Coursera exam typically conducted?

It seems non-obvious to me how one would conduct an exam involving students who might be on different continents.

Having not used Coursera, I do not know what tools they use. However, I have been a part to online exams from both the student and instructor perspective using the Blackboard learning management system. I suspect that features like many (if not all) of the ones Blackboard supports are present in Coursera.

Time limits - The instructor has the ability to set a time limit to the exam (which discourages web browsing to find answers). The instructor can also choose to force the student to complete the exam in one sitting or allow students to leave and return.
Flexible scheduling - The exam does not have to happen at a specific time, but may be accessible over a time period, perhaps 24 hours or more. The instructor can still enforce time limits and so on.
Lockdown - The implementation of Blackboard my institution uses comes with Respondus Lockdown (there are other products), which prevents students from navigating away from the exam once it is started. These products can also prevent such things as minimization of the window, opening new tabs, etc.
Proctoring - I have proctored an online exam for another instructor. I had to enter my credentials and a code before the student could start the exam, and I had to enter a different code when the exam was completed.

Features like these give instructors flexibility in offering the exam to students around the world, while still making it harder to cheat.

They will "cheat", however. No online course management system can prevent the student from using their text, notes, or another computer or electronic device to look up answers. The best defense against infractions of this nature are well-written tests (the kind you might write for an open-book or take-home exam).


What is the proper etiquette for requesting speakers from industry for an academic seminar? I am in a program that has a seminar class where the students are strongly encouraged to get people to come and present. I was wondering if anyone else ever had to find speakers and if so had a sample form letter. I ask because I can offer nothing in terms of compensations so I am not sure how to go about doing this.

I don't think using or even adapting a sample form letter would be very helpful, just as a canned letter wouldn't be very successful in a job application.

A couple of thoughts:

In cases like these, a good network definitely helps. If you know someone, even only slightly, that gives you a better starting position that just cold calling someone. Think through your network, and even if you don't know anyone you could meaningfully invite, maybe someone from your network knows someone she or he could introduce you to.
Can you at least offer reimbursement of travel costs? If not, look for people working close to you. Budgets are tight, and your speaker may have a hard time getting reimbursed for such a talk from his company.
Just as for a job application: when you do contact someone, be brief and to the point. Introduce yourself (if necessary), briefly describe your class and ask whether your candidate would in principle be interested. Offer to follow up with details - don't include them in the first email. People in industry are busy (just as everyone else).
However, you should definitely include a tidbit that (a) makes speaking interesting for your candidate and (b) helps him/her get permission/budget from the employer. Are your classmates close to graduation? Then the company can present itself as an interesting employer. Do you have any interesting projects? Are you working in a field that is related to your candidate's employer or even better to you candidate's own work? Are you perhaps potential customers? Any kind of motivation is good.
Above all, don't worry overmuch. Everyone's ego is tickled at being invited to speak, even if they don't accept the invitation. And established people, whether in industry or in academia, often are happy to accept such invitations and help students out. The worst that could happen is a polite refusal (or no answer at all). The best would be a nice talk and an interesting contact for later on.

I kind of wonder whether this question wouldn't be better at workplace.SE.com. You'll get more answers from industry there than at academia.SE.com. Perhaps you want to consider flagging it for migration.


Is reviewing papers mandatory? I am baffled by this question. Elsevier boycott aside, is one supposed to review a paper every time he/she is asked? And somebody will be upset if he/she declines the request to review? Or is this only maths thing?

Reviewing paper is unpaid, while it takes a lot of time and effort (at least for me). As such, I expect someone in editorial board to be thankful if one accepts to review a paper, and move on if his/her request for reviewing is declined.

To be angry with a (junior) researcher for not reviewing a paper is unacceptable behaviour for me. We are not slave.

Note: Until now, I am happy every time I am asked to review a paper.

No, reviewing is not mandatory, it's just good community service.

When I'm soliciting reviews, as an editor or program chair, I would actually much rather have people who don't want to review simply decline to review.  It does mean that I have to search for more reviewers, but it's much preferable to getting low-quality reviews or no review at all.

Moreover, there is always a limit to the amount of service that one should be expected to do.  If you're reviewing a good amount of papers (see discussion in this question about how much is enough), you should feel free to triage. Just be polite when you decline: even with things you don't want to deal with, it's usually better to simply say "I don't have time right now" (true enough) than to offend a person by completing the sentence with something like "... for your crappy journal" or "... for this horribly tedious-looking paper."

Of course, there is always the possibility of encountering an ego-centric jerk on a power-trip, but life is too short to spend all of fearing that you might encounter such.


Is it ethical for PhD supervisor to forbid publication in a given topic Six months after my PhD graduation, I submitted a paper to an SCI journal as a sole author. Apparently, my PhD supervisor is the technical editor for this journal. He wasn't pleased that I submitted a sole-author paper without informing him.
I formulated the idea and wrote everything from scratch. However, he claimed that's a generalization of what he's currently working on. After I proved to him that they aren't related he went ahead to forbid me from publishing in that area as it's likely to interfere with his. That's after he made me divulge all my on-going investigations. He said it's better we are collaborators than competitors. I didn't set out to compete with anyone. Most ideas I gave him during my PhD were suppressed only to be given to other students two years later. He made me the last author in those anyway.

Question:
1) Does he have the power to do this?
2) Being that he sits on the board of top SCI journals in my field, how do I overcome this?

Your former supervisor's behaviour sounds entirely unethical. I'm sorry to hear that he is unnecessarily causing you distress. So, to answer the title question: No, it is not ethical to forbid anyone from publishing in a given topic.

The justification given -- that it is better to collaborate than compete -- is entirely beside the point. Yes, it is good to collaborate. However, once the work is complete, it should be published and the authors should be those who contributed.

It is understandable that your former supervisor would have liked to be informed. Everyone wants to be kept in the loop. But he has no automatic "right" to be informed of your activities after you graduate. (I'm assuming none of this work happened while you were his student.) Furthermore, there is no justification for blocking publication because it would interfere with his work.

Moving on to your real question: He has a lot of power over you both because he is senior and because he was your supervisor. Thus you should proceed with caution. Perhaps you can reason with him and seek a compromise. If that doesn't work, you can escalate -- appeal to the other editors of the journal, who presumably would not agree with this behaviour.

In the long term, you should consider slowly moving your research away from his to avoid repeating this situation. And you should work with other people. The situation would look a bit different if you had senior coauthors to fight back on your behalf.


Can non-peer-reviewed work be recognized by the community? A number of years ago I was enrolled in a university as a PhD student and was working on a specific thesis topic. My intent was to earn my PhD with this work. Due to lack of funding, I was unable to continue, but I have continued this work independently for a number of years.

I have managed to complete this work now but finding the right place to publish it seems ever more causa perduta for me. I am thinking about simply publishing it for free and trying to distribute it on the Internet. I am also thinking of making translations into several languages myself. Besides publishing in my mother tongue I am thinking to translate it into English and Russian and possibly German, too. I hope this can make it available for as wide range of specialists as possible. But yet the problem of peer review remains. Even if accessible to everyone on the Internet it isn't going to be something gone through the peer review process and it is likely my thesis itself would cause controversy.

As such, my question is, can research be accepted "in any form" by the scientific community? Does anybody know of cases within the past two decades when such a thing (research first published "free on the internet" being eventually accepted as mainstream) has happened ? I just want to know is this even possible in modern science or would it just "disappear" in the huge noise of the net.

It sounds like there are several questions going on here, so I'm going to try and break them down one at a time.

  As such, my question is, can research be accepted "in any form" by the
  scientific community?

Yes. While the scientific community at large is much more likely to accept research that has been peer-reviewed and published, within a community of researchers things are a bit more loose. Some ideas get passed around on list servers and through emails via pre-prints long before they are published.

  Does anybody know of cases within the past two decades when such a
  thing (research first published "free on the internet" being
  eventually accepted as mainstream) has happened ?

As noted by zibadawa timmy in the comments to the question, the work of Grigori Perelman appeared on arXiv, was well received and is highly cited. However, as the commenter also pointed out, Perelman is a well established mathematician so their work gets much more notice when something is published to arXiv.

  I just want to know is this even possible in modern science or would
  it just "disappear" in the huge noise of the net.

There is no guarantee that this will happen, nor is this a modern phenomenon due to the internet. Always remember the history of science. Gregor Mendel's "Experiments on Plant Hybridization" is considered to be a seminal paper, but was published in the fairly obscure Proceedings of the Natural History Society of Brünn and it wasn't until after his death that his work was rediscovered and he was properly credited.

To address your work directly based upon the comments to your answer. I would suggest that your best approach would be to get back into university for your PhD so you can receive mentorship and guidance. If that is not possible, your second best bet might be put together a manuscript and send it off for peer review in various journals. If it get bench rejected by the editor then they may provide feedback on better venues for publication. Likewise, reviewers who think the work is worthy of publication in a different venue will also do the same. This could help to find a home for your work.

Also, based upon some of the things you have mentioned with regards to complexity, I would highly recommend looking into the work of Stuart Kauffman and their book "The Origins of Order: Self-Organization and Selection in Evolution" in particular. Some of what you are describing sounds like work that is actively being done and published by scholars that investigate complexity in the context of complex adaptive systems. If that work is indeed similar to what you are doing, then that may point you in the direction of venues for your own publications.


Including Results in Dissertation Before Publication in a Journal I am in the final phase of my Ph.D. research. I need to defend my thesis before my fellowship funding runs out in a few months.

I won't have time to carefully prepare and polish my results for journal papers before I defend. I need to include some preliminary, unpublished results in my thesis, as per the work I agreed to do in my thesis proposal.

But is submitting results (to a journal) that are already "published" in my Ph.D. thesis an issue? One issue I'm wondering about: journals run a "plagiarism" check, and I wonder if "self-plagiarism" will be an issue.

Good question! No, your thesis does not count as published (yay). Self-plagiarism is definitely not an issue here. Good on you for clarifying though!


When applying to a Phd in Physics or Math , do grades in unrelated courses I took have any effect on my admission? I'm currently studying (Undergraduate) Physics in a University where, regardless of their department, every student must take some English, Turkish and History courses, which I don't want to attend. Turkish and History courses are non-credit but not English, so it affects my GPA. Moreover, I will take violin, astrophysics and philosophy courses as non-included.

So here is my question: when I am applying for a PhD in Physics or Mathematics, does any of these courses have any effect on my admission?

Note: My main concern is whether having  low grades in English ,which is not a non-credit course, affect my Phd admission ?

If you are applying to programs in the US, more important than your grades in English classes is your performance on the TOEFL. Many universities have a minimum TOEFL score required before the department can even consider your application, and these rules are often difficult or impossible for the department to bend, even for an exceptionally attractive candidate.

There is more information in the answers to this question. (For example, someone there mentions that the minimums at "Yale and Stanford are about 100, Harvard is 109" -- out of 120 points total.)

Given the quality of the English in your original question (before it was improved by helpful editors), I don't think you can afford to blow off your English classes if you have any hope of studying in the US.


Do I point to mistakes in a paper if I cannot contact the authors? I am about to submit a manuscript in which I point to some methodological errors that I found in some literature. The error may significantly change part of the results and conclusions if those papers.

I thought I should first contact the authors of those papers to discuss the issue with them. Especially, to check if they actually made that mistake or if their methods were not detailed enough.

However, most of the authors that I tried to contact did not answer back (I checked their actual email address) or did not remember the details of their analysis.

What should I do? Am I "allowed" to point to some papers that I repute wrong only on the base of the details given in their method section?

Of course you can publish it if you think someone is wrong. This is the entire point of science. Always do so in a nice way though: it is very well possible that everything appeared to be correct with the knowledge at the time the paper was published. Or that it is you who misinterpreted the methods (possibly because the paper was a little vague), as you suggest in your question.

Even if it was really a mistake: everybody makes mistakes from time to time and that is nothing to be ashamed about. You did the right thing by contacting the authors first. Not only is it the correct thing to do, but I have also seen this lead to new collaborations that resulted in multiple papers.

If both the paper and the errors were important, it is your responsibility as a scientist to correct the errors. But if the errors are minor, the result is "unimportant", or you are not 100% sure that there actually is a mistake, you could also decide to simply ignore the paper. There are plenty of bad and/or unimportant papers out there and frankly, they do not deserve the attention even if it is to correct mistakes.


Switching REU recommender, good excuse? My professor who I thought would write me a stellar recommendation recently ceded that he feels he must be up front in my recommendation letter and say that I am disorganized.

I have confronted him and asked him to overlook my pitfalls, which he cited as: disorganized, asked for web assign extension, and failure to follow his strategies.

I received a 100% on the final and an A in his class and he also told me during the semester I was his favorite student in my class.

I applied to twenty+ programs and can still alter a lot of my recommenders listed. Of those that I cannot, what excuse should I do to switch recommenders?

I have three other professors who are willing to write the recommendation.

Your recommendation letters should help you in any admissions program. They should speak to your strengths, but also be honest. If you feel that this professor will write something that can damage your application and you have the ability to switch out references/recommendations in your application without negatively impact your application, then absolutely, you should have another professor write you a recommendation letter. For the ones where you cannot switch, you should be honest in that you have another professor in mind who can write you a much stronger letter of recommendation - which is not a lie.


How to cite a working paper, preprint, or manuscript? How I can cite a submitted manuscript which I am not supposed to publicly archive (e.g. on arXiv) because the review process is double-blind (i.e. the manuscript is anonymized and should not be archived in a way that reveals authors' identities) and/or the journal has a restrictive archival policy?
This manuscript may therefore not be assigned a permanent link (like it would have been with biorXiv, arXiv, OSF, some institutional repos, etc.). I am aware of platforms such as Zenodo allowing anonymous archival but these do not necessarily imply a citation format to be used. However, I'd like to share the manuscript among colleagues who might want to refer to it. So, I want to suggest to them a citation format while it's under review.
I found this, suggesting me to do that:

Doe, J., & Smith, A. (2012). A study on the difficulty of getting manuscripts published. Unpublished manuscript, Department of Sociology, The Top University, New York.

where manuscript can be substituted by something like working paper or preprint. See also that SE comment. However, I am not sure whether this is the best way to do it. Any better suggestions?
Thank you.

I'm not sure this is a better solution, but you can be cited by name (and possibly place), with the paper described as "private communication.". Include a date (29 Aug. 2018) but not the name of the manuscript.

  Doe, J., & Smith, A.. Private communication, (29 Aug. 2018). Department of Sociology, The Top University, New York.

Once the publication becomes official contact your circle with the information and an updated reference. They may be able to update their own work in some cases, depending on timing, etc.

I'll note that it isn't impossible that the title of your work will change after review, making a more specific title obsolete.


Can I get into computer science grad school without a strong math background? I took an undergraduate degree in Bachelors of Science which did not go over a lot of mathematics. I did not even take calculus. I only took up to the highest level of algebra. Is it not possible for me to get into a grad program for comp sci, or electrical engineering? How is it going to work? Will I have to go back and take calc? I'm incredibly stupid at math, and I'm almost 25 years old. Do I have any chance to even get in? The weird thing is, I actually have produced more tangible things than my friends who have taken Comp Sci. I have made websites, video games, published them, and have even been referred to gaming studios as a software engineer by people who work there at major companies such as Activision. But I don't know calculus and I feel really retarded. What should I do? I want to get into grad school but I'm scared I'm too stupid to do it.

I'm embarrassed to admit that my math skills are maxed out at the highest level algebra. I never took calculus. Am I just screwed?

The only way to know if you can get in is to apply to a few programs and make your best case. There are some aspects of computing that require less of mathematics and others that require more.

But, don't make the mistake of conflating computer science and computer programming. Programming is only a tool, if a necessary one, for more important things. In particular, some of the things you have probably missed are deep study of algorithms and, especially, algorithmic efficiency and complexity. These are pretty much dependent on mathematics. If you were to be accepted into a CS grad program you would be competing with people who have studied this before, never mind graph theory, for example.

There are, however, some aspects of CS that are very tied up in things like human psychology and physiology more than mathematics. There are universities that focus, especially, on human factors. Even language design can learn from such things.

All is not lost, but it would be a pretty hard road even if you are accepted. You will need plenty of other evidence of the likelihood of your success to get in the gate, however. There is a lot of competition and most of it has followed a more standard path, so many graduate programs expect and depend on that background.

As for the usefulness of math in CS, note that discrete math, probability, and logic are more central than calculus, which has some, direct application, but is only occasionally essential (say, in theoretical work).

And for advanced work, Category Theory may be needed. Deep stuff.


Can I transition from 3 years out of school to a master's in computer science? To erase any confusion, this question is geared entirely towards requirements and expectations of academicians. I am not asking for recommendations for universities or research topics, nor am I asking about preparation for a non-academic career. Additionally, I am speaking from a United States point of view.

Briefly, here is my backstory. A few years ago I graduated with a bachelor's in computer science. During that time I took a part-time adjunct instructor position with a local community college, where I quickly discovered that I loved teaching and the academic environment. In short, I have decided that I would like to make it a full-time career.

On to my question/concern... I am currently looking into research-focused masters degree programs so that one day I can pursue a doctoral degree. I have discovered that a lot of the computer science masters degree programs can require a certain level of mathematical knowledge or even taking research focused math classes.

Is there anything I need to do in order to prepare for my CS masters degree journey in terms of brushing up on mathematics, or other subject areas for that matter? Is it possible to sign up for a program anyway, and just go back through some of my books and notes on an "as needed" basis? I would prefer the second option, not sure if either is possible at this point!

Sure it's possible and some small fraction of people have industry experience (or teaching experience or military service or what have you).  Has always been this way.  It's a minority but normal.  (Actually in good MBA programs its the expectation.  And in law and medicine its very normal, not as rare.  In research it's rare but just because of the population not going that way, not because of schools discouraging it.)

In terms of math prep, I donno.  Guess you should look at different programs and talk to them (good chance to talk about other things in general also).  Maybe there are programs where it matters more/less your math background. Maybe you can get some individual calibration on your specifics, which this forum sometimes discourages.

Finally, your title and then question text itself are a little confusing.  Are you asking about math requirements for CS MS (which would be an issue regardless of your interregnum) or for how the interregnum is looked at.


What does it mean when APS editors ask us to "list first page" for some refferences? Basically the title. I don't understand what the editors are asking from us? Are they asking us to make a list out of the first page of these references, e.g. by copying and pasting them into a file and then submit it??

Needless to say, English isn't my first language. Any help is appreciated.

I believe they mean that the complete citation in the back of the paper should include the page number of the reference in the journal/book where it was published.

For instance, in APA style:

Einstein, A. (1918). Prinzipielles zur allgemeinen Relativitätstheorie. Annalen der Physik, 360(4), 241-244.

Here 241-244 are the page numbers of the journal where the paper was published, and 241 is the first page.


How should you deal with a teacher who is difficult to understand? Related but not a dupe. One of my Japanese teachers often explains things in a difficult to understand way, or because she uses a lot of Japanese quite quickly, sometimes with constructions we haven't quite covered. I often don't understand the tasks that are set. Usually I can ask, but there's a point where I feel like I'm annoying my classmates, and there are a few lessons where I've walked out and everyone was confused. It's just this teacher, the other four communicate very well in general. I'm not going to say anything yet, but the question is: what should I do if this is a persistent issue? What is the most polite and appropriate way to approach her out of hours and tell her that I am struggling to understand her.

I was in a similar position as your classmates in my language course. I'll describe the situation so you can "step into my shoes" and see how it looks from the other side. Hopefully, this will help you understand your situation a bit more.

I'm fluent in spoken Chinese, but being illiterate in would prevent me from passing the equivalency exam, so I took the Intro 101 course with most of the class not being able to speak any Chinese.

Our professor was a grad student originally from China. Her English was acceptable as she was a native Chinese speaker, and she had only come to the US after college.

I had no issues with other students (the class was probably ~15 people) asking for directions to be repeated again more slowly.

Reason? Because, from experience, I know languages are hard to learn. I may be fluent in Chinese, but if I were to take a French class, I'd be in the same boat.

The other students in your class should be able to recognize that you are a new learner. Now, leaving the class might not have been the best response, but you can't change that now. I would recommend not leaving class in the future. That's counter-productive.

Have you tried talking to the other students or asking them for help? I'm sure they're willing to help you learn Japanese as well. Certainly, if they already know the material, they might not even want to be in a rush to go through all the material.

I guess a final concrete example is in order.

  If you were an English teacher with a college mastery of English, and teaching a 1st grade English class, would you be annoyed when the 1th graders asked 1st grade English questions?


Should you provide citation for an professional organization or learned society? I am writing a paper in which I refer to a database maintained by a learned society. Something like:

  We performed this analysis on 7,195 structures taken at random from the Poisonous Substances Database [1] maintained by the Democratic Chemical Society [2].

Ref. 1 will be the URL of the database, but I am wondering about the learned society: should I include its URL as a reference? Or should I simply not give any citation along with its name?

It usually depends on how well the data source/database is known in the field. In some cases the database is the primary source of data for nearly all publications in that field that no one ever cites it formally (i.e., it's a waste of space). Usually, they just mention in the article that the data was obtained from Foo and perhaps again in the acknowledgments, if they're feeling generous.

As always, check with your specific data source/society to know what they require from you in terms of citation. As an example, these guys only expect a blurb acknowledging them, not a full citation.


How much do bench skills matter for a postdoc? If you're hiring a postdoc, how much do you care about the techniques they've used in the PhD?

I'm thinking ahead to the postdoc search (will probably start in earnest in summer/fall). My current field is a somewhat obscure area of human molecular genetics, lots of old-school techniques. I'm very interested in moving to a model organism that will provide quick output during the postdoc and let me transition to a career at a primarily undergraduate institution. I've also had very little opportunity for bioinformatics training, which I would like to learn. (I see lots of online ads for postdocs listing a slew of particular skills, but I've heard these are less common paths compared to personal networks so I'm wondering if they're representative.)

I'm not hiring a postdoc, but:  Bench skills/experience matter a lot.  PIs want to hire someone who can use the existing lab to produce data without training.

That said, it is difficult to anticipate what skills PIs will be looking for at the moment you need a job.


Alphabetical authorship order in graduate admissions (particularly high energy physics) I would like to know how graduate admission committees at US Universities look at alphabetical authorship publications in a CV (particularly in high energy physics). Since the convention in high energy physics is to have authors in alphabetical order, how do the committees determine the contribution of the applicant (I guess recommendation letters is one way)? Also, do the committees actually read the papers (mentioned on the CV) on arXiv or the journal website to check the quality of the papers?

I am applying to US universities for a Ph.D. in high energy physics. Because my surname starts with one of the ending letters in the English alphabet, however, my name on all of my publications is last in the sequence. Could this create confusion in committee members about my contributions?

I can't speak to how every department does it, but in my department (and I think typically) your application would be read mostly by people working in a similar field who are aware of the conventions. You could always add a note to the CV pointing out the alphabetical author convention if you're concerned about it.


Is this our fault? corringendum vs erratum We have been advised that a recent article of ours was incorrectly published as article type y instead of article type x. Article type x and y are very similar, having the same word counts, similar structure, and the same fees. It is just that the name of the article type (x vs y) is different.
It was our error for selecting the incorrect article type when submitting the article, but the article's title and some of the responses to the reviewer made it clear which article type we were aiming for.
The journal would now like us to issue a corringendum that states 'This article was supposed to be published as an x type article rather than a y type article'. However, I am wondering if this is more suitable as an erratum? i.e. that the journal was to blame for this error.

Don't argue with the journal over something as minor as this. Nothing good can come out of it. Just do it and forget about the matter.
Trying to fault someone for this kind of minor error is never a winning strategy in any case, because finding fault in someone is one of the easiest ways to destroy a relationship.


Gamification for theses and papers It’s always been hard for me to stay focused and motivated when writing any kind of a longer text, e.g. an article, paper or gasp thesis, even if I’m interested in the topic and enjoy the work. The Stack Exchange and Wikia gamification systems with points and badges being awarded work well for me. I tried to reward myself for certain research and writing accomplishments, but realized early on that I’m not good at defining milestones and choosing bounties. Therefore, I hope someone else has done it.

Is gamificated thesis writing a thing?
Are there integrated software solutions to support that?

(I don’t use MS Word, but I could easily see how a plugin would detect the first quotation or the 10000th word etc. there. It would be great if it worked with Pandoc/Markdown or LaTeX instead.)

Related questions that are missing the gamification aspect

How to make thesis-writing feel less tedious? – Writing up existing results, mentioning techniques like divide and conquer or pomodoro time
Motivation to write the dreaded dissertation – What to do if you’re not interested in or convinced by the subject and degree, external motivation
Optimizing a thesis writing workflow for Bachelor and Master theses – General advice on structure and workflow

Are there integrated software solutions to support that?

Beeminder integrates with Github or Bitbucket, so if you keep your Latex or Markdown in either of those, you can automatically gamify your writing without having to do any manual data entry.
Beeminder is a commitment tracking service that plots your progress towards your goals, like this:

(image source)
There's also negative reinforcement: if you consistently fail to meet your goal, you "fall off the yellow brick road" and you pay actual money. Beeminder is good at tracking your progress without punishing you for small temporal variations in productivity.
In this context, your goal would be to make a consistent habit of adding to or editing your thesis.
With git integration you can set goals like "N commits per week" and data points are added to your Beeminder graph automatically when you commit.
There's also integration with Draft, if you prefer to count words edited rather than commits.  I haven't used Draft myself, but it looks like you can use it to write in Markdown.


Is it impolite to ask a professor who was not my master's thesis advisor (but with similar research field) to help me to work on a research topic? I have finished my master's thesis and graduated from the university in which I used to study for my masters degree. Now I have two or three months free time and I am searching for a PhD position; in this period of time I want to work on research topic, I see two professors at that university, whose research fields are really interesting to me. Their research field is really near to that of my master's thesis advisor.

Is it considered impoliteness to my master's thesis advisor if I ask another professor in his department (with similar research field to him) to help me work on a research topic?

Not at all. You are not committed to doing your PhD with the same advisor. Even if you did want to work with the same advisor, he/she should encourage that you talk to others to hear out their ideas. I highly doubt your advisor would be offended to hear that you were interested in speaking to other professors about their research interests. After all, a PhD is a long road, and you need to be really happy with your advisor, and your work, to survive it.

In fact, I think it looks positive, even to your advisor, knowing that you have multiple options. I once had a job interview where, upon disclosing that I was also interviewing at other places, that "they would be worried if I wasn't".


How much does it matter if my Masters is in Stats or Math (in Stats track) I have a choice of Master's programs in statistics, one of which is formally a program in applied statistics, the other is formally in math with an applied statistics "track".

The courses in the 2 programs are about the same, so I am wondering how much the label of the degree really matters (I most likely will not work in academia unless I am doing contract work).

Thank you for any insights you may have,

Matt

Well, do you want to end up applying for a job that is looking for a "Degree in Statistics (or related field)," or a job that is looking for a "Degree in Mathematics (or related field)?"

Employers don't usually ask for transcripts and don't look at your list of courses, they just look at your resume/CV, which will just have the title of your degree and perhaps your GPA (or some other summary grade if not in the US). If you look like you don't quite have the right qualifications on paper, you'll need to explain how a "mathematics" degree qualifies you for a job in statistics, or vice versa.


Is it appropriate for reviewer to offer cooperation on a reviewed paper? I am currently reviewing a paper for a journal (area of ecology, organism-environment interactions at various spatiotemporal scales, so including macroecology and evolutionary ecology). Now I am doing a second review of this paper (after resubmission). They submitted a valuable manuscript, but they ran into challenges which are quite difficult to solve. In particular, their statistical population models didn't converge properly; the models would need at least 10x, preferably 20x or 50x as much iterations to run, but they are very slow - taking 2 weeks to run already. I already investigated a bit and found an approach which would make the models run 1000x faster - this would solve the issue. I don't think this approach has been used yet (currently investigating this).
I am about to give them very detailed instructions on how to implement this approach in their models. I am not an experienced reviewer (this is my first paper to review), but (1) I think this is a bit beyond the usual work done by the reviewers? It is also possible that this work will be very challenging for them, since not every biologist is skilled with models and it's much easier for me since I am a specialist in development of new population models. So, (2) is it appropriate for me to offer them cooperation on their paper, with the possibility of becoming a co-author? (3) Should I ask for co-authorship for this? Or, is it better to just contribute and wait if they offer co-authorship to me? If this happens then the editor would probably need to find another reviewer instead of me for the next revision, because of conflicts of interest.
(The review is currently double blinded, so I don't know their names, but I signed the first review and offered my email already, so they know mine.)

Since this is your first review, you probably ought to keep the following in mind:
It is not the job of the referee to fix the paper, it is the job of the referee to provide grounds for the editor to decide whether to accept or reject it. Presumably you have research of your own, and while it is no doubt very kind of you to offer very detailed instructions for how to carry out a new analysis, this is ultimately not what you are tasked to do.
What you can do in your review (which is to be addressed to the editor), is to point out that their current analysis has a flaw, and whether or not you think the paper is publishable with this flaw. If not, then you can suggest that the authors (and not you!) revise the paper using a better method. Here you can give a comment stating your suggestion, and point them to a reference.
And to answer your question concretely: No, it is not appropriate. It would place you in a double role, where the authors might feel pressured into accepting you, to have their paper accepted. If you are very keen on publishing your method under your own name (provided that it is, in fact, novel), you have to wait until their paper is published, and then write a paper of your own. Note that you cannot use privileged information obtained as a referee.
Finally, don't sign your reviews. I would hope that the editor removed your signature. If you don't like giving blind reviews, you should abstain from accepting them, and provide reviews on open platforms which allows this. Like it or not, blind reviews is the name of the game.


Correction of Diploma Having Two Types of Honors Last semester, I was graduated from a four-year university, and am now a Ph.D student at another university.  I received two separate degrees: one in Pure Mathematics and one in Computer Science, both Bachelors of Science.  The honors in question are:

Summa Cum Laude (1): This is a direct, university-wide, GPA-related thing; it applies to both degrees.  I fulfill these requirements and so deserve the honor.
Summa Cum Laude (2): This is applied if the student does a Mathematics thesis.  I did not do this, so I do not deserve this honor.
Computer Science Departmental Honors: This is applied if the student does a CS thesis.  I did do this, working independently to produce not just one but two theses, containing publishable work.  One won best paper at a small conference.

The two separate diplomas were shipped well after graduation, and well after I had moved to a different state.  They contain:

Mathematics: Summa Cum Laude
CS: <nothing extra>

Clearly, there is a problem.  Since I didn't do a mathematics thesis, the "summa cum laude" on the mathematics degree refers to the strict GPA thing (the mathematics department confirmed this).  However, by the same reasoning, I should clearly have gotten the same on my CS diploma.  And, in any case, I might have expected the departmental honors to show up too.

The first thing I did was ask the university help office, which directed me to the (single) email contact at the registrar's office.  This email contact ignored repeated, direct questions asking to clarify the above; replies consisted mostly of one-line, semi-incoherent, half-caps, half-cut-and-paste of irrelevant information I'd already seen on the University's webpage.

Were it not for the typos, this lady wouldn't pass the Turing Test.

The mathematics diploma is correct (since I do meet one of the options for having the honor).  However, the CS diploma needs to be fixed.  I have surmised that the only way to get a fix is to send the original diploma back with a somewhat ambiguous correction form.

This leads me to two questions for the academic community:

Is it common practice to include both a summa cum laude honor and a lesser honor?  In my opinion, my theses represent far more value, especially research value, than a stupid GPA.  The contact was . . . unable to clarify whether the university has an established policy on this--but my impression is that it does not.  The CS department says it's not their format, so they don't know.

Under these assumptions, I am forced to conclude that there is no established format at my university.  Further, as it seems they are taking suggestions, I will submit my correction form to list both honors.  If they really do have a policy, they'll know and can contact me.

I am having trouble thinking up a good way of stating the honors, however.  If this contact was representative of the registrar's office at large, then I definitely want my correction to be verbatim.  What is a simple phrasing of the honors that makes them clear that they are distinct?

In my opinion, the most important statement in your question is "I ... am now a Ph.D student."  Assuming that you follow through in your doctoral program, everything about your undergraduate career will rapidly fade into insignificance.  Please understand that I do not mean to downplay your accomplishments in any way: it is simply that you are entering a new realm in which you will be judged very differently on a very different type of accomplishment.

Given that, what's important here is to make sure that nothing on your C.V. could be interpreted as a lie in the unlikely case that somebody bothers to check with your undergraduate institution.  Check what the CS department believes about you, and write that down on your C.V.  You can always update it later if the bureaucracy gets fixed.

Beyond that, it's really more for your own personal satisfaction than for any career value, particularly as regards the pieces of paper that you were shipped.  My own personal experience as a working scientist... I recently rediscovered my degrees while going through a box throwing out old papers, and they have now been relocated from a box in a closet to a box in the attic.